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Diff for /imach/src/imach.c between versions 1.125 and 1.163

-version 1.125, 2006/04/04 15:20:31
+version 1.163, 2014/12/16 10:30:11
  Line 1
  /* $Id$
    $State$
    $Log$
+   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>
- extern int errno;
- /* #include <sys/time.h> */
+ #include <math.h>
- #include <time.h>
+ #include <stdio.h>
- #include "timeval.h"
+ #include <stdlib.h>
+ #include <string.h>
- /* #include <libintl.h> */
- /* #define _(String) gettext (String) */
+ #ifdef _WIN32
+ #include <io.h>
- #define MAXLINE 256
+ #else
+ #include <unistd.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #endif
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 132
+ #include <limits.h>
+ #include <sys/types.h>
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ #include <sys/stat.h>
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #include <errno.h>
+ /* extern int errno; */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ /* #ifdef LINUX */
+ /* #include <time.h> */
- #define NINTERVMAX 8
+ /* #include "timeval.h" */
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ /* #else */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ /* #include <sys/time.h> */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ /* #endif */
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #include <time.h>
- #define AGESUP 130
- #define AGEBASE 40
+ #ifdef GSL
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #include <gsl/gsl_errno.h>
- #ifdef UNIX
+ #include <gsl/gsl_multimin.h>
- #define DIRSEPARATOR '/'
+ #endif
- #define CHARSEPARATOR "/"
- #define ODIRSEPARATOR '\\'
+ #ifdef NLOPT
- #else
+ #include <nlopt.h>
- #define DIRSEPARATOR '\\'
+ typedef struct {
- #define CHARSEPARATOR "\\"
+   double (* function)(double [] );
- #define ODIRSEPARATOR '/'
+ } myfunc_data ;
  #endif
- /* $Id$ */
+ /* #include <libintl.h> */
- /* $State$ */
+ /* #define _(String) gettext (String) */
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- char fullversion[]="$Revision$ $Date$";
- char strstart[80];
+ #define GNUPLOTPROGRAM "gnuplot"
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ #define FILENAMELENGTH 132
- int nvar;
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- int npar=NPARMAX;
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- int nlstate=2; /* Number of live states */
- int ndeath=1; /* Number of dead states */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int popbased=0;
+ #define NINTERVMAX 8
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int maxwav; /* Maxim number of waves */
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define MAXN 20000
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define YEARM 12. /**< Number of months per year */
- int mle, weightopt;
+ #define AGESUP 130
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define AGEBASE 40
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #ifdef _WIN32
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #define DIRSEPARATOR '\\'
- double jmean; /* Mean space between 2 waves */
+ #define CHARSEPARATOR "\\"
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ #define ODIRSEPARATOR '/'
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ #else
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ #define DIRSEPARATOR '/'
- FILE *ficlog, *ficrespow;
+ #define CHARSEPARATOR "/"
- int globpr; /* Global variable for printing or not */
+ #define ODIRSEPARATOR '\\'
- double fretone; /* Only one call to likelihood */
+ #endif
- long ipmx; /* Number of contributions */
- double sw; /* Sum of weights */
+ /* $Id$ */
- char filerespow[FILENAMELENGTH];
+ /* $State$ */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- FILE *ficresilk;
+ 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 *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ char fullversion[]="$Revision$ $Date$";
- FILE *ficresprobmorprev;
+ char strstart[80];
- FILE *fichtm, *fichtmcov; /* Html File */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- FILE *ficreseij;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char filerese[FILENAMELENGTH];
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- FILE *ficresstdeij;
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- char fileresstde[FILENAMELENGTH];
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- FILE *ficrescveij;
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- char filerescve[FILENAMELENGTH];
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- FILE  *ficresvij;
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- char fileresv[FILENAMELENGTH];
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- FILE  *ficresvpl;
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- char fileresvpl[FILENAMELENGTH];
+ int cptcov=0; /* Working variable */
- char title[MAXLINE];
+ int npar=NPARMAX;
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int nlstate=2; /* Number of live states */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char command[FILENAMELENGTH];
+ int popbased=0;
- int  outcmd=0;
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ int maxwav=0; /* Maxim number of waves */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- char filelog[FILENAMELENGTH]; /* Log file */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- char filerest[FILENAMELENGTH];
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- char fileregp[FILENAMELENGTH];
+                    to the likelihood and the sum of weights (done by funcone)*/
- char popfile[FILENAMELENGTH];
+ int mle=1, weightopt=0;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- struct timezone tzp;
+ int countcallfunc=0;  /* Count the number of calls to func */
- extern int gettimeofday();
+ double jmean=1; /* Mean space between 2 waves */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ double **matprod2(); /* test */
- long time_value;
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- extern long time();
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- char strcurr[80], strfor[80];
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- char *endptr;
+ FILE *ficlog, *ficrespow;
- long lval;
+ int globpr=0; /* Global variable for printing or not */
- double dval;
+ double fretone; /* Only one call to likelihood */
+ long ipmx=0; /* Number of contributions */
- #define NR_END 1
+ double sw; /* Sum of weights */
- #define FREE_ARG char*
+ char filerespow[FILENAMELENGTH];
- #define FTOL 1.0e-10
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
- #define NRANSI
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- #define ITMAX 200
+ FILE *ficresprobmorprev;
+ FILE *fichtm, *fichtmcov; /* Html File */
- #define TOL 2.0e-4
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
- #define CGOLD 0.3819660
+ FILE *ficresstdeij;
- #define ZEPS 1.0e-10
+ char fileresstde[FILENAMELENGTH];
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
- #define GOLD 1.618034
+ FILE  *ficresvij;
- #define GLIMIT 100.0
+ char fileresv[FILENAMELENGTH];
- #define TINY 1.0e-20
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- static double maxarg1,maxarg2;
+ char title[MAXLINE];
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char command[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ int  outcmd=0;
- static double sqrarg;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char filelog[FILENAMELENGTH]; /* Log file */
- int agegomp= AGEGOMP;
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
- int imx;
+ char popfile[FILENAMELENGTH];
- int stepm=1;
- /* Stepm, step in month: minimum step interpolation*/
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- int estepm;
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ /* struct timezone tzp; */
+ /* extern int gettimeofday(); */
- int m,nb;
+ struct tm tml, *gmtime(), *localtime();
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ extern time_t time();
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- double *ageexmed,*agecens;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- double dateintmean=0;
+ struct tm tm;
- double *weight;
+ char strcurr[80], strfor[80];
- int **s; /* Status */
- double *agedc, **covar, idx;
+ char *endptr;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ long lval;
- double *lsurv, *lpop, *tpop;
+ double dval;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ #define NR_END 1
- double ftolhess; /* Tolerance for computing hessian */
+ #define FREE_ARG char*
+ #define FTOL 1.0e-10
- /**************** split *************************/
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ #define NRANSI
- {
+ #define ITMAX 200
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ #define TOL 2.0e-4
-   */
-   char  *ss;                            /* pointer */
+ #define CGOLD 0.3819660
-   int   l1, l2;                         /* length counters */
+ #define ZEPS 1.0e-10
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-   l1 = strlen(path );                   /* length of path */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define GOLD 1.618034
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define GLIMIT 100.0
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ #define TINY 1.0e-20
-     strcpy( name, path );               /* we got the fullname name because no directory */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ static double maxarg1,maxarg2;
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-     /* get current working directory */
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-     /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-       return( GLOCK_ERROR_GETCWD );
+ #define rint(a) floor(a+0.5)
-     }
-     /* got dirc from getcwd*/
+ static double sqrarg;
-     printf(" DIRC = %s \n",dirc);
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   } else {                              /* strip direcotry from path */
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     ss++;                               /* after this, the filename */
+ int agegomp= AGEGOMP;
-     l2 = strlen( ss );                  /* length of filename */
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ int imx;
-     strcpy( name, ss );         /* save file name */
+ int stepm=1;
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ /* Stepm, step in month: minimum step interpolation*/
-     dirc[l1-l2] = 0;                    /* add zero */
-     printf(" DIRC2 = %s \n",dirc);
+ int estepm;
-   }
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-   /* We add a separator at the end of dirc if not exists */
-   l1 = strlen( dirc );                  /* length of directory */
+ int m,nb;
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ long *num;
-     dirc[l1] =  DIRSEPARATOR;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-     dirc[l1+1] = 0;
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-     printf(" DIRC3 = %s \n",dirc);
+ double **pmmij, ***probs;
-   }
+ double *ageexmed,*agecens;
-   ss = strrchr( name, '.' );            /* find last / */
+ double dateintmean=0;
-   if (ss >0){
-     ss++;
+ double *weight;
-     strcpy(ext,ss);                     /* save extension */
+ int **s; /* Status */
-     l1= strlen( name);
+ double *agedc;
-     l2= strlen(ss)+1;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-     strncpy( finame, name, l1-l2);
+                   * covar=matrix(0,NCOVMAX,1,n);
-     finame[l1-l2]= 0;
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   }
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-   return( 0 );                          /* we're done */
+ int *Ndum; /** Freq of modality (tricode */
- }
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *lsurv, *lpop, *tpop;
- /******************************************/
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- void replace_back_to_slash(char *s, char*t)
+ double ftolhess; /**< Tolerance for computing hessian */
- {
-   int i;
+ /**************** split *************************/
-   int lg=0;
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   i=0;
+ {
-   lg=strlen(t);
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   for(i=0; i<= lg; i++) {
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-     (s[i] = t[i]);
+   */
-     if (t[i]== '\\') s[i]='/';
+   char  *ss;                            /* pointer */
-   }
+   int   l1, l2;                         /* length counters */
- }
+   l1 = strlen(path );                   /* length of path */
- int nbocc(char *s, char occ)
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- {
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   int i,j=0;
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   int lg=20;
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   i=0;
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   lg=strlen(s);
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   for(i=0; i<= lg; i++) {
+     /* get current working directory */
-   if  (s[i] == occ ) j++;
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   }
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   return j;
+       return( GLOCK_ERROR_GETCWD );
- }
+     }
+     /* got dirc from getcwd*/
- void cutv(char *u,char *v, char*t, char occ)
+     printf(" DIRC = %s \n",dirc);
- {
+   } else {                              /* strip direcotry from path */
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     ss++;                               /* after this, the filename */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+     l2 = strlen( ss );                  /* length of filename */
-      gives u="abcedf" and v="ghi2j" */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   int i,lg,j,p=0;
+     strcpy( name, ss );         /* save file name */
-   i=0;
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   for(j=0; j<=strlen(t)-1; j++) {
+     dirc[l1-l2] = 0;                    /* add zero */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     printf(" DIRC2 = %s \n",dirc);
    }
+   /* We add a separator at the end of dirc if not exists */
-   lg=strlen(t);
+   l1 = strlen( dirc );                  /* length of directory */
-   for(j=0; j<p; j++) {
+   if( dirc[l1-1] != DIRSEPARATOR ){
-     (u[j] = t[j]);
+     dirc[l1] =  DIRSEPARATOR;
-   }
+     dirc[l1+1] = 0;
-      u[p]='\0';
+     printf(" DIRC3 = %s \n",dirc);
+   }
-    for(j=0; j<= lg; j++) {
+   ss = strrchr( name, '.' );            /* find last / */
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+   if (ss >0){
-   }
+     ss++;
- }
+     strcpy(ext,ss);                     /* save extension */
+     l1= strlen( name);
- /********************** nrerror ********************/
+     l2= strlen(ss)+1;
+     strncpy( finame, name, l1-l2);
- void nrerror(char error_text[])
+     finame[l1-l2]= 0;
- {
+   }
-   fprintf(stderr,"ERREUR ...\n");
-   fprintf(stderr,"%s\n",error_text);
+   return( 0 );                          /* we're done */
-   exit(EXIT_FAILURE);
+ }
- }
- /*********************** vector *******************/
- double *vector(int nl, int nh)
+ /******************************************/
- {
-   double *v;
+ void replace_back_to_slash(char *s, char*t)
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ {
-   if (!v) nrerror("allocation failure in vector");
+   int i;
-   return v-nl+NR_END;
+   int lg=0;
- }
+   i=0;
+   lg=strlen(t);
- /************************ free vector ******************/
+   for(i=0; i<= lg; i++) {
- void free_vector(double*v, int nl, int nh)
+     (s[i] = t[i]);
- {
+     if (t[i]== '\\') s[i]='/';
-   free((FREE_ARG)(v+nl-NR_END));
+   }
  }
- /************************ivector *******************************/
+ char *trimbb(char *out, char *in)
- int *ivector(long nl,long nh)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
- {
+   char *s;
-   int *v;
+   s=out;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   while (*in != '\0'){
-   if (!v) nrerror("allocation failure in ivector");
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-   return v-nl+NR_END;
+       in++;
- }
+     }
+     *out++ = *in++;
- /******************free ivector **************************/
+   }
- void free_ivector(int *v, long nl, long nh)
+   *out='\0';
- {
+   return s;
-   free((FREE_ARG)(v+nl-NR_END));
+ }
- }
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- /************************lvector *******************************/
+ {
- long *lvector(long nl,long nh)
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
- {
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   long *v;
+      gives blocc="abcdef2ghi" and alocc="j".
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-   if (!v) nrerror("allocation failure in ivector");
+   */
-   return v-nl+NR_END;
+   char *s, *t;
- }
+   t=in;s=in;
+   while ((*in != occ) && (*in != '\0')){
- /******************free lvector **************************/
+     *alocc++ = *in++;
- void free_lvector(long *v, long nl, long nh)
+   }
- {
+   if( *in == occ){
-   free((FREE_ARG)(v+nl-NR_END));
+     *(alocc)='\0';
- }
+     s=++in;
+   }
- /******************* imatrix *******************************/
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   if (s == t) {/* occ not found */
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+     *(alocc-(in-s))='\0';
- {
+     in=s;
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   }
-   int **m;
+   while ( *in != '\0'){
+     *blocc++ = *in++;
-   /* allocate pointers to rows */
+   }
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   *blocc='\0';
-   m += NR_END;
+   return t;
-   m -= nrl;
+ }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
-   /* allocate rows and set pointers to them */
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+      gives blocc="abcdef2ghi" and alocc="j".
-   m[nrl] += NR_END;
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   m[nrl] -= ncl;
+   */
+   char *s, *t;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   t=in;s=in;
+   while (*in != '\0'){
-   /* return pointer to array of pointers to rows */
+     while( *in == occ){
-   return m;
+       *blocc++ = *in++;
- }
+       s=in;
+     }
- /****************** free_imatrix *************************/
+     *blocc++ = *in++;
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   }
-       int **m;
+   if (s == t) /* occ not found */
-       long nch,ncl,nrh,nrl;
+     *(blocc-(in-s))='\0';
-      /* free an int matrix allocated by imatrix() */
+   else
- {
+     *(blocc-(in-s)-1)='\0';
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   in=s;
-   free((FREE_ARG) (m+nrl-NR_END));
+   while ( *in != '\0'){
- }
+     *alocc++ = *in++;
+   }
- /******************* matrix *******************************/
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   *alocc='\0';
- {
+   return s;
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ }
-   double **m;
+ int nbocc(char *s, char occ)
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ {
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   int i,j=0;
-   m += NR_END;
+   int lg=20;
-   m -= nrl;
+   i=0;
+   lg=strlen(s);
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   for(i=0; i<= lg; i++) {
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   if  (s[i] == occ ) j++;
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   return j;
+ }
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   return m;
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ /* { */
-    */
+ /*   /\* 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') */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
- /*************************free matrix ************************/
+ /*   int i,lg,j,p=0; */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ /*   i=0; */
- {
+ /*   lg=strlen(t); */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ /*   for(j=0; j<=lg-1; j++) { */
-   free((FREE_ARG)(m+nrl-NR_END));
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
- }
+ /*   } */
- /******************* ma3x *******************************/
+ /*   for(j=0; j<p; j++) { */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+ /*     (u[j] = t[j]); */
- {
+ /*   } */
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ /*      u[p]='\0'; */
-   double ***m;
+ /*    for(j=0; j<= lg; j++) { */
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*   } */
-   m += NR_END;
+ /* } */
-   m -= nrl;
+ #ifdef _WIN32
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ char * strsep(char **pp, const char *delim)
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ {
-   m[nrl] += NR_END;
+   char *p, *q;
-   m[nrl] -= ncl;
+   if ((p = *pp) == NULL)
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+     return 0;
+   if ((q = strpbrk (p, delim)) != NULL)
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+   {
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+     *pp = q + 1;
-   m[nrl][ncl] += NR_END;
+     *q = '\0';
-   m[nrl][ncl] -= nll;
+   }
-   for (j=ncl+1; j<=nch; j++)
+   else
-     m[nrl][j]=m[nrl][j-1]+nlay;
+     *pp = 0;
+   return p;
-   for (i=nrl+1; i<=nrh; i++) {
+ }
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ #endif
-     for (j=ncl+1; j<=nch; j++)
-       m[i][j]=m[i][j-1]+nlay;
+ /********************** nrerror ********************/
-   }
-   return m;
+ void nrerror(char error_text[])
-   /*  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)
+   fprintf(stderr,"ERREUR ...\n");
-   */
+   fprintf(stderr,"%s\n",error_text);
- }
+   exit(EXIT_FAILURE);
+ }
- /*************************free ma3x ************************/
+ /*********************** vector *******************/
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ double *vector(int nl, int nh)
  {
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   double *v;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   free((FREE_ARG)(m+nrl-NR_END));
+   if (!v) nrerror("allocation failure in vector");
- }
+   return v-nl+NR_END;
+ }
- /*************** function subdirf ***********/
- char *subdirf(char fileres[])
+ /************************ free vector ******************/
- {
+ void free_vector(double*v, int nl, int nh)
-   /* Caution optionfilefiname is hidden */
+ {
-   strcpy(tmpout,optionfilefiname);
+   free((FREE_ARG)(v+nl-NR_END));
-   strcat(tmpout,"/"); /* Add to the right */
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /************************ivector *******************************/
- }
+ int *ivector(long nl,long nh)
+ {
- /*************** function subdirf2 ***********/
+   int *v;
- char *subdirf2(char fileres[], char *preop)
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- {
+   if (!v) nrerror("allocation failure in ivector");
+   return v-nl+NR_END;
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+ /******************free ivector **************************/
-   strcat(tmpout,preop);
+ void free_ivector(int *v, long nl, long nh)
-   strcat(tmpout,fileres);
+ {
-   return tmpout;
+   free((FREE_ARG)(v+nl-NR_END));
  }
- /*************** function subdirf3 ***********/
+ /************************lvector *******************************/
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ long *lvector(long nl,long nh)
  {
+   long *v;
-   /* Caution optionfilefiname is hidden */
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   strcpy(tmpout,optionfilefiname);
+   if (!v) nrerror("allocation failure in ivector");
-   strcat(tmpout,"/");
+   return v-nl+NR_END;
-   strcat(tmpout,preop);
+ }
-   strcat(tmpout,preop2);
-   strcat(tmpout,fileres);
+ /******************free lvector **************************/
-   return tmpout;
+ void free_lvector(long *v, long nl, long nh)
- }
+ {
+   free((FREE_ARG)(v+nl-NR_END));
- /***************** f1dim *************************/
+ }
- extern int ncom;
- extern double *pcom,*xicom;
+ /******************* imatrix *******************************/
- extern double (*nrfunc)(double []);
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
- double f1dim(double x)
+ {
- {
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   int j;
+   int **m;
-   double f;
-   double *xt;
+   /* allocate pointers to rows */
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   xt=vector(1,ncom);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   m += NR_END;
-   f=(*nrfunc)(xt);
+   m -= nrl;
-   free_vector(xt,1,ncom);
-   return f;
- }
+   /* allocate rows and set pointers to them */
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
- /*****************brent *************************/
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   m[nrl] += NR_END;
- {
+   m[nrl] -= ncl;
-   int iter;
-   double a,b,d,etemp;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   double fu,fv,fw,fx;
-   double ftemp;
+   /* return pointer to array of pointers to rows */
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   return m;
-   double e=0.0;
+ }
-   a=(ax < cx ? ax : cx);
+ /****************** free_imatrix *************************/
-   b=(ax > cx ? ax : cx);
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   x=w=v=bx;
+       int **m;
-   fw=fv=fx=(*f)(x);
+       long nch,ncl,nrh,nrl;
-   for (iter=1;iter<=ITMAX;iter++) {
+      /* free an int matrix allocated by imatrix() */
-     xm=0.5*(a+b);
+ {
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   free((FREE_ARG) (m+nrl-NR_END));
-     printf(".");fflush(stdout);
+ }
-     fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+ /******************* matrix *******************************/
-     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);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ {
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
- #endif
+   double **m;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       *xmin=x;
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       return fx;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     }
+   m += NR_END;
-     ftemp=fu;
+   m -= nrl;
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       q=(x-v)*(fx-fw);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       p=(x-v)*q-(x-w)*r;
+   m[nrl] += NR_END;
-       q=2.0*(q-r);
+   m[nrl] -= ncl;
-       if (q > 0.0) p = -p;
-       q=fabs(q);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-       etemp=e;
+   return m;
-       e=d;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-       else {
+    */
-         d=p/q;
+ }
-         u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+ /*************************free matrix ************************/
-           d=SIGN(tol1,xm-x);
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-       }
+ {
-     } else {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   free((FREE_ARG)(m+nrl-NR_END));
-     }
+ }
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-     fu=(*f)(u);
+ /******************* ma3x *******************************/
-     if (fu <= fx) {
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-       if (u >= x) a=x; else b=x;
+ {
-       SHFT(v,w,x,u)
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-         SHFT(fv,fw,fx,fu)
+   double ***m;
-         } else {
-           if (u < x) a=u; else b=u;
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-           if (fu <= fw || w == x) {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-             v=w;
+   m += NR_END;
-             w=u;
+   m -= nrl;
-             fv=fw;
-             fw=fu;
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-           } else if (fu <= fv || v == x || v == w) {
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-             v=u;
+   m[nrl] += NR_END;
-             fv=fu;
+   m[nrl] -= ncl;
-           }
-         }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   }
-   nrerror("Too many iterations in brent");
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   *xmin=x;
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   return fx;
+   m[nrl][ncl] += NR_END;
- }
+   m[nrl][ncl] -= nll;
+   for (j=ncl+1; j<=nch; j++)
- /****************** mnbrak ***********************/
+     m[nrl][j]=m[nrl][j-1]+nlay;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   for (i=nrl+1; i<=nrh; i++) {
-             double (*func)(double))
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- {
+     for (j=ncl+1; j<=nch; j++)
-   double ulim,u,r,q, dum;
+       m[i][j]=m[i][j-1]+nlay;
-   double fu;
+   }
+   return m;
-   *fa=(*func)(*ax);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   *fb=(*func)(*bx);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   if (*fb > *fa) {
+   */
-     SHFT(dum,*ax,*bx,dum)
+ }
-       SHFT(dum,*fb,*fa,dum)
-       }
+ /*************************free ma3x ************************/
-   *cx=(*bx)+GOLD*(*bx-*ax);
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   *fc=(*func)(*cx);
+ {
-   while (*fb > *fc) {
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-     r=(*bx-*ax)*(*fb-*fc);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     q=(*bx-*cx)*(*fb-*fa);
+   free((FREE_ARG)(m+nrl-NR_END));
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+ }
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+ /*************** function subdirf ***********/
-     if ((*bx-u)*(u-*cx) > 0.0) {
+ char *subdirf(char fileres[])
-       fu=(*func)(u);
+ {
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+   /* Caution optionfilefiname is hidden */
-       fu=(*func)(u);
+   strcpy(tmpout,optionfilefiname);
-       if (fu < *fc) {
+   strcat(tmpout,"/"); /* Add to the right */
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   strcat(tmpout,fileres);
-           SHFT(*fb,*fc,fu,(*func)(u))
+   return tmpout;
-           }
+ }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-       u=ulim;
+ /*************** function subdirf2 ***********/
-       fu=(*func)(u);
+ char *subdirf2(char fileres[], char *preop)
-     } else {
+ {
-       u=(*cx)+GOLD*(*cx-*bx);
-       fu=(*func)(u);
+   /* Caution optionfilefiname is hidden */
-     }
+   strcpy(tmpout,optionfilefiname);
-     SHFT(*ax,*bx,*cx,u)
+   strcat(tmpout,"/");
-       SHFT(*fa,*fb,*fc,fu)
+   strcat(tmpout,preop);
-       }
+   strcat(tmpout,fileres);
- }
+   return tmpout;
+ }
- /*************** linmin ************************/
+ /*************** function subdirf3 ***********/
- int ncom;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
- double *pcom,*xicom;
+ {
- double (*nrfunc)(double []);
+   /* Caution optionfilefiname is hidden */
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   strcpy(tmpout,optionfilefiname);
- {
+   strcat(tmpout,"/");
-   double brent(double ax, double bx, double cx,
+   strcat(tmpout,preop);
-                double (*f)(double), double tol, double *xmin);
+   strcat(tmpout,preop2);
-   double f1dim(double x);
+   strcat(tmpout,fileres);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   return tmpout;
-               double *fc, double (*func)(double));
+ }
-   int j;
-   double xx,xmin,bx,ax;
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   double fx,fb,fa;
+ {
+   long sec_left, days, hours, minutes;
-   ncom=n;
+   days = (time_sec) / (60*60*24);
-   pcom=vector(1,n);
+   sec_left = (time_sec) % (60*60*24);
-   xicom=vector(1,n);
+   hours = (sec_left) / (60*60) ;
-   nrfunc=func;
+   sec_left = (sec_left) %(60*60);
-   for (j=1;j<=n;j++) {
+   minutes = (sec_left) /60;
-     pcom[j]=p[j];
+   sec_left = (sec_left) % (60);
-     xicom[j]=xi[j];
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-   }
+   return ascdiff;
-   ax=0.0;
+ }
-   xx=1.0;
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ /***************** f1dim *************************/
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ extern int ncom;
- #ifdef DEBUG
+ extern double *pcom,*xicom;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ extern double (*nrfunc)(double []);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- #endif
+ double f1dim(double x)
-   for (j=1;j<=n;j++) {
+ {
-     xi[j] *= xmin;
+   int j;
-     p[j] += xi[j];
+   double f;
-   }
+   double *xt;
-   free_vector(xicom,1,n);
-   free_vector(pcom,1,n);
+   xt=vector(1,ncom);
- }
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   f=(*nrfunc)(xt);
- char *asc_diff_time(long time_sec, char ascdiff[])
+   free_vector(xt,1,ncom);
- {
+   return f;
-   long sec_left, days, hours, minutes;
+ }
-   days = (time_sec) / (60*60*24);
-   sec_left = (time_sec) % (60*60*24);
+ /*****************brent *************************/
-   hours = (sec_left) / (60*60) ;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-   sec_left = (sec_left) %(60*60);
+ {
-   minutes = (sec_left) /60;
+   int iter;
-   sec_left = (sec_left) % (60);
+   double a,b,d,etemp;
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   double fu=0,fv,fw,fx;
-   return ascdiff;
+   double ftemp;
- }
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   double e=0.0;
- /*************** powell ************************/
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+   a=(ax < cx ? ax : cx);
-             double (*func)(double []))
+   b=(ax > cx ? ax : cx);
- {
+   x=w=v=bx;
-   void linmin(double p[], double xi[], int n, double *fret,
+   fw=fv=fx=(*f)(x);
-               double (*func)(double []));
+   for (iter=1;iter<=ITMAX;iter++) {
-   int i,ibig,j;
+     xm=0.5*(a+b);
-   double del,t,*pt,*ptt,*xit;
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   double fp,fptt;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-   double *xits;
+     printf(".");fflush(stdout);
-   int niterf, itmp;
+     fprintf(ficlog,".");fflush(ficlog);
+ #ifdef DEBUGBRENT
-   pt=vector(1,n);
+     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);
-   ptt=vector(1,n);
+     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);
-   xit=vector(1,n);
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-   xits=vector(1,n);
+ #endif
-   *fret=(*func)(p);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-   for (j=1;j<=n;j++) pt[j]=p[j];
+       *xmin=x;
-   for (*iter=1;;++(*iter)) {
+       return fx;
-     fp=(*fret);
+     }
-     ibig=0;
+     ftemp=fu;
-     del=0.0;
+     if (fabs(e) > tol1) {
-     last_time=curr_time;
+       r=(x-w)*(fx-fv);
-     (void) gettimeofday(&curr_time,&tzp);
+       q=(x-v)*(fx-fw);
-     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);
+       p=(x-v)*q-(x-w)*r;
-     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);
+       q=2.0*(q-r);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+       if (q > 0.0) p = -p;
-    for (i=1;i<=n;i++) {
+       q=fabs(q);
-       printf(" %d %.12f",i, p[i]);
+       etemp=e;
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+       e=d;
-       fprintf(ficrespow," %.12lf", p[i]);
+       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));
-     printf("\n");
+       else {
-     fprintf(ficlog,"\n");
+         d=p/q;
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+         u=x+d;
-     if(*iter <=3){
+         if (u-a < tol2 || b-u < tol2)
-       tm = *localtime(&curr_time.tv_sec);
+           d=SIGN(tol1,xm-x);
-       strcpy(strcurr,asctime(&tm));
+       }
- /*       asctime_r(&tm,strcurr); */
+     } else {
-       forecast_time=curr_time;
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       itmp = strlen(strcurr);
+     }
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-         strcurr[itmp-1]='\0';
+     fu=(*f)(u);
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     if (fu <= fx) {
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       if (u >= x) a=x; else b=x;
-       for(niterf=10;niterf<=30;niterf+=10){
+       SHFT(v,w,x,u)
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+         SHFT(fv,fw,fx,fu)
-         tmf = *localtime(&forecast_time.tv_sec);
+         } else {
- /*      asctime_r(&tmf,strfor); */
+           if (u < x) a=u; else b=u;
-         strcpy(strfor,asctime(&tmf));
+           if (fu <= fw || w == x) {
-         itmp = strlen(strfor);
+             v=w;
-         if(strfor[itmp-1]=='\n')
+             w=u;
-         strfor[itmp-1]='\0';
+             fv=fw;
-         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);
+             fw=fu;
-         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);
+           } else if (fu <= fv || v == x || v == w) {
-       }
+             v=u;
-     }
+             fv=fu;
-     for (i=1;i<=n;i++) {
+           }
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+         }
-       fptt=(*fret);
+   }
- #ifdef DEBUG
+   nrerror("Too many iterations in brent");
-       printf("fret=%lf \n",*fret);
+   *xmin=x;
-       fprintf(ficlog,"fret=%lf \n",*fret);
+   return fx;
- #endif
+ }
-       printf("%d",i);fflush(stdout);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+ /****************** mnbrak ***********************/
-       linmin(p,xit,n,fret,func);
-       if (fabs(fptt-(*fret)) > del) {
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         del=fabs(fptt-(*fret));
+             double (*func)(double))
-         ibig=i;
+ {
-       }
+   double ulim,u,r,q, dum;
- #ifdef DEBUG
+   double fu;
-       printf("%d %.12e",i,(*fret));
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   *fa=(*func)(*ax);
-       for (j=1;j<=n;j++) {
+   *fb=(*func)(*bx);
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   if (*fb > *fa) {
-         printf(" x(%d)=%.12e",j,xit[j]);
+     SHFT(dum,*ax,*bx,dum)
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+       SHFT(dum,*fb,*fa,dum)
        }
-       for(j=1;j<=n;j++) {
+   *cx=(*bx)+GOLD*(*bx-*ax);
-         printf(" p=%.12e",p[j]);
+   *fc=(*func)(*cx);
-         fprintf(ficlog," p=%.12e",p[j]);
+   while (*fb > *fc) { /* Declining fa, fb, fc */
-       }
+     r=(*bx-*ax)*(*fb-*fc);
-       printf("\n");
+     q=(*bx-*cx)*(*fb-*fa);
-       fprintf(ficlog,"\n");
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
- #endif
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     }
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
- #ifdef DEBUG
+       fu=(*func)(u);
-       int k[2],l;
+ #ifdef DEBUG
-       k[0]=1;
+       /* f(x)=A(x-u)**2+f(u) */
-       k[1]=-1;
+       double A, fparabu;
-       printf("Max: %.12e",(*func)(p));
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
-       for (j=1;j<=n;j++) {
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-         printf(" %.12e",p[j]);
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
-         fprintf(ficlog," %.12e",p[j]);
+ #endif
-       }
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-       printf("\n");
+       fu=(*func)(u);
-       fprintf(ficlog,"\n");
+       if (fu < *fc) {
-       for(l=0;l<=1;l++) {
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         for (j=1;j<=n;j++) {
+           SHFT(*fb,*fc,fu,(*func)(u))
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+           }
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       u=ulim;
-         }
+       fu=(*func)(u);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     } else {
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       u=(*cx)+GOLD*(*cx-*bx);
-       }
+       fu=(*func)(u);
- #endif
+     }
+     SHFT(*ax,*bx,*cx,u)
+       SHFT(*fa,*fb,*fc,fu)
-       free_vector(xit,1,n);
+       }
-       free_vector(xits,1,n);
+ }
-       free_vector(ptt,1,n);
-       free_vector(pt,1,n);
+ /*************** linmin ************************/
-       return;
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
-     }
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
-     for (j=1;j<=n;j++) {
+ the value of func at the returned location p . This is actually all accomplished by calling the
-       ptt[j]=2.0*p[j]-pt[j];
+ routines mnbrak and brent .*/
-       xit[j]=p[j]-pt[j];
+ int ncom;
-       pt[j]=p[j];
+ double *pcom,*xicom;
-     }
+ double (*nrfunc)(double []);
-     fptt=(*func)(ptt);
-     if (fptt < fp) {
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ {
-       if (t < 0.0) {
+   double brent(double ax, double bx, double cx,
-         linmin(p,xit,n,fret,func);
+                double (*f)(double), double tol, double *xmin);
-         for (j=1;j<=n;j++) {
+   double f1dim(double x);
-           xi[j][ibig]=xi[j][n];
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-           xi[j][n]=xit[j];
+               double *fc, double (*func)(double));
-         }
+   int j;
- #ifdef DEBUG
+   double xx,xmin,bx,ax;
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   double fx,fb,fa;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         for(j=1;j<=n;j++){
+   ncom=n;
-           printf(" %.12e",xit[j]);
+   pcom=vector(1,n);
-           fprintf(ficlog," %.12e",xit[j]);
+   xicom=vector(1,n);
-         }
+   nrfunc=func;
-         printf("\n");
+   for (j=1;j<=n;j++) {
-         fprintf(ficlog,"\n");
+     pcom[j]=p[j];
- #endif
+     xicom[j]=xi[j];
-       }
+   }
-     }
+   ax=0.0;
-   }
+   xx=1.0;
- }
+   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 */
- /**** Prevalence limit (stable or period prevalence)  ****************/
+ #ifdef DEBUG
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- {
+ #endif
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   for (j=1;j<=n;j++) {
-      matrix by transitions matrix until convergence is reached */
+     xi[j] *= xmin;
+     p[j] += xi[j];
-   int i, ii,j,k;
+   }
-   double min, max, maxmin, maxmax,sumnew=0.;
+   free_vector(xicom,1,n);
-   double **matprod2();
+   free_vector(pcom,1,n);
-   double **out, cov[NCOVMAX], **pmij();
+ }
-   double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+ /*************** powell ************************/
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+ /*
-     for (j=1;j<=nlstate+ndeath;j++){
+ Minimization of a function func of n variables. Input consists of an initial starting point
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-     }
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-    cov[1]=1.;
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+  */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-     newm=savm;
+             double (*func)(double []))
-     /* Covariates have to be included here again */
+ {
-      cov[2]=agefin;
+   void linmin(double p[], double xi[], int n, double *fret,
+               double (*func)(double []));
-       for (k=1; k<=cptcovn;k++) {
+   int i,ibig,j;
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   double del,t,*pt,*ptt,*xit;
-         /*      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]]);*/
+   double fp,fptt;
-       }
+   double *xits;
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   int niterf, itmp;
-       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]]];
+   pt=vector(1,n);
+   ptt=vector(1,n);
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+   xit=vector(1,n);
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+   xits=vector(1,n);
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+   *fret=(*func)(p);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+   for (j=1;j<=n;j++) pt[j]=p[j];
+     rcurr_time = time(NULL);
-     savm=oldm;
+   for (*iter=1;;++(*iter)) {
-     oldm=newm;
+     fp=(*fret);
-     maxmax=0.;
+     ibig=0;
-     for(j=1;j<=nlstate;j++){
+     del=0.0;
-       min=1.;
+     rlast_time=rcurr_time;
-       max=0.;
+     /* (void) gettimeofday(&curr_time,&tzp); */
-       for(i=1; i<=nlstate; i++) {
+     rcurr_time = time(NULL);
-         sumnew=0;
+     curr_time = *localtime(&rcurr_time);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-         max=FMAX(max,prlim[i][j]);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-         min=FMIN(min,prlim[i][j]);
+    for (i=1;i<=n;i++) {
-       }
+       printf(" %d %.12f",i, p[i]);
-       maxmin=max-min;
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-       maxmax=FMAX(maxmax,maxmin);
+       fprintf(ficrespow," %.12lf", p[i]);
      }
-     if(maxmax < ftolpl){
+     printf("\n");
-       return prlim;
+     fprintf(ficlog,"\n");
-     }
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-   }
+     if(*iter <=3){
- }
+       tml = *localtime(&rcurr_time);
+       strcpy(strcurr,asctime(&tml));
- /*************** transition probabilities ***************/
+       rforecast_time=rcurr_time;
+       itmp = strlen(strcurr);
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
- {
+         strcurr[itmp-1]='\0';
-   double s1, s2;
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-   /*double t34;*/
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-   int i,j,j1, nc, ii, jj;
+       for(niterf=10;niterf<=30;niterf+=10){
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-     for(i=1; i<= nlstate; i++){
+         forecast_time = *localtime(&rforecast_time);
-       for(j=1; j<i;j++){
+         strcpy(strfor,asctime(&forecast_time));
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         itmp = strlen(strfor);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+         if(strfor[itmp-1]=='\n')
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+         strfor[itmp-1]='\0';
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-         }
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-         ps[i][j]=s2;
+       }
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+     }
-       }
+     for (i=1;i<=n;i++) {
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       fptt=(*fret);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ #ifdef DEBUG
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+       printf("fret=%lf \n",*fret);
-         }
+       fprintf(ficlog,"fret=%lf \n",*fret);
-         ps[i][j]=s2;
+ #endif
-       }
+       printf("%d",i);fflush(stdout);
-     }
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     /*ps[3][2]=1;*/
+       linmin(p,xit,n,fret,func);
+       if (fabs(fptt-(*fret)) > del) {
-     for(i=1; i<= nlstate; i++){
+         del=fabs(fptt-(*fret));
-       s1=0;
+         ibig=i;
-       for(j=1; j<i; j++)
+       }
-         s1+=exp(ps[i][j]);
+ #ifdef DEBUG
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       printf("%d %.12e",i,(*fret));
-         s1+=exp(ps[i][j]);
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       ps[i][i]=1./(s1+1.);
+       for (j=1;j<=n;j++) {
-       for(j=1; j<i; j++)
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         printf(" x(%d)=%.12e",j,xit[j]);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       }
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       for(j=1;j<=n;j++) {
-     } /* end i */
+         printf(" p(%d)=%.12e",j,p[j]);
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       printf("\n");
-         ps[ii][jj]=0;
+       fprintf(ficlog,"\n");
-         ps[ii][ii]=1;
+ #endif
-       }
+     } /* end i */
-     }
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+ #ifdef DEBUG
+       int k[2],l;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       k[0]=1;
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       k[1]=-1;
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       printf("Max: %.12e",(*func)(p));
- /*       } */
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
- /*       printf("\n "); */
+       for (j=1;j<=n;j++) {
- /*        } */
+         printf(" %.12e",p[j]);
- /*        printf("\n ");printf("%lf ",cov[2]); */
+         fprintf(ficlog," %.12e",p[j]);
-        /*
+       }
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       printf("\n");
-       goto end;*/
+       fprintf(ficlog,"\n");
-     return ps;
+       for(l=0;l<=1;l++) {
- }
+         for (j=1;j<=n;j++) {
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
- /**************** Product of 2 matrices ******************/
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+         }
- {
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+       }
-   /* in, b, out are matrice of pointers which should have been initialized
+ #endif
-      before: only the contents of out is modified. The function returns
-      a pointer to pointers identical to out */
-   long i, j, k;
+       free_vector(xit,1,n);
-   for(i=nrl; i<= nrh; i++)
+       free_vector(xits,1,n);
-     for(k=ncolol; k<=ncoloh; k++)
+       free_vector(ptt,1,n);
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+       free_vector(pt,1,n);
-         out[i][k] +=in[i][j]*b[j][k];
+       return;
+     }
-   return out;
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
- }
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
+       ptt[j]=2.0*p[j]-pt[j];
+       xit[j]=p[j]-pt[j];
- /************* Higher Matrix Product ***************/
+       pt[j]=p[j];
+     }
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+     fptt=(*func)(ptt);
- {
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-   /* Computes the transition matrix starting at age 'age' over
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-      'nhstepm*hstepm*stepm' months (i.e. until
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
-      nhstepm*hstepm matrices.
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-      (typically every 2 years instead of every month which is too big
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
-      for the memory).
+       /* Thus we compare delta(2h) with observed f1-f3 */
-      Model is determined by parameters x and covariates have to be
+       /* or best gain on one ancient line 'del' with total  */
-      included manually here.
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-      */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-   int i, j, d, h, k;
+       t= t- del*SQR(fp-fptt);
-   double **out, cov[NCOVMAX];
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-   double **newm;
+       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);
+ #ifdef DEBUG
-   /* Hstepm could be zero and should return the unit matrix */
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   for (i=1;i<=nlstate+ndeath;i++)
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-     for (j=1;j<=nlstate+ndeath;j++){
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       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);
-     }
+       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);
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ #endif
-   for(h=1; h <=nhstepm; h++){
+       if (t < 0.0) { /* Then we use it for last direction */
-     for(d=1; d <=hstepm; d++){
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
-       newm=savm;
+         for (j=1;j<=n;j++) {
-       /* Covariates have to be included here again */
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-       cov[1]=1.;
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+         }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-       for (k=1; k<=cptcovage;k++)
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+ #ifdef DEBUG
-         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<=n;j++){
+           printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+         }
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+         printf("\n");
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+         fprintf(ficlog,"\n");
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ #endif
-       savm=oldm;
+       } /* end of t negative */
-       oldm=newm;
+     } /* end if (fptt < fp)  */
-     }
+   }
-     for(i=1; i<=nlstate+ndeath; i++)
+ }
-       for(j=1;j<=nlstate+ndeath;j++) {
-         po[i][j][h]=newm[i][j];
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
-          */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-       }
+ {
-   } /* end h */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-   return po;
+      matrix by transitions matrix until convergence is reached */
- }
+   int i, ii,j,k;
+   double min, max, maxmin, maxmax,sumnew=0.;
- /*************** log-likelihood *************/
+   /* double **matprod2(); */ /* test */
- double func( double *x)
+   double **out, cov[NCOVMAX+1], **pmij();
- {
+   double **newm;
-   int i, ii, j, k, mi, d, kk;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
-   double **out;
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-   double sw; /* Sum of weights */
+     for (j=1;j<=nlstate+ndeath;j++){
-   double lli; /* Individual log likelihood */
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int s1, s2;
+     }
-   double bbh, survp;
-   long ipmx;
+    cov[1]=1.;
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-   /*for(i=1;i<imx;i++)
+     newm=savm;
-     printf(" %d\n",s[4][i]);
+     /* Covariates have to be included here again */
-   */
+     cov[2]=agefin;
-   cov[1]=1.;
+     for (k=1; k<=cptcovn;k++) {
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       /*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]]);*/
-   if(mle==1){
+     }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-       for(mi=1; mi<= wav[i]-1; mi++){
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-           }
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-         for(d=0; d<dh[mi][i]; d++){
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-           newm=savm;
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
+     savm=oldm;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     oldm=newm;
-           }
+     maxmax=0.;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     for(j=1;j<=nlstate;j++){
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       min=1.;
-           savm=oldm;
+       max=0.;
-           oldm=newm;
+       for(i=1; i<=nlstate; i++) {
-         } /* end mult */
+         sumnew=0;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+         max=FMAX(max,prlim[i][j]);
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+         min=FMIN(min,prlim[i][j]);
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+       }
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+       maxmin=max-min;
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       maxmax=FMAX(maxmax,maxmin);
-          * probability in order to take into account the bias as a fraction of the way
+     }
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+     if(maxmax < ftolpl){
-          * -stepm/2 to stepm/2 .
+       return prlim;
-          * 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.
+   }
-          */
+ }
-         s1=s[mw[mi][i]][i];
-         s2=s[mw[mi+1][i]][i];
+ /*************** transition probabilities ***************/
-         bbh=(double)bh[mi][i]/(double)stepm;
-         /* bias bh is positive if real duration
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-          * is higher than the multiple of stepm and negative otherwise.
+ {
-          */
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+      computes the probability to be observed in state j being in state i by appying the
-         if( s2 > nlstate){
+      model to the ncovmodel covariates (including constant and age).
-           /* i.e. if s2 is a death state and if the date of death is known
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-              then the contribution to the likelihood is the probability to
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-              die between last step unit time and current  step unit time,
+      ncth covariate in the global vector x is given by the formula:
-              which is also equal to probability to die before dh
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-              minus probability to die before dh-stepm .
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-              In version up to 0.92 likelihood was computed
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         as if date of death was unknown. Death was treated as any other
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         health state: the date of the interview describes the actual state
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-         and not the date of a change in health state. The former idea was
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         to consider that at each interview the state was recorded
+   */
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   double s1, lnpijopii;
-         introduced the exact date of death then we should have modified
+   /*double t34;*/
-         the contribution of an exact death to the likelihood. This new
+   int i,j,j1, nc, ii, jj;
-         contribution is smaller and very dependent of the step unit
-         stepm. It is no more the probability to die between last interview
+     for(i=1; i<= nlstate; i++){
-         and month of death but the probability to survive from last
+       for(j=1; j<i;j++){
-         interview up to one month before death multiplied by the
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         probability to die within a month. Thanks to Chris
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         Jackson for correcting this bug.  Former versions increased
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-         mortality artificially. The bad side is that we add another loop
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         which slows down the processing. The difference can be up to 10%
+         }
-         lower mortality.
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-           */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         } else if  (s2==-2) {
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-           for (j=1,survp=0. ; j<=nlstate; j++)
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-           /*survp += out[s1][j]; */
+         }
-           lli= log(survp);
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         }
+       }
+     }
-         else if  (s2==-4) {
-           for (j=3,survp=0. ; j<=nlstate; 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 if  (s2==-5) {
+       }
-           for (j=1,survp=0. ; j<=2; j++)
+       for(j=i+1; j<=nlstate+ndeath; j++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           lli= log(survp);
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         }
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         else{
+       ps[i][i]=1./(s1+1.);
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       /* Computing other pijs */
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+       for(j=1; j<i; j++)
-         }
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         /*if(lli ==000.0)*/
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         /*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][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         ipmx +=1;
+     } /* end i */
-         sw += weight[i];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       } /* end of wave */
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-     } /* end of individual */
+         ps[ii][jj]=0;
-   }  else if(mle==2){
+         ps[ii][ii]=1;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     }
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-           }
+     /*   } */
-         for(d=0; d<=dh[mi][i]; d++){
+     /*   printf("\n "); */
-           newm=savm;
+     /* } */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+     /*
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-           }
+       goto end;*/
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+     return ps;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ }
-           savm=oldm;
-           oldm=newm;
+ /**************** Product of 2 matrices ******************/
-         } /* end mult */
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         s1=s[mw[mi][i]][i];
+ {
-         s2=s[mw[mi+1][i]][i];
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-         bbh=(double)bh[mi][i]/(double)stepm;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+   /* in, b, out are matrice of pointers which should have been initialized
-         ipmx +=1;
+      before: only the contents of out is modified. The function returns
-         sw += weight[i];
+      a pointer to pointers identical to out */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   int i, j, k;
-       } /* end of wave */
+   for(i=nrl; i<= nrh; i++)
-     } /* end of individual */
+     for(k=ncolol; k<=ncoloh; k++){
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+       out[i][k]=0.;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for(j=ncl; j<=nch; j++)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         out[i][k] +=in[i][j]*b[j][k];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   return out;
-           for (j=1;j<=nlstate+ndeath;j++){
+ }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           }
+ /************* Higher Matrix Product ***************/
-         for(d=0; d<dh[mi][i]; d++){
-           newm=savm;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ {
-           for (kk=1; kk<=cptcovage;kk++) {
+   /* Computes the transition matrix starting at age 'age' over
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      'nhstepm*hstepm*stepm' months (i.e. until
-           }
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      nhstepm*hstepm matrices.
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-           savm=oldm;
+      (typically every 2 years instead of every month which is too big
-           oldm=newm;
+      for the memory).
-         } /* end mult */
+      Model is determined by parameters x and covariates have to be
+      included manually here.
-         s1=s[mw[mi][i]][i];
-         s2=s[mw[mi+1][i]][i];
+      */
-         bbh=(double)bh[mi][i]/(double)stepm;
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+   int i, j, d, h, k;
-         ipmx +=1;
+   double **out, cov[NCOVMAX+1];
-         sw += weight[i];
+   double **newm;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       } /* end of wave */
+   /* Hstepm could be zero and should return the unit matrix */
-     } /* end of individual */
+   for (i=1;i<=nlstate+ndeath;i++)
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+     for (j=1;j<=nlstate+ndeath;j++){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-           for (j=1;j<=nlstate+ndeath;j++){
+   for(h=1; h <=nhstepm; h++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for(d=1; d <=hstepm; d++){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       newm=savm;
-           }
+       /* Covariates have to be included here again */
-         for(d=0; d<dh[mi][i]; d++){
+       cov[1]=1.;
-           newm=savm;
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       for (k=1; k<=cptcovn;k++)
-           for (kk=1; kk<=cptcovage;kk++) {
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for (k=1; k<=cptcovage;k++)
-           }
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
-           oldm=newm;
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-         } /* end mult */
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-         s1=s[mw[mi][i]][i];
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-         s2=s[mw[mi+1][i]][i];
+       savm=oldm;
-         if( s2 > nlstate){
+       oldm=newm;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+     }
-         }else{
+     for(i=1; i<=nlstate+ndeath; i++)
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       for(j=1;j<=nlstate+ndeath;j++) {
-         }
+         po[i][j][h]=newm[i][j];
-         ipmx +=1;
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-         sw += weight[i];
+       }
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     /*printf("h=%d ",h);*/
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+   } /* end h */
-       } /* end of wave */
+ /*     printf("\n H=%d \n",h); */
-     } /* end of individual */
+   return po;
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+ }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ #ifdef NLOPT
-       for(mi=1; mi<= wav[i]-1; mi++){
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   double fret;
-           for (j=1;j<=nlstate+ndeath;j++){
+   double *xt;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   int j;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   myfunc_data *d2 = (myfunc_data *) pd;
-           }
+ /* xt = (p1-1); */
-         for(d=0; d<dh[mi][i]; d++){
+   xt=vector(1,n);
-           newm=savm;
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-           }
+   printf("Function = %.12lf ",fret);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   printf("\n");
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+  free_vector(xt,1,n);
-           savm=oldm;
+   return fret;
-           oldm=newm;
+ }
-         } /* end mult */
+ #endif
-         s1=s[mw[mi][i]][i];
+ /*************** log-likelihood *************/
-         s2=s[mw[mi+1][i]][i];
+ double func( double *x)
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ {
-         ipmx +=1;
+   int i, ii, j, k, mi, d, kk;
-         sw += weight[i];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   double **out;
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+   double sw; /* Sum of weights */
-       } /* end of wave */
+   double lli; /* Individual log likelihood */
-     } /* end of individual */
+   int s1, s2;
-   } /* End of if */
+   double bbh, survp;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   long ipmx;
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   /*extern weight */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   /* We are differentiating ll according to initial status */
-   return -l;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- }
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
- /*************** log-likelihood *************/
+   */
- double funcone( double *x)
- {
+   ++countcallfunc;
-   /* Same as likeli but slower because of a lot of printf and if */
-   int i, ii, j, k, mi, d, kk;
+   cov[1]=1.;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
-   double **out;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   double lli; /* Individual log likelihood */
-   double llt;
+   if(mle==1){
-   int s1, s2;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double bbh, survp;
+       /* Computes the values of the ncovmodel covariates of the model
-   /*extern weight */
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-   /* We are differentiating ll according to initial status */
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+          to be observed in j being in i according to the model.
-   /*for(i=1;i<imx;i++)
+        */
-     printf(" %d\n",s[4][i]);
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-   */
+         cov[2+k]=covar[Tvar[k]][i];
-   cov[1]=1.;
+       }
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for(mi=1; mi<= wav[i]-1; mi++){
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for(mi=1; mi<= wav[i]-1; mi++){
+           for (j=1;j<=nlstate+ndeath;j++){
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+             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[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++){
-         }
+           newm=savm;
-       for(d=0; d<dh[mi][i]; d++){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         newm=savm;
+           for (kk=1; kk<=cptcovage;kk++) {
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-         for (kk=1; kk<=cptcovage;kk++) {
+           }
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           savm=oldm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           oldm=newm;
-         savm=oldm;
+         } /* end mult */
-         oldm=newm;
-       } /* end mult */
+         /*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.
-       s1=s[mw[mi][i]][i];
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-       s2=s[mw[mi+1][i]][i];
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-       bbh=(double)bh[mi][i]/(double)stepm;
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-       /* bias is positive if real duration
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-        * is higher than the multiple of stepm and negative otherwise.
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-        */
+          * probability in order to take into account the bias as a fraction of the way
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         lli=log(out[s1][s2] - savm[s1][s2]);
+          * -stepm/2 to stepm/2 .
-       } else if  (s2==-2) {
+          * For stepm=1 the results are the same as for previous versions of Imach.
-         for (j=1,survp=0. ; j<=nlstate; j++)
+          * For stepm > 1 the results are less biased than in previous versions.
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+          */
-         lli= log(survp);
+         s1=s[mw[mi][i]][i];
-       }else if (mle==1){
+         s2=s[mw[mi+1][i]][i];
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         bbh=(double)bh[mi][i]/(double)stepm;
-       } else if(mle==2){
+         /* bias bh is positive if real duration
-         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 */
+          * is higher than the multiple of stepm and negative otherwise.
-       } 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 */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         if( s2 > nlstate){
-         lli=log(out[s1][s2]); /* Original formula */
+           /* i.e. if s2 is a death state and if the date of death is known
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+              then the contribution to the likelihood is the probability to
-         lli=log(out[s1][s2]); /* Original formula */
+              die between last step unit time and current  step unit time,
-       } /* End of if */
+              which is also equal to probability to die before dh
-       ipmx +=1;
+              minus probability to die before dh-stepm .
-       sw += weight[i];
+              In version up to 0.92 likelihood was computed
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         as if date of death was unknown. Death was treated as any other
- /*       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]); */
+         health state: the date of the interview describes the actual state
-       if(globpr){
+         and not the date of a change in health state. The former idea was
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         to consider that at each interview the state was recorded
-  %11.6f %11.6f %11.6f ", \
+         (healthy, disable or death) and IMaCh was corrected; but when we
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+         introduced the exact date of death then we should have modified
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         the contribution of an exact death to the likelihood. This new
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         contribution is smaller and very dependent of the step unit
-           llt +=ll[k]*gipmx/gsw;
+         stepm. It is no more the probability to die between last interview
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         and month of death but the probability to survive from last
-         }
+         interview up to one month before death multiplied by the
-         fprintf(ficresilk," %10.6f\n", -llt);
+         probability to die within a month. Thanks to Chris
-       }
+         Jackson for correcting this bug.  Former versions increased
-     } /* end of wave */
+         mortality artificially. The bad side is that we add another loop
-   } /* end of individual */
+         which slows down the processing. The difference can be up to 10%
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         lower mortality.
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   if(globpr==0){ /* First time we count the contributions and weights */
-     gipmx=ipmx;
-     gsw=sw;
+         } else if  (s2==-2) {
-   }
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   return -l;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- }
+           /*survp += out[s1][j]; */
+           lli= log(survp);
+         }
- /*************** function likelione ***********/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+         else if  (s2==-4) {
- {
+           for (j=3,survp=0. ; j<=nlstate; j++)
-   /* This routine should help understanding what is done with
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[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==-5) {
-   int k;
+           for (j=1,survp=0. ; j<=2; 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{
-       printf("Problem with resultfile: %s\n", fileresilk);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-     }
+         }
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+         /*if(lli ==000.0)*/
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-     for(k=1; k<=nlstate; k++)
+         ipmx +=1;
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+         sw += weight[i];
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   }
+       } /* end of wave */
+     } /* end of individual */
-   *fretone=(*funcone)(p);
+   }  else if(mle==2){
-   if(*globpri !=0){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     fclose(ficresilk);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       for(mi=1; mi<= wav[i]-1; mi++){
-     fflush(fichtm);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+           for (j=1;j<=nlstate+ndeath;j++){
-   return;
+             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++){
- /*********** Maximum Likelihood Estimation ***************/
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+           for (kk=1; kk<=cptcovage;kk++) {
- {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   int i,j, iter;
+           }
-   double **xi;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   double fret;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   double fretone; /* Only one call to likelihood */
+           savm=oldm;
-   /*  char filerespow[FILENAMELENGTH];*/
+           oldm=newm;
-   xi=matrix(1,npar,1,npar);
+         } /* end mult */
-   for (i=1;i<=npar;i++)
-     for (j=1;j<=npar;j++)
+         s1=s[mw[mi][i]][i];
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         s2=s[mw[mi+1][i]][i];
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         bbh=(double)bh[mi][i]/(double)stepm;
-   strcpy(filerespow,"pow");
+         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 */
-   strcat(filerespow,fileres);
+         ipmx +=1;
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         sw += weight[i];
-     printf("Problem with resultfile: %s\n", filerespow);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+       } /* end of wave */
-   }
+     } /* end of individual */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-   for (i=1;i<=nlstate;i++)
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for(j=1;j<=nlstate+ndeath;j++)
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   fprintf(ficrespow,"\n");
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (j=1;j<=nlstate+ndeath;j++){
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   free_matrix(xi,1,npar,1,npar);
+           }
-   fclose(ficrespow);
+         for(d=0; d<dh[mi][i]; d++){
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+           newm=savm;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- /**** Computes Hessian and covariance matrix ***/
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+           savm=oldm;
- {
+           oldm=newm;
-   double  **a,**y,*x,pd;
+         } /* end mult */
-   double **hess;
-   int i, j,jk;
+         s1=s[mw[mi][i]][i];
-   int *indx;
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+         ipmx +=1;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+         sw += weight[i];
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double gompertz(double p[]);
+       } /* end of wave */
-   hess=matrix(1,npar,1,npar);
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   for (i=1;i<=npar;i++){
+       for(mi=1; mi<= wav[i]-1; mi++){
-     printf("%d",i);fflush(stdout);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-     /*  printf(" %f ",p[i]);
+         for(d=0; d<dh[mi][i]; d++){
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+           newm=savm;
-   }
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
-   for (i=1;i<=npar;i++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     for (j=1;j<=npar;j++)  {
+           }
-       if (j>i) {
-         printf(".%d%d",i,j);fflush(stdout);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+           savm=oldm;
+           oldm=newm;
-         hess[j][i]=hess[i][j];
+         } /* end mult */
-         /*printf(" %lf ",hess[i][j]);*/
-       }
+         s1=s[mw[mi][i]][i];
-     }
+         s2=s[mw[mi+1][i]][i];
-   }
+         if( s2 > nlstate){
-   printf("\n");
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   fprintf(ficlog,"\n");
+         }else{
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+         }
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+         ipmx +=1;
+         sw += weight[i];
-   a=matrix(1,npar,1,npar);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   y=matrix(1,npar,1,npar);
+ /*      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]); */
-   x=vector(1,npar);
+       } /* end of wave */
-   indx=ivector(1,npar);
+     } /* end of individual */
-   for (i=1;i<=npar;i++)
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   ludcmp(a,npar,indx,&pd);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-   for (j=1;j<=npar;j++) {
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1;i<=npar;i++) x[i]=0;
+           for (j=1;j<=nlstate+ndeath;j++){
-     x[j]=1;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     lubksb(a,npar,indx,x);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for (i=1;i<=npar;i++){
+           }
-       matcov[i][j]=x[i];
+         for(d=0; d<dh[mi][i]; d++){
-     }
+           newm=savm;
-   }
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           for (kk=1; kk<=cptcovage;kk++) {
-   printf("\n#Hessian matrix#\n");
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+           }
-   for (i=1;i<=npar;i++) {
-     for (j=1;j<=npar;j++) {
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       printf("%.3e ",hess[i][j]);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+           savm=oldm;
-     }
+           oldm=newm;
-     printf("\n");
+         } /* end mult */
-     fprintf(ficlog,"\n");
-   }
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-   /* Recompute Inverse */
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   for (i=1;i<=npar;i++)
+         ipmx +=1;
-     for (j=1;j<=npar;j++) a[i][j]=matcov[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]);*/
-   /*  printf("\n#Hessian matrix recomputed#\n");
+       } /* end of wave */
+     } /* end of individual */
-   for (j=1;j<=npar;j++) {
+   } /* End of if */
-     for (i=1;i<=npar;i++) x[i]=0;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     x[j]=1;
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     lubksb(a,npar,indx,x);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     for (i=1;i<=npar;i++){
+   return -l;
-       y[i][j]=x[i];
+ }
-       printf("%.3e ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
+ /*************** log-likelihood *************/
-     }
+ double funcone( double *x)
-     printf("\n");
+ {
-     fprintf(ficlog,"\n");
+   /* Same as likeli but slower because of a lot of printf and if */
-   }
+   int i, ii, j, k, mi, d, kk;
-   */
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
-   free_matrix(a,1,npar,1,npar);
+   double lli; /* Individual log likelihood */
-   free_matrix(y,1,npar,1,npar);
+   double llt;
-   free_vector(x,1,npar);
+   int s1, s2;
-   free_ivector(indx,1,npar);
+   double bbh, survp;
-   free_matrix(hess,1,npar,1,npar);
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- }
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
- /*************** hessian matrix ****************/
+   */
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   cov[1]=1.;
- {
-   int i;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   int l=1, lmax=20;
-   double k1,k2;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double p2[NPARMAX+1];
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   double res;
+     for(mi=1; mi<= wav[i]-1; mi++){
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-   double fx;
+         for (j=1;j<=nlstate+ndeath;j++){
-   int k=0,kmax=10;
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double l1;
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
-   fx=func(x);
+       for(d=0; d<dh[mi][i]; d++){
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+         newm=savm;
-   for(l=0 ; l <=lmax; l++){
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     l1=pow(10,l);
+         for (kk=1; kk<=cptcovage;kk++) {
-     delts=delt;
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     for(k=1 ; k <kmax; k=k+1){
+         }
-       delt = delta*(l1*k);
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-       p2[theta]=x[theta] +delt;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       k1=func(p2)-fx;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       p2[theta]=x[theta]-delt;
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-       k2=func(p2)-fx;
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+         savm=oldm;
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+         oldm=newm;
+       } /* end mult */
- #ifdef DEBUG
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       s1=s[mw[mi][i]][i];
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+       s2=s[mw[mi+1][i]][i];
- #endif
+       bbh=(double)bh[mi][i]/(double)stepm;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+       /* bias is positive if real duration
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+        * is higher than the multiple of stepm and negative otherwise.
-         k=kmax;
+        */
-       }
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+         lli=log(out[s1][s2] - savm[s1][s2]);
-         k=kmax; l=lmax*10.;
+       } else if  (s2==-2) {
-       }
+         for (j=1,survp=0. ; j<=nlstate; j++)
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         delts=delt;
+         lli= log(survp);
-       }
+       }else if (mle==1){
-     }
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   }
+       } else if(mle==2){
-   delti[theta]=delts;
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   return res;
+       } 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 */
- }
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         lli=log(out[s1][s2]); /* Original formula */
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+       } else{  /* mle=0 back to 1 */
- {
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   int i;
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   int l=1, l1, lmax=20;
+       } /* End of if */
-   double k1,k2,k3,k4,res,fx;
+       ipmx +=1;
-   double p2[NPARMAX+1];
+       sw += weight[i];
-   int k;
+       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]); */
-   fx=func(x);
+       if(globpr){
-   for (k=1; k<=2; k++) {
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+  %11.6f %11.6f %11.6f ", \
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     k1=func(p2)-fx;
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+         }
-     k2=func(p2)-fx;
+         fprintf(ficresilk," %10.6f\n", -llt);
+       }
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     } /* end of wave */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   } /* end of individual */
-     k3=func(p2)-fx;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   if(globpr==0){ /* First time we count the contributions and weights */
-     k4=func(p2)-fx;
+     gipmx=ipmx;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     gsw=sw;
- #ifdef DEBUG
+   }
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+   return -l;
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ }
- #endif
-   }
-   return res;
+ /*************** function likelione ***********/
- }
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ {
- /************** Inverse of matrix **************/
+   /* This routine should help understanding what is done with
- void ludcmp(double **a, int n, int *indx, double *d)
+      the selection of individuals/waves and
- {
+      to check the exact contribution to the likelihood.
-   int i,imax,j,k;
+      Plotting could be done.
-   double big,dum,sum,temp;
+    */
-   double *vv;
+   int k;
-   vv=vector(1,n);
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-   *d=1.0;
+     strcpy(fileresilk,"ilk");
-   for (i=1;i<=n;i++) {
+     strcat(fileresilk,fileres);
-     big=0.0;
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-     for (j=1;j<=n;j++)
+       printf("Problem with resultfile: %s\n", fileresilk);
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     }
-     vv[i]=1.0/big;
+     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 ");
-   for (j=1;j<=n;j++) {
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-     for (i=1;i<j;i++) {
+     for(k=1; k<=nlstate; k++)
-       sum=a[i][j];
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-       a[i][j]=sum;
+   }
-     }
-     big=0.0;
+   *fretone=(*funcone)(p);
-     for (i=j;i<=n;i++) {
+   if(*globpri !=0){
-       sum=a[i][j];
+     fclose(ficresilk);
-       for (k=1;k<j;k++)
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-         sum -= a[i][k]*a[k][j];
+     fflush(fichtm);
-       a[i][j]=sum;
+   }
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   return;
-         big=dum;
+ }
-         imax=i;
-       }
-     }
+ /*********** Maximum Likelihood Estimation ***************/
-     if (j != imax) {
-       for (k=1;k<=n;k++) {
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-         dum=a[imax][k];
+ {
-         a[imax][k]=a[j][k];
+   int i,j, iter;
-         a[j][k]=dum;
+   double **xi;
-       }
+   double fret;
-       *d = -(*d);
+   double fretone; /* Only one call to likelihood */
-       vv[imax]=vv[j];
+   /*  char filerespow[FILENAMELENGTH];*/
-     }
-     indx[j]=imax;
+ #ifdef NLOPT
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   int creturn;
-     if (j != n) {
+   nlopt_opt opt;
-       dum=1.0/(a[j][j]);
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   double *lb;
-     }
+   double minf; /* the minimum objective value, upon return */
-   }
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-   free_vector(vv,1,n);  /* Doesn't work */
+   myfunc_data dinst, *d = &dinst;
- ;
+ #endif
- }
- void lubksb(double **a, int n, int *indx, double b[])
+   xi=matrix(1,npar,1,npar);
- {
+   for (i=1;i<=npar;i++)
-   int i,ii=0,ip,j;
+     for (j=1;j<=npar;j++)
-   double sum;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   for (i=1;i<=n;i++) {
+   strcpy(filerespow,"pow");
-     ip=indx[i];
+   strcat(filerespow,fileres);
-     sum=b[ip];
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     b[ip]=b[i];
+     printf("Problem with resultfile: %s\n", filerespow);
-     if (ii)
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+   }
-     else if (sum) ii=i;
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     b[i]=sum;
+   for (i=1;i<=nlstate;i++)
-   }
+     for(j=1;j<=nlstate+ndeath;j++)
-   for (i=n;i>=1;i--) {
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     sum=b[i];
+   fprintf(ficrespow,"\n");
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+ #ifdef POWELL
-     b[i]=sum/a[i][i];
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-   }
+ #endif
- }
+ #ifdef NLOPT
- void pstamp(FILE *fichier)
+ #ifdef NEWUOA
- {
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ #else
- }
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+ #endif
- /************ Frequencies ********************/
+   lb=vector(0,npar-1);
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
- {  /* Some frequencies */
+   nlopt_set_lower_bounds(opt, lb);
+   nlopt_set_initial_step1(opt, 0.1);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
-   int first;
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
-   double ***freq; /* Frequencies */
+   d->function = func;
-   double *pp, **prop;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   nlopt_set_min_objective(opt, myfunc, d);
-   char fileresp[FILENAMELENGTH];
+   nlopt_set_xtol_rel(opt, ftol);
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
-   pp=vector(1,nlstate);
+     printf("nlopt failed! %d\n",creturn);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   }
-   strcpy(fileresp,"p");
+   else {
-   strcat(fileresp,fileres);
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+     iter=1; /* not equal */
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   }
-     exit(0);
+   nlopt_destroy(opt);
-   }
+ #endif
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   free_matrix(xi,1,npar,1,npar);
-   j1=0;
+   fclose(ficrespow);
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   j=cptcoveff;
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   first=1;
+ }
-   for(k1=1; k1<=j;k1++){
+ /**** Computes Hessian and covariance matrix ***/
-     for(i1=1; i1<=ncodemax[k1];i1++){
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-       j1++;
+ {
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   double  **a,**y,*x,pd;
-         scanf("%d", i);*/
+   double **hess;
-       for (i=-5; i<=nlstate+ndeath; i++)
+   int i, j,jk;
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   int *indx;
-           for(m=iagemin; m <= iagemax+3; m++)
-             freq[i][jk][m]=0;
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-     for (i=1; i<=nlstate; i++)
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-       for(m=iagemin; m <= iagemax+3; m++)
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-         prop[i][m]=0;
+   double gompertz(double p[]);
+   hess=matrix(1,npar,1,npar);
-       dateintsum=0;
-       k2cpt=0;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-       for (i=1; i<=imx; i++) {
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-         bool=1;
+   for (i=1;i<=npar;i++){
-         if  (cptcovn>0) {
+     printf("%d",i);fflush(stdout);
-           for (z1=1; z1<=cptcoveff; z1++)
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-         }
-         if (bool==1){
+     /*  printf(" %f ",p[i]);
-           for(m=firstpass; m<=lastpass; m++){
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-             k2=anint[m][i]+(mint[m][i]/12.);
+   }
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   for (i=1;i<=npar;i++) {
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     for (j=1;j<=npar;j++)  {
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+       if (j>i) {
-               if (m<lastpass) {
+         printf(".%d%d",i,j);fflush(stdout);
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-               }
+         hess[j][i]=hess[i][j];
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+         /*printf(" %lf ",hess[i][j]);*/
-                 dateintsum=dateintsum+k2;
+       }
-                 k2cpt++;
+     }
-               }
+   }
-               /*}*/
+   printf("\n");
-           }
+   fprintf(ficlog,"\n");
-         }
-       }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
+   a=matrix(1,npar,1,npar);
-       if  (cptcovn>0) {
+   y=matrix(1,npar,1,npar);
-         fprintf(ficresp, "\n#********** Variable ");
+   x=vector(1,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   indx=ivector(1,npar);
-         fprintf(ficresp, "**********\n#");
+   for (i=1;i<=npar;i++)
-       }
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-       for(i=1; i<=nlstate;i++)
+   ludcmp(a,npar,indx,&pd);
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresp, "\n");
+   for (j=1;j<=npar;j++) {
+     for (i=1;i<=npar;i++) x[i]=0;
-       for(i=iagemin; i <= iagemax+3; i++){
+     x[j]=1;
-         if(i==iagemax+3){
+     lubksb(a,npar,indx,x);
-           fprintf(ficlog,"Total");
+     for (i=1;i<=npar;i++){
-         }else{
+       matcov[i][j]=x[i];
-           if(first==1){
+     }
-             first=0;
+   }
-             printf("See log file for details...\n");
-           }
+   printf("\n#Hessian matrix#\n");
-           fprintf(ficlog,"Age %d", i);
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-         }
+   for (i=1;i<=npar;i++) {
-         for(jk=1; jk <=nlstate ; jk++){
+     for (j=1;j<=npar;j++) {
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       printf("%.3e ",hess[i][j]);
-             pp[jk] += freq[jk][m][i];
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-         }
+     }
-         for(jk=1; jk <=nlstate ; jk++){
+     printf("\n");
-           for(m=-1, pos=0; m <=0 ; m++)
+     fprintf(ficlog,"\n");
-             pos += freq[jk][m][i];
+   }
-           if(pp[jk]>=1.e-10){
-             if(first==1){
+   /* Recompute Inverse */
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   for (i=1;i<=npar;i++)
-             }
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   ludcmp(a,npar,indx,&pd);
-           }else{
-             if(first==1)
+   /*  printf("\n#Hessian matrix recomputed#\n");
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (j=1;j<=npar;j++) {
-           }
+     for (i=1;i<=npar;i++) x[i]=0;
-         }
+     x[j]=1;
+     lubksb(a,npar,indx,x);
-         for(jk=1; jk <=nlstate ; jk++){
+     for (i=1;i<=npar;i++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+       y[i][j]=x[i];
-             pp[jk] += freq[jk][m][i];
+       printf("%.3e ",y[i][j]);
-         }
+       fprintf(ficlog,"%.3e ",y[i][j]);
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+     }
-           pos += pp[jk];
+     printf("\n");
-           posprop += prop[jk][i];
+     fprintf(ficlog,"\n");
-         }
+   }
-         for(jk=1; jk <=nlstate ; jk++){
+   */
-           if(pos>=1.e-5){
-             if(first==1)
+   free_matrix(a,1,npar,1,npar);
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   free_matrix(y,1,npar,1,npar);
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+   free_vector(x,1,npar);
-           }else{
+   free_ivector(indx,1,npar);
-             if(first==1)
+   free_matrix(hess,1,npar,1,npar);
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-           }
+ }
-           if( i <= iagemax){
-             if(pos>=1.e-5){
+ /*************** hessian matrix ****************/
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int 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]);*/
+   int i;
-             }
+   int l=1, lmax=20;
-             else
+   double k1,k2;
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   double p2[MAXPARM+1]; /* identical to x */
-           }
+   double res;
-         }
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   double fx;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+   int k=0,kmax=10;
-           for(m=-1; m <=nlstate+ndeath; m++)
+   double l1;
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+   fx=func(x);
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-             }
+     l1=pow(10,l);
-         if(i <= iagemax)
+     delts=delt;
-           fprintf(ficresp,"\n");
+     for(k=1 ; k <kmax; k=k+1){
-         if(first==1)
+       delt = delta*(l1*k);
-           printf("Others in log...\n");
+       p2[theta]=x[theta] +delt;
-         fprintf(ficlog,"\n");
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-       }
+       p2[theta]=x[theta]-delt;
-     }
+       k2=func(p2)-fx;
-   }
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   dateintmean=dateintsum/k2cpt;
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   fclose(ficresp);
+ #ifdef DEBUGHESS
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+       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);
-   free_vector(pp,1,nlstate);
+       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);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+ #endif
-   /* End of Freq */
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
- }
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+         k=kmax;
- /************ Prevalence ********************/
+       }
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
- {
+         k=kmax; l=lmax*10.;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+       }
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-      We still use firstpass and lastpass as another selection.
+         delts=delt;
-   */
+       }
+     }
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   }
-   double ***freq; /* Frequencies */
+   delti[theta]=delts;
-   double *pp, **prop;
+   return res;
-   double pos,posprop;
-   double  y2; /* in fractional years */
+ }
-   int iagemin, iagemax;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-   iagemin= (int) agemin;
+ {
-   iagemax= (int) agemax;
+   int i;
-   /*pp=vector(1,nlstate);*/
+   int l=1, l1, lmax=20;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   double k1,k2,k3,k4,res,fx;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+   double p2[MAXPARM+1];
-   j1=0;
+   int k;
-   j=cptcoveff;
+   fx=func(x);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   for (k=1; k<=2; k++) {
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-   for(k1=1; k1<=j;k1++){
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-       j1++;
+     k1=func(p2)-fx;
-       for (i=1; i<=nlstate; i++)
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-         for(m=iagemin; m <= iagemax+3; m++)
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-           prop[i][m]=0.0;
+     k2=func(p2)-fx;
-       for (i=1; i<=imx; i++) { /* Each individual */
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-         bool=1;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-         if  (cptcovn>0) {
+     k3=func(p2)-fx;
-           for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-               bool=0;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-         }
+     k4=func(p2)-fx;
-         if (bool==1) {
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+ #ifdef DEBUG
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+     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);
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+     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);
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+ #endif
-               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);
+   return res;
-               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];
+ /************** Inverse of matrix **************/
-                 prop[s[m][i]][iagemax+3] += weight[i];
+ void ludcmp(double **a, int n, int *indx, double *d)
-               }
+ {
-             }
+   int i,imax,j,k;
-           } /* end selection of waves */
+   double big,dum,sum,temp;
-         }
+   double *vv;
-       }
-       for(i=iagemin; i <= iagemax+3; i++){
+   vv=vector(1,n);
+   *d=1.0;
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+   for (i=1;i<=n;i++) {
-           posprop += prop[jk][i];
+     big=0.0;
-         }
+     for (j=1;j<=n;j++)
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-         for(jk=1; jk <=nlstate ; jk++){
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-           if( i <=  iagemax){
+     vv[i]=1.0/big;
-             if(posprop>=1.e-5){
+   }
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+   for (j=1;j<=n;j++) {
-             }
+     for (i=1;i<j;i++) {
-           }
+       sum=a[i][j];
-         }/* end jk */
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-       }/* end i */
+       a[i][j]=sum;
-     } /* end i1 */
+     }
-   } /* end k1 */
+     big=0.0;
+     for (i=j;i<=n;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<j;k++)
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+         sum -= a[i][k]*a[k][j];
- }  /* End of prevalence */
+       a[i][j]=sum;
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
- /************* Waves Concatenation ***************/
+         big=dum;
+         imax=i;
- void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+       }
- {
+     }
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+     if (j != imax) {
-      Death is a valid wave (if date is known).
+       for (k=1;k<=n;k++) {
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+         dum=a[imax][k];
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+         a[imax][k]=a[j][k];
-      and mw[mi+1][i]. dh depends on stepm.
+         a[j][k]=dum;
-      */
+       }
+       *d = -(*d);
-   int i, mi, m;
+       vv[imax]=vv[j];
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+     }
-      double sum=0., jmean=0.;*/
+     indx[j]=imax;
-   int first;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   int j, k=0,jk, ju, jl;
+     if (j != n) {
-   double sum=0.;
+       dum=1.0/(a[j][j]);
-   first=0;
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-   jmin=1e+5;
+     }
-   jmax=-1;
+   }
-   jmean=0.;
+   free_vector(vv,1,n);  /* Doesn't work */
-   for(i=1; i<=imx; i++){
+ ;
-     mi=0;
+ }
-     m=firstpass;
-     while(s[m][i] <= nlstate){
+ void lubksb(double **a, int n, int *indx, double b[])
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+ {
-         mw[++mi][i]=m;
+   int i,ii=0,ip,j;
-       if(m >=lastpass)
+   double sum;
-         break;
-       else
+   for (i=1;i<=n;i++) {
-         m++;
+     ip=indx[i];
-     }/* end while */
+     sum=b[ip];
-     if (s[m][i] > nlstate){
+     b[ip]=b[i];
-       mi++;     /* Death is another wave */
+     if (ii)
-       /* if(mi==0)  never been interviewed correctly before death */
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-          /* Only death is a correct wave */
+     else if (sum) ii=i;
-       mw[mi][i]=m;
+     b[i]=sum;
-     }
+   }
+   for (i=n;i>=1;i--) {
-     wav[i]=mi;
+     sum=b[i];
-     if(mi==0){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       nbwarn++;
+     b[i]=sum/a[i][i];
-       if(first==0){
+   }
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+ }
-         first=1;
-       }
+ void pstamp(FILE *fichier)
-       if(first==1){
+ {
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-       }
+ }
-     } /* end mi==0 */
-   } /* End individuals */
+ /************ Frequencies ********************/
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-   for(i=1; i<=imx; i++){
+ {  /* Some frequencies */
-     for(mi=1; mi<wav[i];mi++){
-       if (stepm <=0)
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-         dh[mi][i]=1;
+   int first;
-       else{
+   double ***freq; /* Frequencies */
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+   double *pp, **prop;
-           if (agedc[i] < 2*AGESUP) {
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+   char fileresp[FILENAMELENGTH];
-             if(j==0) j=1;  /* Survives at least one month after exam */
-             else if(j<0){
+   pp=vector(1,nlstate);
-               nberr++;
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-               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]);
+   strcpy(fileresp,"p");
-               j=1; /* Temporary Dangerous patch */
+   strcat(fileresp,fileres);
-               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);
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-               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]);
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-               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);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-             }
+     exit(0);
-             k=k+1;
+   }
-             if (j >= jmax){
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-               jmax=j;
+   j1=0;
-               ijmax=i;
-             }
+   j=cptcoveff;
-             if (j <= jmin){
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-               jmin=j;
-               ijmin=i;
+   first=1;
-             }
-             sum=sum+j;
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   /*    j1++;
-           }
+ */
-         }
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-         else{
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+         scanf("%d", i);*/
- /*        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 (i=-5; i<=nlstate+ndeath; i++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           k=k+1;
+           for(m=iagemin; m <= iagemax+3; m++)
-           if (j >= jmax) {
+             freq[i][jk][m]=0;
-             jmax=j;
-             ijmax=i;
+       for (i=1; i<=nlstate; i++)
-           }
+         for(m=iagemin; m <= iagemax+3; m++)
-           else if (j <= jmin){
+           prop[i][m]=0;
-             jmin=j;
-             ijmin=i;
+       dateintsum=0;
-           }
+       k2cpt=0;
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+       for (i=1; i<=imx; 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]);*/
+         bool=1;
-           if(j<0){
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-             nberr++;
+           for (z1=1; z1<=cptcoveff; z1++)
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-             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]);
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-           }
+               bool=0;
-           sum=sum+j;
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-         }
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-         jk= j/stepm;
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-         jl= j -jk*stepm;
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-         ju= j -(jk+1)*stepm;
+             }
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+         }
-           if(jl==0){
-             dh[mi][i]=jk;
+         if (bool==1){
-             bh[mi][i]=0;
+           for(m=firstpass; m<=lastpass; m++){
-           }else{ /* We want a negative bias in order to only have interpolation ie
+             k2=anint[m][i]+(mint[m][i]/12.);
-                   * at the price of an extra matrix product in likelihood */
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-             dh[mi][i]=jk+1;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-             bh[mi][i]=ju;
+               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];
-         }else{
+               if (m<lastpass) {
-           if(jl <= -ju){
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-             dh[mi][i]=jk;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-             bh[mi][i]=jl;       /* bias is positive if real duration
+               }
-                                  * is higher than the multiple of stepm and negative otherwise.
-                                  */
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-           }
+                 dateintsum=dateintsum+k2;
-           else{
+                 k2cpt++;
-             dh[mi][i]=jk+1;
+               }
-             bh[mi][i]=ju;
+               /*}*/
            }
-           if(dh[mi][i]==0){
+         }
-             dh[mi][i]=1; /* At least one step */
+       } /* end i */
-             bh[mi][i]=ju; /* At least one step */
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-           }
+       pstamp(ficresp);
-         } /* end if mle */
+       if  (cptcovn>0) {
-       }
+         fprintf(ficresp, "\n#********** Variable ");
-     } /* end wave */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   }
+         fprintf(ficresp, "**********\n#");
-   jmean=sum/k;
+         fprintf(ficlog, "\n#********** Variable ");
-   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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   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);
+         fprintf(ficlog, "**********\n#");
-  }
+       }
+       for(i=1; i<=nlstate;i++)
- /*********** Tricode ****************************/
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- void tricode(int *Tvar, int **nbcode, int imx)
+       fprintf(ficresp, "\n");
- {
+       for(i=iagemin; i <= iagemax+3; i++){
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+         if(i==iagemax+3){
-   int cptcode=0;
+           fprintf(ficlog,"Total");
-   cptcoveff=0;
+         }else{
+           if(first==1){
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+             first=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+             printf("See log file for details...\n");
+           }
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+           fprintf(ficlog,"Age %d", i);
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+         }
-                                modality*/
+         for(jk=1; jk <=nlstate ; jk++){
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-       Ndum[ij]++; /*store the modality */
+             pp[jk] += freq[jk][m][i];
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+         }
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+         for(jk=1; jk <=nlstate ; jk++){
-                                        Tvar[j]. If V=sex and male is 0 and
+           for(m=-1, pos=0; m <=0 ; m++)
-                                        female is 1, then  cptcode=1.*/
+             pos += freq[jk][m][i];
-     }
+           if(pp[jk]>=1.e-10){
+             if(first==1){
-     for (i=0; i<=cptcode; i++) {
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+             }
-     }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           }else{
-     ij=1;
+             if(first==1)
-     for (i=1; i<=ncodemax[j]; i++) {
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-       for (k=0; k<= maxncov; k++) {
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         if (Ndum[k] != 0) {
+           }
-           nbcode[Tvar[j]][ij]=k;
+         }
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+         for(jk=1; jk <=nlstate ; jk++){
-           ij++;
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-         }
+             pp[jk] += freq[jk][m][i];
-         if (ij > ncodemax[j]) break;
+         }
-       }
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-     }
+           pos += pp[jk];
-   }
+           posprop += prop[jk][i];
+         }
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+         for(jk=1; jk <=nlstate ; jk++){
+           if(pos>=1.e-5){
-  for (i=1; i<=ncovmodel-2; i++) {
+             if(first==1)
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-    ij=Tvar[i];
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-    Ndum[ij]++;
+           }else{
-  }
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-  ij=1;
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-  for (i=1; i<= maxncov; i++) {
+           }
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+           if( i <= iagemax){
-      Tvaraff[ij]=i; /*For printing */
+             if(pos>=1.e-5){
-      ij++;
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-    }
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-  }
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
-  cptcoveff=ij-1; /*Number of simple covariates*/
+             else
- }
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+           }
- /*********** Health Expectancies ****************/
+         }
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
+           for(m=-1; m <=nlstate+ndeath; m++)
- {
+             if(freq[jk][m][i] !=0 ) {
-   /* Health expectancies, no variances */
+             if(first==1)
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   double age, agelim, hf;
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   double ***p3mat;
+             }
-   double eip;
+         if(i <= iagemax)
+           fprintf(ficresp,"\n");
-   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("Others in log...\n");
-   fprintf(ficreseij,"# Age");
+         fprintf(ficlog,"\n");
-   for(i=1; i<=nlstate;i++){
+       }
-     for(j=1; j<=nlstate;j++){
+       /*}*/
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   }
-     }
+   dateintmean=dateintsum/k2cpt;
-     fprintf(ficreseij," e%1d. ",i);
-   }
+   fclose(ficresp);
-   fprintf(ficreseij,"\n");
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   free_vector(pp,1,nlstate);
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-   if(estepm < stepm){
+   /* End of Freq */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
-   }
-   else  hstepm=estepm;
+ /************ Prevalence ********************/
-   /* We compute the life expectancy from trapezoids spaced every estepm 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)
-    * This is mainly to measure the difference between two models: for example
+ {
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-    * progression in between and thus overestimating or underestimating according
+      We still use firstpass and lastpass as another selection.
-    * to the curvature of the survival function. If, for the same date, we
+   */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-    * to compare the new estimate of Life expectancy with the same linear
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-    * hypothesis. A more precise result, taking into account a more precise
+   double ***freq; /* Frequencies */
-    * curvature will be obtained if estepm is as small as stepm. */
+   double *pp, **prop;
+   double pos,posprop;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   double  y2; /* in fractional years */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   int iagemin, iagemax;
-      nhstepm is the number of hstepm from age to agelim
+   int first; /** to stop verbosity which is redirected to log file */
-      nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+   iagemin= (int) agemin;
-      and note for a fixed period like estepm months */
+   iagemax= (int) agemax;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   /*pp=vector(1,nlstate);*/
-      survival function given by stepm (the optimization length). Unfortunately it
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-      means that if the survival funtion is printed only each two years of age and if
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   j1=0;
-      results. So we changed our mind and took the option of the best precision.
-   */
+   /*j=cptcoveff;*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   agelim=AGESUP;
+   first=1;
-   /* If stepm=6 months */
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       j1++;*/
- /* nhstepm age range expressed in number of stepm */
+       for (i=1; i<=nlstate; i++)
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         for(m=iagemin; m <= iagemax+3; m++)
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+           prop[i][m]=0.0;
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       for (i=1; i<=imx; i++) { /* Each individual */
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         bool=1;
+         if  (cptcovn>0) {
-   for (age=bage; age<=fage; age ++){
+           for (z1=1; z1<=cptcoveff; z1++)
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               bool=0;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+         }
+         if (bool==1) {
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-     printf("%d|",(int)age);fflush(stdout);
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-     /* Computing expectancies */
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-     for(i=1; i<=nlstate;i++)
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-       for(j=1; j<=nlstate;j++)
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+                 prop[s[m][i]][iagemax+3] += weight[i];
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[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]);*/
+           } /* end selection of waves */
+         }
-         }
+       }
+       for(i=iagemin; i <= iagemax+3; i++){
-     fprintf(ficreseij,"%3.0f",age );
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-     for(i=1; i<=nlstate;i++){
+           posprop += prop[jk][i];
-       eip=0;
+         }
-       for(j=1; j<=nlstate;j++){
-         eip +=eij[i][j][(int)age];
+         for(jk=1; jk <=nlstate ; jk++){
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+           if( i <=  iagemax){
-       }
+             if(posprop>=1.e-5){
-       fprintf(ficreseij,"%9.4f", eip );
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-     }
+             } else{
-     fprintf(ficreseij,"\n");
+               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]);
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               }
-   printf("\n");
+             }
-   fprintf(ficlog,"\n");
+           }
+         }/* end jk */
- }
+       }/* end i */
+     /*} *//* end i1 */
- 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[] )
+   } /* end j1 */
- {
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   /* Covariances of health expectancies eij and of total life expectancies according
+   /*free_vector(pp,1,nlstate);*/
-    to initial status i, ei. .
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-   */
+ }  /* End of prevalence */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   double age, agelim, hf;
+ /************* Waves Concatenation ***************/
-   double ***p3matp, ***p3matm, ***varhe;
-   double **dnewm,**doldm;
+ 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)
-   double *xp, *xm;
+ {
-   double **gp, **gm;
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-   double ***gradg, ***trgradg;
+      Death is a valid wave (if date is known).
-   int theta;
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   double eip, vip;
+      and mw[mi+1][i]. dh depends on stepm.
+      */
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   xp=vector(1,npar);
+   int i, mi, m;
-   xm=vector(1,npar);
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+      double sum=0., jmean=0.;*/
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   int first;
+   int j, k=0,jk, ju, jl;
-   pstamp(ficresstdeij);
+   double sum=0.;
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   first=0;
-   fprintf(ficresstdeij,"# Age");
+   jmin=1e+5;
-   for(i=1; i<=nlstate;i++){
+   jmax=-1;
-     for(j=1; j<=nlstate;j++)
+   jmean=0.;
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   for(i=1; i<=imx; i++){
-     fprintf(ficresstdeij," e%1d. ",i);
+     mi=0;
-   }
+     m=firstpass;
-   fprintf(ficresstdeij,"\n");
+     while(s[m][i] <= nlstate){
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-   pstamp(ficrescveij);
+         mw[++mi][i]=m;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+       if(m >=lastpass)
-   fprintf(ficrescveij,"# Age");
+         break;
-   for(i=1; i<=nlstate;i++)
+       else
-     for(j=1; j<=nlstate;j++){
+         m++;
-       cptj= (j-1)*nlstate+i;
+     }/* end while */
-       for(i2=1; i2<=nlstate;i2++)
+     if (s[m][i] > nlstate){
-         for(j2=1; j2<=nlstate;j2++){
+       mi++;     /* Death is another wave */
-           cptj2= (j2-1)*nlstate+i2;
+       /* if(mi==0)  never been interviewed correctly before death */
-           if(cptj2 <= cptj)
+          /* Only death is a correct wave */
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+       mw[mi][i]=m;
-         }
+     }
-     }
-   fprintf(ficrescveij,"\n");
+     wav[i]=mi;
+     if(mi==0){
-   if(estepm < stepm){
+       nbwarn++;
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       if(first==0){
-   }
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-   else  hstepm=estepm;
+         first=1;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+       }
-    * This is mainly to measure the difference between two models: for example
+       if(first==1){
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       }
-    * progression in between and thus overestimating or underestimating according
+     } /* end mi==0 */
-    * to the curvature of the survival function. If, for the same date, we
+   } /* End individuals */
-    * 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
+   for(i=1; i<=imx; i++){
-    * hypothesis. A more precise result, taking into account a more precise
+     for(mi=1; mi<wav[i];mi++){
-    * curvature will be obtained if estepm is as small as stepm. */
+       if (stepm <=0)
+         dh[mi][i]=1;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+       else{
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-      nhstepm is the number of hstepm from age to agelim
+           if (agedc[i] < 2*AGESUP) {
-      nstepm is the number of stepm from age to agelin.
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-      Look at hpijx to understand the reason of that which relies in memory size
+             if(j==0) j=1;  /* Survives at least one month after exam */
-      and note for a fixed period like estepm months */
+             else if(j<0){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+               nberr++;
-      survival function given by stepm (the optimization length). Unfortunately it
+               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]);
-      means that if the survival funtion is printed only each two years of age and if
+               j=1; /* Temporary Dangerous patch */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+               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);
-      results. So we changed our mind and took the option of the best precision.
+               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);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+             }
+             k=k+1;
-   /* If stepm=6 months */
+             if (j >= jmax){
-   /* nhstepm age range expressed in number of stepm */
+               jmax=j;
-   agelim=AGESUP;
+               ijmax=i;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+             }
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+             if (j <= jmin){
-   /* if (stepm >= YEARM) hstepm=1;*/
+               jmin=j;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+               ijmin=i;
+             }
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             sum=sum+j;
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+           }
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+         }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+         else{
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-   for (age=bage; age<=fage; age ++){
+ /*        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]); */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           k=k+1;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+           if (j >= jmax) {
+             jmax=j;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             ijmax=i;
+           }
-     /* Computing  Variances of health expectancies */
+           else if (j <= jmin){
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+             jmin=j;
-        decrease memory allocation */
+             ijmin=i;
-     for(theta=1; theta <=npar; theta++){
+           }
-       for(i=1; i<=npar; i++){
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+           /*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]);*/
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+           if(j<0){
-       }
+             nberr++;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+             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]);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
-       for(j=1; j<= nlstate; j++){
+           sum=sum+j;
-         for(i=1; i<=nlstate; i++){
+         }
-           for(h=0; h<=nhstepm-1; h++){
+         jk= j/stepm;
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+         jl= j -jk*stepm;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+         ju= j -(jk+1)*stepm;
-           }
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-         }
+           if(jl==0){
-       }
+             dh[mi][i]=jk;
+             bh[mi][i]=0;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+           }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 */
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+             dh[mi][i]=jk+1;
-         }
+             bh[mi][i]=ju;
-     }/* End theta */
+           }
+         }else{
+           if(jl <= -ju){
-     for(h=0; h<=nhstepm-1; h++)
+             dh[mi][i]=jk;
-       for(j=1; j<=nlstate*nlstate;j++)
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         for(theta=1; theta <=npar; theta++)
+                                  * is higher than the multiple of stepm and negative otherwise.
-           trgradg[h][j][theta]=gradg[h][theta][j];
+                                  */
+           }
+           else{
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+             dh[mi][i]=jk+1;
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+             bh[mi][i]=ju;
-         varhe[ij][ji][(int)age] =0.;
+           }
+           if(dh[mi][i]==0){
-      printf("%d|",(int)age);fflush(stdout);
+             dh[mi][i]=1; /* At least one step */
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+             bh[mi][i]=ju; /* At least one step */
-      for(h=0;h<=nhstepm-1;h++){
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-       for(k=0;k<=nhstepm-1;k++){
+           }
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+         } /* end if mle */
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+       }
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+     } /* end wave */
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+   }
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+   jmean=sum/k;
-       }
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-     }
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+  }
-     /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+ /*********** Tricode ****************************/
-     for(i=1; i<=nlstate;i++)
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-       for(j=1; j<=nlstate;j++)
+ {
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
-           /* 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]);*/
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+   /* nbcode[Tvar[j]][1]=
-         }
+   */
-     fprintf(ficresstdeij,"%3.0f",age );
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-     for(i=1; i<=nlstate;i++){
+   int modmaxcovj=0; /* Modality max of covariates j */
-       eip=0.;
+   int cptcode=0; /* Modality max of covariates j */
-       vip=0.;
+   int modmincovj=0; /* Modality min of covariates j */
-       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) */
+   cptcoveff=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]) );
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-       }
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-     }
+   /* Loop on covariates without age and products */
-     fprintf(ficresstdeij,"\n");
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-     fprintf(ficrescveij,"%3.0f",age );
+                                modality of this covariate Vj*/
-     for(i=1; i<=nlstate;i++)
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-       for(j=1; j<=nlstate;j++){
+                                     * If product of Vn*Vm, still boolean *:
-         cptj= (j-1)*nlstate+i;
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-         for(i2=1; i2<=nlstate;i2++)
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-           for(j2=1; j2<=nlstate;j2++){
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-             cptj2= (j2-1)*nlstate+i2;
+                                       modality of the nth covariate of individual i. */
-             if(cptj2 <= cptj)
+       if (ij > modmaxcovj)
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+         modmaxcovj=ij;
-           }
+       else if (ij < modmincovj)
-       }
+         modmincovj=ij;
-     fprintf(ficrescveij,"\n");
+       if ((ij < -1) && (ij > NCOVMAX)){
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   }
+         exit(1);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+       }else
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* getting the maximum value of the modality of the covariate
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   printf("\n");
+          female is 1, then modmaxcovj=1.*/
-   fprintf(ficlog,"\n");
+     }
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   free_vector(xm,1,npar);
+     cptcode=modmaxcovj;
-   free_vector(xp,1,npar);
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+    /*for (i=0; i<=cptcode; i++) {*/
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
- }
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
- /************ 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[])
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
- {
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   /* Variance of health expectancies */
+     } /* Ndum[-1] number of undefined modalities */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   /* double **newm;*/
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-   double **dnewm,**doldm;
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-   double **dnewmp,**doldmp;
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+        modmincovj=3; modmaxcovj = 7;
-   int k, cptcode;
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
-   double *xp;
+        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 **gp, **gm;  /* for var eij */
+        variables V1_1 and V1_2.
-   double ***gradg, ***trgradg; /*for var eij */
+        nbcode[Tvar[j]][ij]=k;
-   double **gradgp, **trgradgp; /* for var p point j */
+        nbcode[Tvar[j]][1]=0;
-   double *gpp, *gmp; /* for var p point j */
+        nbcode[Tvar[j]][2]=1;
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+        nbcode[Tvar[j]][3]=2;
-   double ***p3mat;
+     */
-   double age,agelim, hf;
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   double ***mobaverage;
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   int theta;
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-   char digit[4];
+         /*recode from 0 */
-   char digitp[25];
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   char fileresprobmorprev[FILENAMELENGTH];
+                                      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; */
-   if(popbased==1){
+           ij++;
-     if(mobilav!=0)
+         }
-       strcpy(digitp,"-populbased-mobilav-");
+         if (ij > ncodemax[j]) break;
-     else strcpy(digitp,"-populbased-nomobil-");
+       }  /* end of loop on */
-   }
+     } /* end of loop on modality */
-   else
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-     strcpy(digitp,"-stablbased-");
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+    Ndum[ij]++;
-     }
+  }
-   }
+  ij=1;
-   strcpy(fileresprobmorprev,"prmorprev");
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-   sprintf(digit,"%-d",ij);
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+      Tvaraff[ij]=i; /*For printing (unclear) */
-   strcat(fileresprobmorprev,fileres);
+      ij++;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+    }else
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+        Tvaraff[ij]=0;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+  }
-   }
+  ij--;
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+  cptcoveff=ij; /*Number of total covariates*/
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ }
-   pstamp(ficresprobmorprev);
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+ /*********** Health Expectancies ****************/
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+ {
-   }
+   /* Health expectancies, no variances */
-   fprintf(ficresprobmorprev,"\n");
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-   fprintf(ficgp,"\n# Routine varevsij");
+   int nhstepma, nstepma; /* Decreasing with age */
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   double age, agelim, hf;
-   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");
+   double ***p3mat;
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+   double eip;
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficreseij);
-   pstamp(ficresvij);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   fprintf(ficreseij,"# Age");
-   if(popbased==1)
+   for(i=1; i<=nlstate;i++){
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+     for(j=1; j<=nlstate;j++){
-   else
+       fprintf(ficreseij," e%1d%1d ",i,j);
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+     }
-   fprintf(ficresvij,"# Age");
+     fprintf(ficreseij," e%1d. ",i);
-   for(i=1; i<=nlstate;i++)
+   }
-     for(j=1; j<=nlstate;j++)
+   fprintf(ficreseij,"\n");
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   fprintf(ficresvij,"\n");
+   if(estepm < stepm){
-   xp=vector(1,npar);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   dnewm=matrix(1,nlstate,1,npar);
+   }
-   doldm=matrix(1,nlstate,1,nlstate);
+   else  hstepm=estepm;
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   gpp=vector(nlstate+1,nlstate+ndeath);
+    * progression in between and thus overestimating or underestimating according
-   gmp=vector(nlstate+1,nlstate+ndeath);
+    * to the curvature of the survival function. If, for the same date, we
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    * 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(estepm < stepm){
+    * hypothesis. A more precise result, taking into account a more precise
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    * curvature will be obtained if estepm is as small as stepm. */
-   }
-   else  hstepm=estepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* 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.
-   /* 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
-      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
-      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
-      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
-      and note for a fixed period like k years */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
-      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
-      means that if the survival funtion is printed every two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      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.
-      results. So we changed our mind and took the option of the best precision.
+   */
-   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
+   agelim=AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+ /* nhstepm age range expressed in number of stepm */
-     gp=matrix(0,nhstepm,1,nlstate);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     gm=matrix(0,nhstepm,1,nlstate);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     for(theta=1; theta <=npar; theta++){
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   for (age=bage; age<=fage; age ++){
-       }
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       if (popbased==1) {
-         if(mobilav ==0){
+     /* If stepm=6 months */
-           for(i=1; i<=nlstate;i++)
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-             prlim[i][i]=probs[(int)age][i][ij];
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       }
+     printf("%d|",(int)age);fflush(stdout);
-       for(j=1; j<= nlstate; j++){
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+     /* Computing expectancies */
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+     for(i=1; i<=nlstate;i++)
-         }
+       for(j=1; j<=nlstate;j++)
-       }
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-       /* This for computing probability of death (h=1 means
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+           /* 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(j=nlstate+1;j<=nlstate+ndeath;j++){
+         }
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+     fprintf(ficreseij,"%3.0f",age );
-       }
+     for(i=1; i<=nlstate;i++){
-       /* end probability of death */
+       eip=0;
+       for(j=1; j<=nlstate;j++){
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+         eip +=eij[i][j][(int)age];
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       fprintf(ficreseij,"%9.4f", eip );
+     }
-       if (popbased==1) {
+     fprintf(ficreseij,"\n");
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
+   }
-             prlim[i][i]=probs[(int)age][i][ij];
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }else{ /* mobilav */
+   printf("\n");
-           for(i=1; i<=nlstate;i++)
+   fprintf(ficlog,"\n");
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+ }
-       }
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+ {
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+   /* Covariances of health expectancies eij and of total life expectancies according
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+    to initial status i, ei. .
-         }
+   */
-       }
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-       /* This for computing probability of death (h=1 means
+   int nhstepma, nstepma; /* Decreasing with age */
-          computed over hstepm matrices product = hstepm*stepm months)
+   double age, agelim, hf;
-          as a weighted average of prlim.
+   double ***p3matp, ***p3matm, ***varhe;
-       */
+   double **dnewm,**doldm;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   double *xp, *xm;
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+   double **gp, **gm;
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   double ***gradg, ***trgradg;
-       }
+   int theta;
-       /* end probability of death */
+   double eip, vip;
-       for(j=1; j<= nlstate; j++) /* vareij */
-         for(h=0; h<=nhstepm; h++){
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   xp=vector(1,npar);
-         }
+   xm=vector(1,npar);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-       }
+   pstamp(ficresstdeij);
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     } /* End theta */
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-     for(h=0; h<=nhstepm; h++) /* veij */
+     fprintf(ficresstdeij," e%1d. ",i);
-       for(j=1; j<=nlstate;j++)
+   }
-         for(theta=1; theta <=npar; theta++)
+   fprintf(ficresstdeij,"\n");
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   pstamp(ficrescveij);
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-       for(theta=1; theta <=npar; theta++)
+   fprintf(ficrescveij,"# Age");
-         trgradgp[j][theta]=gradgp[theta][j];
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       for(i2=1; i2<=nlstate;i2++)
-     for(i=1;i<=nlstate;i++)
+         for(j2=1; j2<=nlstate;j2++){
-       for(j=1;j<=nlstate;j++)
+           cptj2= (j2-1)*nlstate+i2;
-         vareij[i][j][(int)age] =0.;
+           if(cptj2 <= cptj)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-     for(h=0;h<=nhstepm;h++){
+         }
-       for(k=0;k<=nhstepm;k++){
+     }
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+   fprintf(ficrescveij,"\n");
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for(i=1;i<=nlstate;i++)
+   if(estepm < stepm){
-           for(j=1;j<=nlstate;j++)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+   }
-       }
+   else  hstepm=estepm;
-     }
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-     /* pptj */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+    * progression in between and thus overestimating or underestimating according
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+    * to the curvature of the survival function. If, for the same date, we
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-         varppt[j][i]=doldmp[j][i];
+    * to compare the new estimate of Life expectancy with the same linear
-     /* end ppptj */
+    * hypothesis. A more precise result, taking into account a more precise
-     /*  x centered again */
+    * curvature will be obtained if estepm is as small as stepm. */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     if (popbased==1) {
+      nhstepm is the number of hstepm from age to agelim
-       if(mobilav ==0){
+      nstepm is the number of stepm from age to agelin.
-         for(i=1; i<=nlstate;i++)
+      Look at hpijx to understand the reason of that which relies in memory size
-           prlim[i][i]=probs[(int)age][i][ij];
+      and note for a fixed period like estepm months */
-       }else{ /* mobilav */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         for(i=1; i<=nlstate;i++)
+      survival function given by stepm (the optimization length). Unfortunately it
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+      means that if the survival funtion is printed only each two years of age and if
-       }
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     }
+      results. So we changed our mind and took the option of the best precision.
+   */
-     /* This for computing probability of death (h=1 means
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
+   /* If stepm=6 months */
-     */
+   /* nhstepm age range expressed in number of stepm */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   agelim=AGESUP;
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     }
+   /* if (stepm >= YEARM) hstepm=1;*/
-     /* end probability of death */
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       for(i=1; i<=nlstate;i++){
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-       }
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     }
-     fprintf(ficresprobmorprev,"\n");
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     fprintf(ficresvij,"%.0f ",age );
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     for(i=1; i<=nlstate;i++)
+     /* if (stepm >= YEARM) hstepm=1;*/
-       for(j=1; j<=nlstate;j++){
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-       }
+     /* If stepm=6 months */
-     fprintf(ficresvij,"\n");
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-     free_matrix(gp,0,nhstepm,1,nlstate);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     free_matrix(gm,0,nhstepm,1,nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /* Computing  Variances of health expectancies */
-   } /* End age */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+        decrease memory allocation */
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+     for(theta=1; theta <=npar; theta++){
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+       for(i=1; i<=npar; i++){
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+       }
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       for(j=1; j<= nlstate; j++){
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+         for(i=1; i<=nlstate; i++){
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+           for(h=0; h<=nhstepm-1; h++){
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   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);
+         }
- */
+       }
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       for(ij=1; ij<= nlstate*nlstate; ij++)
+         for(h=0; h<=nhstepm-1; h++){
-   free_vector(xp,1,npar);
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   free_matrix(doldm,1,nlstate,1,nlstate);
+         }
-   free_matrix(dnewm,1,nlstate,1,npar);
+     }/* End theta */
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     for(h=0; h<=nhstepm-1; h++)
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for(j=1; j<=nlstate*nlstate;j++)
-   fclose(ficresprobmorprev);
+         for(theta=1; theta <=npar; theta++)
-   fflush(ficgp);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   fflush(fichtm);
- }  /* end varevsij */
+      for(ij=1;ij<=nlstate*nlstate;ij++)
- /************ Variance of prevlim ******************/
+       for(ji=1;ji<=nlstate*nlstate;ji++)
- 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[])
+         varhe[ij][ji][(int)age] =0.;
- {
-   /* Variance of prevalence limit */
+      printf("%d|",(int)age);fflush(stdout);
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   double **newm;
+      for(h=0;h<=nhstepm-1;h++){
-   double **dnewm,**doldm;
+       for(k=0;k<=nhstepm-1;k++){
-   int i, j, nhstepm, hstepm;
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-   int k, cptcode;
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   double *xp;
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   double *gp, *gm;
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   double **gradg, **trgradg;
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   double age,agelim;
+       }
-   int theta;
+     }
-   pstamp(ficresvpl);
+     /* Computing expectancies */
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   fprintf(ficresvpl,"# Age");
+     for(i=1; i<=nlstate;i++)
-   for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++)
-       fprintf(ficresvpl," %1d-%1d",i,i);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   fprintf(ficresvpl,"\n");
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   xp=vector(1,npar);
+           /* 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]);*/
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
+         }
-   hstepm=1*YEARM; /* Every year of age */
+     fprintf(ficresstdeij,"%3.0f",age );
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     for(i=1; i<=nlstate;i++){
-   agelim = AGESUP;
+       eip=0.;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+       vip=0.;
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       for(j=1; j<=nlstate;j++){
-     if (stepm >= YEARM) hstepm=1;
+         eip += eij[i][j][(int)age];
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-     gradg=matrix(1,npar,1,nlstate);
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-     gp=vector(1,nlstate);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-     gm=vector(1,nlstate);
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-     for(theta=1; theta <=npar; theta++){
+     }
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     fprintf(ficresstdeij,"\n");
-         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++){
-         gp[i] = prlim[i][i];
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-       for(i=1; i<=npar; i++) /* Computes gradient */
+           for(j2=1; j2<=nlstate;j2++){
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+             cptj2= (j2-1)*nlstate+i2;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+             if(cptj2 <= cptj)
-       for(i=1;i<=nlstate;i++)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-         gm[i] = prlim[i][i];
+           }
+       }
-       for(i=1;i<=nlstate;i++)
+     fprintf(ficrescveij,"\n");
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-     } /* End theta */
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     trgradg =matrix(1,nlstate,1,npar);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     for(j=1; j<=nlstate;j++)
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-       for(theta=1; theta <=npar; theta++)
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         trgradg[j][theta]=gradg[theta][j];
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
-     for(i=1;i<=nlstate;i++)
+   fprintf(ficlog,"\n");
-       varpl[i][(int)age] =0.;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   free_vector(xm,1,npar);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   free_vector(xp,1,npar);
-     for(i=1;i<=nlstate;i++)
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-     fprintf(ficresvpl,"%.0f ",age );
+ }
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+ /************ Variance ******************/
-     fprintf(ficresvpl,"\n");
+ 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(gp,1,nlstate);
+ {
-     free_vector(gm,1,nlstate);
+   /* Variance of health expectancies */
-     free_matrix(gradg,1,npar,1,nlstate);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-     free_matrix(trgradg,1,nlstate,1,npar);
+   /* double **newm;*/
-   } /* End age */
+   double **dnewm,**doldm;
+   double **dnewmp,**doldmp;
-   free_vector(xp,1,npar);
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   free_matrix(doldm,1,nlstate,1,npar);
+   int k, cptcode;
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   double *xp;
+   double **gp, **gm;  /* for var eij */
- }
+   double ***gradg, ***trgradg; /*for var eij */
+   double **gradgp, **trgradgp; /* for var p point j */
- /************ Variance of one-step probabilities  ******************/
+   double *gpp, *gmp; /* for var p point j */
- 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[])
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
- {
+   double ***p3mat;
-   int i, j=0,  i1, k1, l1, t, tj;
+   double age,agelim, hf;
-   int k2, l2, j1,  z1;
+   double ***mobaverage;
-   int k=0,l, cptcode;
+   int theta;
-   int first=1, first1;
+   char digit[4];
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   char digitp[25];
-   double **dnewm,**doldm;
-   double *xp;
+   char fileresprobmorprev[FILENAMELENGTH];
-   double *gp, *gm;
-   double **gradg, **trgradg;
+   if(popbased==1){
-   double **mu;
+     if(mobilav!=0)
-   double age,agelim, cov[NCOVMAX];
+       strcpy(digitp,"-populbased-mobilav-");
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+     else strcpy(digitp,"-populbased-nomobil-");
-   int theta;
+   }
-   char fileresprob[FILENAMELENGTH];
+   else
-   char fileresprobcov[FILENAMELENGTH];
+     strcpy(digitp,"-stablbased-");
-   char fileresprobcor[FILENAMELENGTH];
+   if (mobilav!=0) {
-   double ***varpij;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   strcpy(fileresprob,"prob");
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   strcat(fileresprob,fileres);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     }
-     printf("Problem with resultfile: %s\n", fileresprob);
+   }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-   }
+   strcpy(fileresprobmorprev,"prmorprev");
-   strcpy(fileresprobcov,"probcov");
+   sprintf(digit,"%-d",ij);
-   strcat(fileresprobcov,fileres);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   strcat(fileresprobmorprev,fileres);
-   }
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   strcpy(fileresprobcor,"probcor");
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   strcat(fileresprobcor,fileres);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   }
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   pstamp(ficresprobmorprev);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+     for(i=1; i<=nlstate;i++)
-   pstamp(ficresprob);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   }
-   fprintf(ficresprob,"# Age");
+   fprintf(ficresprobmorprev,"\n");
-   pstamp(ficresprobcov);
+   fprintf(ficgp,"\n# Routine varevsij");
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   fprintf(ficresprobcov,"# Age");
+   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");
-   pstamp(ficresprobcor);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+ /*   } */
-   fprintf(ficresprobcor,"# Age");
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   pstamp(ficresvij);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   for(i=1; i<=nlstate;i++)
+   if(popbased==1)
-     for(j=1; j<=(nlstate+ndeath);j++){
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   else
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   fprintf(ficresvij,"# Age");
-     }
+   for(i=1; i<=nlstate;i++)
-  /* fprintf(ficresprob,"\n");
+     for(j=1; j<=nlstate;j++)
-   fprintf(ficresprobcov,"\n");
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   fprintf(ficresprobcor,"\n");
+   fprintf(ficresvij,"\n");
-  */
-  xp=vector(1,npar);
+   xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   doldm=matrix(1,nlstate,1,nlstate);
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   gpp=vector(nlstate+1,nlstate+ndeath);
-   fprintf(fichtm,"\n");
+   gmp=vector(nlstate+1,nlstate+ndeath);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   if(estepm < stepm){
-   file %s<br>\n",optionfilehtmcov);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+   }
- and drawn. It helps understanding how is the covariance between two incidences.\
+   else  hstepm=estepm;
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   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. \
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+      nhstepm is the number of hstepm from age to agelim
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+      nstepm is the number of stepm from age to agelin.
- standard deviations wide on each axis. <br>\
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+      survival function given by stepm (the optimization length). Unfortunately it
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+      means that if the survival funtion is printed every two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   cov[1]=1;
+      results. So we changed our mind and took the option of the best precision.
-   tj=cptcoveff;
+   */
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   j1=0;
+   agelim = AGESUP;
-   for(t=1; t<=tj;t++){
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     for(i1=1; i1<=ncodemax[t];i1++){
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       j1++;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       if  (cptcovn>0) {
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(ficresprob, "\n#********** Variable ");
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     gp=matrix(0,nhstepm,1,nlstate);
-         fprintf(ficresprob, "**********\n#\n");
+     gm=matrix(0,nhstepm,1,nlstate);
-         fprintf(ficresprobcov, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresprobcov, "**********\n#\n");
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         fprintf(ficgp, "\n#********** Variable ");
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       }
-         fprintf(ficgp, "**********\n#\n");
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+       if (popbased==1) {
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         if(mobilav ==0){
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
-         fprintf(ficresprobcor, "\n#********** Variable ");
+         }else{ /* mobilav */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+           for(i=1; i<=nlstate;i++)
-         fprintf(ficresprobcor, "**********\n#");
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-       }
+         }
+       }
-       for (age=bage; age<=fage; age ++){
-         cov[2]=age;
+       for(j=1; j<= nlstate; j++){
-         for (k=1; k<=cptcovn;k++) {
+         for(h=0; h<=nhstepm; h++){
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-         }
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         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]]];
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+          as a weighted average of prlim.
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-         for(theta=1; theta <=npar; theta++){
+       }
-           for(i=1; i<=npar; i++)
+       /* end probability of death */
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-           k=0;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           for(i=1; i<= (nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+       if (popbased==1) {
-               k=k+1;
+         if(mobilav ==0){
-               gp[k]=pmmij[i][j];
+           for(i=1; i<=nlstate;i++)
-             }
+             prlim[i][i]=probs[(int)age][i][ij];
-           }
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
-           for(i=1; i<=npar; i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+         }
+       }
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           k=0;
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-           for(i=1; i<=(nlstate); i++){
+         for(h=0; h<=nhstepm; h++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-               k=k+1;
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-               gm[k]=pmmij[i][j];
+         }
-             }
+       }
-           }
+       /* This for computing probability of death (h=1 means
+          computed over hstepm matrices product = hstepm*stepm months)
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+          as a weighted average of prlim.
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+       */
-         }
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-           for(theta=1; theta <=npar; theta++)
+       }
-             trgradg[j][theta]=gradg[theta][j];
+       /* end probability of death */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+       for(j=1; j<= nlstate; j++) /* vareij */
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+         for(h=0; h<=nhstepm; h++){
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+         }
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+       }
-         k=0;
+     } /* End theta */
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
+     for(h=0; h<=nhstepm; h++) /* veij */
-           }
+       for(j=1; j<=nlstate;j++)
-         }
+         for(theta=1; theta <=npar; theta++)
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-             varpij[i][j][(int)age] = doldm[i][j];
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
-         /*printf("\n%d ",(int)age);
+         trgradgp[j][theta]=gradgp[theta][j];
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-           }*/
+     for(i=1;i<=nlstate;i++)
+       for(j=1;j<=nlstate;j++)
-         fprintf(ficresprob,"\n%d ",(int)age);
+         vareij[i][j][(int)age] =0.;
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     for(h=0;h<=nhstepm;h++){
+       for(k=0;k<=nhstepm;k++){
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         for(i=1;i<=nlstate;i++)
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           for(j=1;j<=nlstate;j++)
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-         }
+       }
-         i=0;
+     }
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
+     /* pptj */
-             i=i++;
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-             for (j=1; j<=i;j++){
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+         varppt[j][i]=doldmp[j][i];
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+     /* end ppptj */
-             }
+     /*  x centered again */
-           }
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-         }/* end of loop for state */
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-       } /* end of loop for age */
+     if (popbased==1) {
-       /* Confidence intervalle of pij  */
+       if(mobilav ==0){
-       /*
+         for(i=1; i<=nlstate;i++)
-         fprintf(ficgp,"\nset noparametric;unset label");
+           prlim[i][i]=probs[(int)age][i][ij];
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+       }else{ /* mobilav */
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         for(i=1; i<=nlstate;i++)
-         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);
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+       }
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+     }
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       */
+     /* This for computing probability of death (h=1 means
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+        as a weighted average of prlim.
-       first1=1;
+     */
-       for (k2=1; k2<=(nlstate);k2++){
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-           if(l2==k2) continue;
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-           j=(k2-1)*(nlstate+ndeath)+l2;
+     }
-           for (k1=1; k1<=(nlstate);k1++){
+     /* end probability of death */
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-               i=(k1-1)*(nlstate+ndeath)+l1;
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-               if(i<=j) continue;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-               for (age=bage; age<=fage; age ++){
+       for(i=1; i<=nlstate;i++){
-                 if ((int)age %5==0){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+       }
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     }
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     fprintf(ficresprobmorprev,"\n");
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+     fprintf(ficresvij,"%.0f ",age );
-                   c12=cv12/sqrt(v1*v2);
+     for(i=1; i<=nlstate;i++)
-                   /* Computing eigen value of matrix of covariance */
+       for(j=1; j<=nlstate;j++){
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       }
-                   /* Eigen vectors */
+     fprintf(ficresvij,"\n");
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                   v21=(lc1-v1)/cv12*v11;
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                   v12=-v21;
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-                   v22=v11;
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                   tnalp=v21/v11;
+   } /* End age */
-                   if(first1==1){
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                     first1=0;
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                     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_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                   }
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-                   /*printf(fignu*/
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-                   if(first==1){
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                     first=0;
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                     fprintf(ficgp,"\nset parametric;unset label");
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+   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);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+   /*  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);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+ */
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                     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);
+   free_vector(xp,1,npar);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   free_matrix(dnewm,1,nlstate,1,npar);
-                     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",\
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                   }else{
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                     first=0;
+   fclose(ficresprobmorprev);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   fflush(ficgp);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fflush(fichtm);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+ }  /* end varevsij */
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+ /************ Variance of prevlim ******************/
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ 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[])
-                   }/* if first */
+ {
-                 } /* age mod 5 */
+   /* Variance of prevalence limit */
-               } /* end loop age */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   double **newm;
-               first=1;
+   double **dnewm,**doldm;
-             } /*l12 */
+   int i, j, nhstepm, hstepm;
-           } /* k12 */
+   int k, cptcode;
-         } /*l1 */
+   double *xp;
-       }/* k1 */
+   double *gp, *gm;
-     } /* loop covariates */
+   double **gradg, **trgradg;
-   }
+   double age,agelim;
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   int theta;
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   pstamp(ficresvpl);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   free_vector(xp,1,npar);
+   fprintf(ficresvpl,"# Age");
-   fclose(ficresprob);
+   for(i=1; i<=nlstate;i++)
-   fclose(ficresprobcov);
+       fprintf(ficresvpl," %1d-%1d",i,i);
-   fclose(ficresprobcor);
+   fprintf(ficresvpl,"\n");
-   fflush(ficgp);
-   fflush(fichtmcov);
+   xp=vector(1,npar);
- }
+   dnewm=matrix(1,nlstate,1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
- /******************* Printing html file ***********/
+   hstepm=1*YEARM; /* Every year of age */
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-                   int lastpass, int stepm, int weightopt, char model[],\
+   agelim = AGESUP;
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-                   int popforecast, int estepm ,\
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-                   double jprev1, double mprev1,double anprev1, \
+     if (stepm >= YEARM) hstepm=1;
-                   double jprev2, double mprev2,double anprev2){
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-   int jj1, k1, i1, cpt;
+     gradg=matrix(1,npar,1,nlstate);
+     gp=vector(1,nlstate);
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+     gm=vector(1,nlstate);
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
- </ul>");
+     for(theta=1; theta <=npar; theta++){
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+       }
-    fprintf(fichtm,"\
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+       for(i=1;i<=nlstate;i++)
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+         gp[i] = prlim[i][i];
-    fprintf(fichtm,"\
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+       for(i=1; i<=npar; i++) /* Computes gradient */
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-    fprintf(fichtm,"\
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+       for(i=1;i<=nlstate;i++)
-    <a href=\"%s\">%s</a> <br>\n",
+         gm[i] = prlim[i][i];
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-    fprintf(fichtm,"\
+       for(i=1;i<=nlstate;i++)
-  - Population projections by age and states: \
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+     } /* End theta */
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+     trgradg =matrix(1,nlstate,1,npar);
-  m=cptcoveff;
+     for(j=1; j<=nlstate;j++)
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
-  jj1=0;
-  for(k1=1; k1<=m;k1++){
+     for(i=1;i<=nlstate;i++)
-    for(i1=1; i1<=ncodemax[k1];i1++){
+       varpl[i][(int)age] =0.;
-      jj1++;
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-      if (cptcovn > 0) {
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     for(i=1;i<=nlstate;i++)
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+     fprintf(ficresvpl,"%.0f ",age );
-      }
+     for(i=1; i<=nlstate;i++)
-      /* Pij */
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)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%d1.png\">%s%d1.png</a><br> \
+     fprintf(ficresvpl,"\n");
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+     free_vector(gp,1,nlstate);
-      /* Quasi-incidences */
+     free_vector(gm,1,nlstate);
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+     free_matrix(gradg,1,npar,1,nlstate);
-  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> \
+     free_matrix(trgradg,1,nlstate,1,npar);
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   } /* End age */
-        /* Period (stable) prevalence in each health state */
-        for(cpt=1; cpt<nlstate;cpt++){
+   free_vector(xp,1,npar);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+   free_matrix(doldm,1,nlstate,1,npar);
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-        }
-      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> \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ /************ 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[])
-    } /* end i1 */
+ {
-  }/* End k1 */
+   int i, j=0,  i1, k1, l1, t, tj;
-  fprintf(fichtm,"</ul>");
+   int k2, l2, j1,  z1;
+   int k=0,l, cptcode;
+   int first=1, first1, first2;
-  fprintf(fichtm,"\
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   double **dnewm,**doldm;
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   double *xp;
+   double *gp, *gm;
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   double **gradg, **trgradg;
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+   double **mu;
-  fprintf(fichtm,"\
+   double age,agelim, cov[NCOVMAX+1];
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   int theta;
+   char fileresprob[FILENAMELENGTH];
-  fprintf(fichtm,"\
+   char fileresprobcov[FILENAMELENGTH];
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   char fileresprobcor[FILENAMELENGTH];
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   double ***varpij;
-  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): \
+   strcpy(fileresprob,"prob");
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   strcat(fileresprob,fileres);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-  fprintf(fichtm,"\
+     printf("Problem with resultfile: %s\n", fileresprob);
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   }
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   strcpy(fileresprobcov,"probcov");
-  fprintf(fichtm,"\
+   strcat(fileresprobcov,fileres);
-  - 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",
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-  fprintf(fichtm,"\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  - 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",
+   }
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   strcpy(fileresprobcor,"probcor");
-  fprintf(fichtm,"\
+   strcat(fileresprobcor,fileres);
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   }
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- /*      <br>",fileres,fileres,fileres,fileres); */
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- /*  else  */
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- /*    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); */
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-  fflush(fichtm);
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   pstamp(ficresprob);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-  m=cptcoveff;
+   fprintf(ficresprob,"# Age");
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   pstamp(ficresprobcov);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-  jj1=0;
+   fprintf(ficresprobcov,"# Age");
-  for(k1=1; k1<=m;k1++){
+   pstamp(ficresprobcor);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-      jj1++;
+   fprintf(ficresprobcor,"# Age");
-      if (cptcovn > 0) {
-        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]]);
+     for(j=1; j<=(nlstate+ndeath);j++){
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-      }
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+     }
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+  /* fprintf(ficresprob,"\n");
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   fprintf(ficresprobcov,"\n");
-      }
+   fprintf(ficresprobcor,"\n");
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+  */
- health expectancies in states (1) and (2): %s%d.png<br>\
+   xp=vector(1,npar);
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-    } /* end i1 */
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-  }/* End k1 */
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-  fprintf(fichtm,"</ul>");
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-  fflush(fichtm);
+   first=1;
- }
+   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
- /******************* Gnuplot file **************/
+   fprintf(fichtm,"\n");
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   char dirfileres[132],optfileres[132];
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   file %s<br>\n",optionfilehtmcov);
-   int ng;
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ and drawn. It helps understanding how is the covariance between two incidences.\
- /*     printf("Problem with file %s",optionfilegnuplot); */
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   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 \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-   /*#ifdef windows */
+ standard deviations wide on each axis. <br>\
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-     /*#endif */
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-   m=pow(2,cptcoveff);
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   strcpy(dirfileres,optionfilefiname);
+   cov[1]=1;
-   strcpy(optfileres,"vpl");
+   /* tj=cptcoveff; */
-  /* 1eme*/
+   tj = (int) pow(2,cptcoveff);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-    for (k1=1; k1<= m ; k1 ++) {
+   j1=0;
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+   for(j1=1; j1<=tj;j1++){
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+     /*j1++;*/
- set ylabel \"Probability\" \n\
+       if  (cptcovn>0) {
- set ter png small\n\
+         fprintf(ficresprob, "\n#********** Variable ");
- set size 0.65,0.65\n\
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+         fprintf(ficresprob, "**********\n#\n");
+         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\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         for (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\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      for (i=1; i<= nlstate ; i ++) {
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprobcor, "\n#********** Variable ");
-      }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         fprintf(ficresprobcor, "**********\n#");
-    }
+       }
-   }
-   /*2 eme*/
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   for (k1=1; k1<= m ; k1 ++) {
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+       for (age=bage; age<=fage; age ++){
+         cov[2]=age;
-     for (i=1; i<= nlstate+1 ; i ++) {
+         for (k=1; k<=cptcovn;k++) {
-       k=2*i;
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                          * 1  1 1 1 1
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                          * 2  2 1 1 1
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                                                          * 3  1 2 1 1
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                                                          */
-       }
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+         }
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         for (k=1; k<=cptcovprod;k++)
-       for (j=1; j<= nlstate+1 ; j ++) {
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+         for(theta=1; theta <=npar; theta++){
-       fprintf(ficgp,"\" t\"\" w l 0,");
+           for(i=1; i<=npar; i++)
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+           k=0;
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+           for(i=1; i<= (nlstate); i++){
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+             for(j=1; j<=(nlstate+ndeath);j++){
-     }
+               k=k+1;
-   }
+               gp[k]=pmmij[i][j];
+             }
-   /*3eme*/
+           }
-   for (k1=1; k1<= m ; k1 ++) {
+           for(i=1; i<=npar; i++)
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-       /*       k=2+nlstate*(2*cpt-2); */
-       k=2+(nlstate+1)*(cpt-1);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+           k=0;
-       fprintf(ficgp,"set ter png small\n\
+           for(i=1; i<=(nlstate); i++){
- set size 0.65,0.65\n\
+             for(j=1; j<=(nlstate+ndeath);j++){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+               k=k+1;
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+               gm[k]=pmmij[i][j];
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+             }
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           }
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         }
-       */
-       for (i=1; i< nlstate ; i ++) {
+         for(j=1; j<=(nlstate)*(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+i,cpt,i+1);
+           for(theta=1; theta <=npar; theta++)
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+             trgradg[j][theta]=gradg[theta][j];
-       }
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-     }
-   }
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-   /* CV preval stable (period) */
+         k=0;
-   for (k1=1; k1<= m ; k1 ++) {
+         for(i=1; i<=(nlstate); i++){
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+           for(j=1; j<=(nlstate+ndeath);j++){
-       k=3;
+             k=k+1;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+             mu[k][(int) age]=pmmij[i][j];
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+           }
- set ter png small\nset size 0.65,0.65\n\
+         }
- unset log y\n\
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             varpij[i][j][(int)age] = doldm[i][j];
-       for (i=1; i< nlstate ; i ++)
-         fprintf(ficgp,"+$%d",k+i+1);
+         /*printf("\n%d ",(int)age);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-       l=3+(nlstate+ndeath)*cpt;
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+           }*/
-       for (i=1; i< nlstate ; i ++) {
-         l=3+(nlstate+ndeath)*cpt;
+         fprintf(ficresprob,"\n%d ",(int)age);
-         fprintf(ficgp,"+$%d",l+i+1);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-       }
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-     }
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-   }
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-   /* proba elementaires */
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-   for(i=1,jk=1; i <=nlstate; i++){
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-     for(k=1; k <=(nlstate+ndeath); k++){
+         }
-       if (k != i) {
+         i=0;
-         for(j=1; j <=ncovmodel; j++){
+         for (k=1; k<=(nlstate);k++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           for (l=1; l<=(nlstate+ndeath);l++){
-           jk++;
+             i++;
-           fprintf(ficgp,"\n");
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-         }
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-       }
+             for (j=1; j<=i;j++){
-     }
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-    }
+               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]));
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+             }
-      for(jk=1; jk <=m; jk++) {
+           }
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+         }/* end of loop for state */
-        if (ng==2)
+       } /* end of loop for age */
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-        else
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-        i=1;
-        for(k2=1; k2<=nlstate; k2++) {
+       /* Confidence intervalle of pij  */
-          k3=i;
+       /*
-          for(k=1; k<=(nlstate+ndeath); k++) {
+         fprintf(ficgp,"\nunset parametric;unset label");
-            if (k != k2){
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-              if(ng==2)
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-              else
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-              ij=1;
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-              for(j=3; j <=ncovmodel; j++) {
+       */
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-                  ij++;
+       first1=1;first2=2;
-                }
+       for (k2=1; k2<=(nlstate);k2++){
-                else
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+           if(l2==k2) continue;
-              }
+           j=(k2-1)*(nlstate+ndeath)+l2;
-              fprintf(ficgp,")/(1");
+           for (k1=1; k1<=(nlstate);k1++){
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-              for(k1=1; k1 <=nlstate; k1++){
+               if(l1==k1) continue;
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+               i=(k1-1)*(nlstate+ndeath)+l1;
-                ij=1;
+               if(i<=j) continue;
-                for(j=3; j <=ncovmodel; j++){
+               for (age=bage; age<=fage; age ++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                 if ((int)age %5==0){
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                    ij++;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                  }
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                  else
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-                }
+                   c12=cv12/sqrt(v1*v2);
-                fprintf(ficgp,")");
+                   /* Computing eigen value of matrix of covariance */
-              }
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+                   if ((lc2 <0) || (lc1 <0) ){
-              i=i+ncovmodel;
+                     if(first2==1){
-            }
+                       first1=0;
-          } /* end k */
+                     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);
-        } /* end k2 */
+                     }
-      } /* end jk */
+                     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);
-    } /* end ng */
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-    fflush(ficgp);
+                     /* lc2=fabs(lc2); */
- }  /* end gnuplot */
+                   }
+                   /* Eigen vectors */
- /*************** Moving average **************/
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                   /*v21=sqrt(1.-v11*v11); *//* error */
+                   v21=(lc1-v1)/cv12*v11;
-   int i, cpt, cptcod;
+                   v12=-v21;
-   int modcovmax =1;
+                   v22=v11;
-   int mobilavrange, mob;
+                   tnalp=v21/v11;
-   double age;
+                   if(first1==1){
+                     first1=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                     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);
-                            a covariate has 2 modalities */
+                   }
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                   /*printf(fignu*/
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-     if(mobilav==1) mobilavrange=5; /* default */
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-     else mobilavrange=mobilav;
+                   if(first==1){
-     for (age=bage; age<=fage; age++)
+                     first=0;
-       for (i=1; i<=nlstate;i++)
+                     fprintf(ficgp,"\nset parametric;unset label");
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-     /* We keep the original values on the extreme ages bage, fage and for
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-        we use a 5 terms etc. until the borders are no more concerned.
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-     */
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-         for (i=1; i<=nlstate;i++){
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                     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",\
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-               }
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+                   }else{
-           }
+                     first=0;
-         }
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-       }/* end age */
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-     }/* end mob */
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-   }else return -1;
+                     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",\
-   return 0;
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
- }/* End movingaverage */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   }/* if first */
+                 } /* age mod 5 */
- /************** Forecasting ******************/
+               } /* end loop age */
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   /* proj1, year, month, day of starting projection
+               first=1;
-      agemin, agemax range of age
+             } /*l12 */
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+           } /* k12 */
-      anproj2 year of en of projection (same day and month as proj1).
+         } /*l1 */
-   */
+       }/* k1 */
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+       /* } /* loop covariates */
-   int *popage;
+   }
-   double agec; /* generic age */
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-   double *popeffectif,*popcount;
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   double ***p3mat;
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   double ***mobaverage;
+   free_vector(xp,1,npar);
-   char fileresf[FILENAMELENGTH];
+   fclose(ficresprob);
+   fclose(ficresprobcov);
-   agelim=AGESUP;
+   fclose(ficresprobcor);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   fflush(ficgp);
+   fflush(fichtmcov);
-   strcpy(fileresf,"f");
+ }
-   strcat(fileresf,fileres);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+ /******************* Printing html file ***********/
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   }
+                   int lastpass, int stepm, int weightopt, char model[],\
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+                   int popforecast, int estepm ,\
+                   double jprev1, double mprev1,double anprev1, \
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ </ul>");
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-     }
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-   }
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+    fprintf(fichtm,"\
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-   if (stepm<=12) stepsize=1;
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-   if(estepm < stepm){
+    fprintf(fichtm,"\
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-   }
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-   else  hstepm=estepm;
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-   hstepm=hstepm/stepm;
+    <a href=\"%s\">%s</a> <br>\n",
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-                                fractional in yp1 */
+    fprintf(fichtm,"\
-   anprojmean=yp;
+  - Population projections by age and states: \
-   yp2=modf((yp1*12),&yp);
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   mprojmean=yp;
-   yp1=modf((yp2*30.5),&yp);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   jprojmean=yp;
-   if(jprojmean==0) jprojmean=1;
+  m=pow(2,cptcoveff);
-   if(mprojmean==0) jprojmean=1;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   i1=cptcoveff;
+  jj1=0;
-   if (cptcovn < 1){i1=1;}
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+      jj1++;
+      if (cptcovn > 0) {
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
- /*            if (h==(int)(YEARM*yearp)){ */
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      }
-       k=k+1;
+      /* Pij */
-       fprintf(ficresf,"\n#******");
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-       for(j=1;j<=cptcoveff;j++) {
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      /* Quasi-incidences */
-       }
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-       fprintf(ficresf,"******\n");
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-       for(j=1; j<=nlstate+ndeath;j++){
+        /* Period (stable) prevalence in each health state */
-         for(i=1; i<=nlstate;i++)
+        for(cpt=1; cpt<=nlstate;cpt++){
-           fprintf(ficresf," p%d%d",i,j);
+          fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
-         fprintf(ficresf," p.%d",j);
+ <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-       }
+        }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(ficresf,"\n");
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+      }
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+    } /* end i1 */
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+  }/* End k1 */
-           nhstepm = nhstepm/hstepm;
+  fprintf(fichtm,"</ul>");
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+  fprintf(fichtm,"\
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-           for (h=0; h<=nhstepm; h++){
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               for(j=1;j<=cptcoveff;j++)
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  fprintf(fichtm,"\
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-             }
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-             for(j=1; j<=nlstate+ndeath;j++) {
-               ppij=0.;
+  fprintf(fichtm,"\
-               for(i=1; i<=nlstate;i++) {
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-                 if (mobilav==1)
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+  fprintf(fichtm,"\
-                 else {
+  - 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): \
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+    <a href=\"%s\">%s</a> <br>\n</li>",
-                 }
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-                 if (h*hstepm/YEARM*stepm== yearp) {
+  fprintf(fichtm,"\
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+  - (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>",
-               } /* end i */
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-               if (h*hstepm/YEARM*stepm==yearp) {
+  fprintf(fichtm,"\
-                 fprintf(ficresf," %.3f", ppij);
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-               }
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-             }/* end j */
+  fprintf(fichtm,"\
-           } /* end h */
+  - 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",
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-         } /* end agec */
+  fprintf(fichtm,"\
-       } /* end yearp */
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-     } /* end cptcod */
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   } /* end  cptcov */
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-   fclose(ficresf);
+ /*      <br>",fileres,fileres,fileres,fileres); */
- }
+ /*  else  */
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
- /************** Forecasting *****not tested NB*************/
+  fflush(fichtm);
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+  m=pow(2,cptcoveff);
-   int *popage;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
+  jj1=0;
-   double ***p3mat,***tabpop,***tabpopprev;
+  for(k1=1; k1<=m;k1++){
-   double ***mobaverage;
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   char filerespop[FILENAMELENGTH];
+      jj1++;
+      if (cptcovn > 0) {
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   agelim=AGESUP;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+      for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-   strcpy(filerespop,"pop");
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-   strcat(filerespop,fileres);
+      }
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ true period expectancies (those weighted with period prevalences are also\
-   }
+  drawn in addition to the population based expectancies computed using\
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+  observed and cahotic prevalences: %s%d.png<br>\
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+    } /* end i1 */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
-   if (mobilav!=0) {
+  fflush(fichtm);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ }
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /******************* Gnuplot file **************/
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     }
-   }
+   char dirfileres[132],optfileres[132];
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   int ng=0;
-   if (stepm<=12) stepsize=1;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   agelim=AGESUP;
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+ /*   } */
-   hstepm=1;
-   hstepm=hstepm/stepm;
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   if (popforecast==1) {
+     /*#endif */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+   m=pow(2,cptcoveff);
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+   strcpy(dirfileres,optionfilefiname);
-     }
+   strcpy(optfileres,"vpl");
-     popage=ivector(0,AGESUP);
+  /* 1eme*/
-     popeffectif=vector(0,AGESUP);
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-     popcount=vector(0,AGESUP);
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-     i=1;
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-     imx=i;
+ set ylabel \"Probability\" \n\
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ set ter png small size 320, 240\n\
-   }
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+      for (i=1; i<= nlstate ; i ++) {
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       k=k+1;
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-       fprintf(ficrespop,"\n#******");
+      }
-       for(j=1;j<=cptcoveff;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);
-         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\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       for (cpt=0; cpt<=0;cpt++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+      }
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+    }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   }
-           nhstepm = nhstepm/hstepm;
+   /*2 eme*/
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (k1=1; k1<= m ; k1 ++) {
-           oldm=oldms;savm=savms;
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-           for (h=0; h<=nhstepm; h++){
+     for (i=1; i<= nlstate+1 ; i ++) {
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       k=2*i;
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-             }
+       for (j=1; j<= nlstate+1 ; j ++) {
-             for(j=1; j<=nlstate+ndeath;j++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-               kk1=0.;kk2=0;
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-               for(i=1; i<=nlstate;i++) {
+       }
-                 if (mobilav==1)
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-                 else {
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+       for (j=1; j<= nlstate+1 ; j ++) {
-                 }
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-               }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-               if (h==(int)(calagedatem+12*cpt)){
+       }
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-                   /*fprintf(ficrespop," %.3f", kk1);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+       for (j=1; j<= nlstate+1 ; j ++) {
-               }
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-             }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-             for(i=1; i<=nlstate;i++){
+       }
-               kk1=0.;
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-                 for(j=1; j<=nlstate;j++){
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+     }
-                 }
+   }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-             }
+   /*3eme*/
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+   for (k1=1; k1<= m ; k1 ++) {
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-           }
+       /*       k=2+nlstate*(2*cpt-2); */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       k=2+(nlstate+1)*(cpt-1);
-         }
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       }
+       fprintf(ficgp,"set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-   /******/
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           nhstepm = nhstepm/hstepm;
+       */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (i=1; i< nlstate ; i ++) {
-           oldm=oldms;savm=savms;
+         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);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       }
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       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+ndeath;j++) {
+   }
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
+   /* CV preval stable (period) */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-               }
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+       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);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-         }
+ set ter png small size 320, 240\n\
-       }
+ unset log y\n\
-    }
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-   }
+       for (i=1; i<= nlstate ; i ++){
+         if(i==1)
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+         else
-   if (popforecast==1) {
+           fprintf(ficgp,", '' ");
-     free_ivector(popage,0,AGESUP);
+         l=(nlstate+ndeath)*(i-1)+1;
-     free_vector(popeffectif,0,AGESUP);
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-     free_vector(popcount,0,AGESUP);
+         for (j=1; j<= (nlstate-1) ; j ++)
-   }
+           fprintf(ficgp,"+$%d",k+l+j);
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       } /* nlstate */
-   fclose(ficrespop);
+       fprintf(ficgp,"\n");
- } /* End of popforecast */
+     } /* end cpt state*/
+   } /* end covariate */
- int fileappend(FILE *fichier, char *optionfich)
- {
+   /* proba elementaires */
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   for(i=1,jk=1; i <=nlstate; i++){
-     printf("Problem with file: %s\n", optionfich);
+     for(k=1; k <=(nlstate+ndeath); k++){
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+       if (k != i) {
-     return (0);
+         for(j=1; j <=ncovmodel; j++){
-   }
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-   fflush(fichier);
+           jk++;
-   return (1);
+           fprintf(ficgp,"\n");
- }
+         }
+       }
+     }
- /**************** function prwizard **********************/
+    }
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+   /*goto avoid;*/
- {
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
-   /* Wizard to print covariance matrix template */
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+        if (ng==2)
-   char ca[32], cb[32], cc[32];
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+        else
-   int numlinepar;
+          fprintf(ficgp,"\nset title \"Probability\"\n");
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+        i=1;
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+        for(k2=1; k2<=nlstate; k2++) {
-   for(i=1; i <=nlstate; i++){
+          k3=i;
-     jj=0;
+          for(k=1; k<=(nlstate+ndeath); k++) {
-     for(j=1; j <=nlstate+ndeath; j++){
+            if (k != k2){
-       if(j==i) continue;
+              if(ng==2)
-       jj++;
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+              else
-       printf("%1d%1d",i,j);
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-       fprintf(ficparo,"%1d%1d",i,j);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-       for(k=1; k<=ncovmodel;k++){
+              for(j=3; j <=ncovmodel; j++) {
-         /*        printf(" %lf",param[i][j][k]); */
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-         printf(" 0.");
+                /*        ij++; */
-         fprintf(ficparo," 0.");
+                /* } */
-       }
+                /* else */
-       printf("\n");
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       fprintf(ficparo,"\n");
+              }
-     }
+              fprintf(ficgp,")/(1");
-   }
-   printf("# Scales (for hessian or gradient estimation)\n");
+              for(k1=1; k1 <=nlstate; k1++){
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                ij=1;
-   for(i=1; i <=nlstate; i++){
+                for(j=3; j <=ncovmodel; j++){
-     jj=0;
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-     for(j=1; j <=nlstate+ndeath; j++){
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-       if(j==i) continue;
+                  /*   ij++; */
-       jj++;
+                  /* } */
-       fprintf(ficparo,"%1d%1d",i,j);
+                  /* else */
-       printf("%1d%1d",i,j);
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       fflush(stdout);
+                }
-       for(k=1; k<=ncovmodel;k++){
+                fprintf(ficgp,")");
-         /*      printf(" %le",delti3[i][j][k]); */
+              }
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-         printf(" 0.");
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-         fprintf(ficparo," 0.");
+              i=i+ncovmodel;
-       }
+            }
-       numlinepar++;
+          } /* end k */
-       printf("\n");
+        } /* end k2 */
-       fprintf(ficparo,"\n");
+      } /* end jk */
-     }
+    } /* end ng */
-   }
+  avoid:
-   printf("# Covariance matrix\n");
+    fflush(ficgp);
- /* # 121 Var(a12)\n\ */
+ }  /* end gnuplot */
- /* # 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\ */
+ /*************** Moving average **************/
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
- /* # 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\ */
+   int i, cpt, cptcod;
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   int modcovmax =1;
-   fflush(stdout);
+   int mobilavrange, mob;
-   fprintf(ficparo,"# Covariance matrix\n");
+   double age;
-   /* # 121 Var(a12)\n\ */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-   /* #   ...\n\ */
+                            a covariate has 2 modalities */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-   for(itimes=1;itimes<=2;itimes++){
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-     jj=0;
+     if(mobilav==1) mobilavrange=5; /* default */
-     for(i=1; i <=nlstate; i++){
+     else mobilavrange=mobilav;
-       for(j=1; j <=nlstate+ndeath; j++){
+     for (age=bage; age<=fage; age++)
-         if(j==i) continue;
+       for (i=1; i<=nlstate;i++)
-         for(k=1; k<=ncovmodel;k++){
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           jj++;
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-           ca[0]= k+'a'-1;ca[1]='\0';
+     /* We keep the original values on the extreme ages bage, fage and for
-           if(itimes==1){
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-             printf("#%1d%1d%d",i,j,k);
+        we use a 5 terms etc. until the borders are no more concerned.
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+     */
-           }else{
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-             printf("%1d%1d%d",i,j,k);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+         for (i=1; i<=nlstate;i++){
-             /*  printf(" %.5le",matcov[i][j]); */
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-           }
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-           ll=0;
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-           for(li=1;li <=nlstate; li++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               if(lj==li) continue;
+               }
-               for(lk=1;lk<=ncovmodel;lk++){
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-                 ll++;
+           }
-                 if(ll<=jj){
+         }
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+       }/* end age */
-                   if(ll<jj){
+     }/* end mob */
-                     if(itimes==1){
+   }else return -1;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   return 0;
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+ }/* End movingaverage */
-                     }else{
-                       printf(" 0.");
-                       fprintf(ficparo," 0.");
+ /************** Forecasting ******************/
-                     }
+ prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
-                   }else{
+   /* proj1, year, month, day of starting projection
-                     if(itimes==1){
+      agemin, agemax range of age
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+      anproj2 year of en of projection (same day and month as proj1).
-                     }else{
+   */
-                       printf(" 0.");
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-                       fprintf(ficparo," 0.");
+   int *popage;
-                     }
+   double agec; /* generic age */
-                   }
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-                 }
+   double *popeffectif,*popcount;
-               } /* end lk */
+   double ***p3mat;
-             } /* end lj */
+   double ***mobaverage;
-           } /* end li */
+   char fileresf[FILENAMELENGTH];
-           printf("\n");
-           fprintf(ficparo,"\n");
+   agelim=AGESUP;
-           numlinepar++;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-         } /* end k*/
-       } /*end j */
+   strcpy(fileresf,"f");
-     } /* end i */
+   strcat(fileresf,fileres);
-   } /* end itimes */
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
- } /* end of prwizard */
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
- /******************* Gompertz Likelihood ******************************/
+   }
- double gompertz(double x[])
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
- {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   double A,B,L=0.0,sump=0.,num=0.;
-   int i,n=0; /* n is the size of the sample */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   for (i=0;i<=imx-1 ; i++) {
+   if (mobilav!=0) {
-     sump=sump+weight[i];
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     /*    sump=sump+1;*/
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-     num=num+1;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   }
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
+   }
-   /* for (i=0; i<=imx; i++)
-      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   for (i=1;i<=imx ; i++)
+   if(estepm < stepm){
-     {
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       if (cens[i] == 1 && wav[i]>1)
+   }
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   else  hstepm=estepm;
-       if (cens[i] == 0 && wav[i]>1)
+   hstepm=hstepm/stepm;
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+                                fractional in yp1 */
+   anprojmean=yp;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   yp2=modf((yp1*12),&yp);
-       if (wav[i] > 1 ) { /* ??? */
+   mprojmean=yp;
-         L=L+A*weight[i];
+   yp1=modf((yp2*30.5),&yp);
-         /*      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]);*/
+   jprojmean=yp;
-       }
+   if(jprojmean==0) jprojmean=1;
-     }
+   if(mprojmean==0) jprojmean=1;
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   return -2*L*num/sump;
- }
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
- /******************* Printing html file ***********/
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-                   int lastpass, int stepm, int weightopt, char model[],\
+ /*            if (h==(int)(YEARM*yearp)){ */
-                   int imx,  double p[],double **matcov,double agemortsup){
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-   int i,k;
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+       fprintf(ficresf,"\n#******");
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+       for(j=1;j<=cptcoveff;j++) {
-   for (i=1;i<=2;i++)
+         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," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+       }
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+       fprintf(ficresf,"******\n");
-   fprintf(fichtm,"</ul>");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+       for(j=1; j<=nlstate+ndeath;j++){
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresf," p%d%d",i,j);
-  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," p.%d",j);
+       }
-  for (k=agegomp;k<(agemortsup-2);k++)
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-    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,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-   fflush(fichtm);
+         for (agec=fage; agec>=(ageminpar-1); agec--){
- }
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
- /******************* Gnuplot file **************/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+           for (h=0; h<=nhstepm; h++){
-   int ng;
+             if (h*hstepm/YEARM*stepm ==yearp) {
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
-   /*#ifdef windows */
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-     /*#endif */
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               ppij=0.;
-   strcpy(dirfileres,optionfilefiname);
+               for(i=1; i<=nlstate;i++) {
-   strcpy(optfileres,"vpl");
+                 if (mobilav==1)
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+                 else {
-   fprintf(ficgp, "set ter png small\n set log y\n");
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-   fprintf(ficgp, "set size 0.65,0.65\n");
+                 }
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+                 if (h*hstepm/YEARM*stepm== yearp) {
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
- }
+                 }
+               } /* end i */
+               if (h*hstepm/YEARM*stepm==yearp) {
+                 fprintf(ficresf," %.3f", ppij);
+               }
+             }/* end j */
- /***********************************************/
+           } /* end h */
- /**************** Main Program *****************/
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /***********************************************/
+         } /* end agec */
+       } /* end yearp */
- int main(int argc, char *argv[])
+     } /* end cptcod */
- {
+   } /* end  cptcov */
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int linei, month, year,iout;
-   int jj, ll, li, lj, lk, imk;
+   fclose(ficresf);
-   int numlinepar=0; /* Current linenumber of parameter file */
+ }
-   int itimes;
-   int NDIM=2;
+ /************** Forecasting *****not tested NB*************/
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-   char ca[32], cb[32], cc[32];
-   char dummy[]="                         ";
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   /*  FILE *fichtm; *//* Html File */
+   int *popage;
-   /* FILE *ficgp;*/ /*Gnuplot File */
+   double calagedatem, agelim, kk1, kk2;
-   struct stat info;
+   double *popeffectif,*popcount;
-   double agedeb, agefin,hf;
+   double ***p3mat,***tabpop,***tabpopprev;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double ***mobaverage;
+   char filerespop[FILENAMELENGTH];
-   double fret;
-   double **xi,tmp,delta;
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double dum; /* Dummy variable */
+   agelim=AGESUP;
-   double ***p3mat;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   double ***mobaverage;
-   int *indx;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   char line[MAXLINE], linepar[MAXLINE];
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char pathr[MAXLINE], pathimach[MAXLINE];
+   strcpy(filerespop,"pop");
-   char **bp, *tok, *val; /* pathtot */
+   strcat(filerespop,fileres);
-   int firstobs=1, lastobs=10;
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   int sdeb, sfin; /* Status at beginning and end */
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   int c,  h , cpt,l;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   int ju,jl, mi;
+   }
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   int mobilav=0,popforecast=0;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   int hstepm, nhstepm;
-   int agemortsup;
+   if (mobilav!=0) {
-   float  sumlpop=0.;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   double bage, fage, age, agelim, agebase;
+     }
-   double ftolpl=FTOL;
+   }
-   double **prlim;
-   double *severity;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   double ***param; /* Matrix of parameters */
+   if (stepm<=12) stepsize=1;
-   double  *p;
-   double **matcov; /* Matrix of covariance */
+   agelim=AGESUP;
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
+   hstepm=1;
-   double ***eij, ***vareij;
+   hstepm=hstepm/stepm;
-   double **varpl; /* Variances of prevalence limits by age */
-   double *epj, vepp;
+   if (popforecast==1) {
-   double kk1, kk2;
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   double **ximort;
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+     }
-   int *dcwave;
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
-   char z[1]="c", occ;
+     popcount=vector(0,AGESUP);
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+     i=1;
-   char  *strt, strtend[80];
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   char *stratrunc;
-   int lstra;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   long total_usecs;
+   }
- /*   setlocale (LC_ALL, ""); */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- /*   textdomain (PACKAGE); */
+       k=k+1;
- /*   setlocale (LC_CTYPE, ""); */
+       fprintf(ficrespop,"\n#******");
- /*   setlocale (LC_MESSAGES, ""); */
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       }
-   (void) gettimeofday(&start_time,&tzp);
+       fprintf(ficrespop,"******\n");
-   curr_time=start_time;
+       fprintf(ficrespop,"# Age");
-   tm = *localtime(&start_time.tv_sec);
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-   tmg = *gmtime(&start_time.tv_sec);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-   strcpy(strstart,asctime(&tm));
+       for (cpt=0; cpt<=0;cpt++) {
- /*  printf("Localtime (at start)=%s",strstart); */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- /*  tp.tv_sec = tp.tv_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+           nhstepm = nhstepm/hstepm;
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
- /*   tp.tv_sec = mktime(&tmg); */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*   strt=asctime(&tmg); */
+           oldm=oldms;savm=savms;
- /*   printf("Time(after) =%s",strstart);  */
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- /*  (void) time (&time_value);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+           for (h=0; h<=nhstepm; h++){
- *  tm = *localtime(&time_value);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
- *  strstart=asctime(&tm);
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+             }
- */
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   nberr=0; /* Number of errors and warnings */
+               for(i=1; i<=nlstate;i++) {
-   nbwarn=0;
+                 if (mobilav==1)
-   getcwd(pathcd, size);
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
-   printf("\n%s\n%s",version,fullversion);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-   if(argc <=1){
+                 }
-     printf("\nEnter the parameter file name: ");
+               }
-     fgets(pathr,FILENAMELENGTH,stdin);
+               if (h==(int)(calagedatem+12*cpt)){
-     i=strlen(pathr);
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-     if(pathr[i-1]=='\n')
+                   /*fprintf(ficrespop," %.3f", kk1);
-       pathr[i-1]='\0';
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-    for (tok = pathr; tok != NULL; ){
+               }
-       printf("Pathr |%s|\n",pathr);
+             }
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+             for(i=1; i<=nlstate;i++){
-       printf("val= |%s| pathr=%s\n",val,pathr);
+               kk1=0.;
-       strcpy (pathtot, val);
+                 for(j=1; j<=nlstate;j++){
-       if(pathr[0] == '\0') break; /* Dirty */
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-     }
+                 }
-   }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   else{
+             }
-     strcpy(pathtot,argv[1]);
-   }
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   /*cygwin_split_path(pathtot,path,optionfile);
+           }
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* cutv(path,optionfile,pathtot,'\\');*/
+         }
+       }
-   /* Split argv[0], imach program to get pathimach */
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   /******/
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-  /*   strcpy(pathimach,argv[0]); */
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+           nhstepm = nhstepm/hstepm;
-   chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("Current directory %s!\n",pathcd);
+           oldm=oldms;savm=savms;
-   strcpy(command,"mkdir ");
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   strcat(command,optionfilefiname);
+           for (h=0; h<=nhstepm; h++){
-   if((outcmd=system(command)) != 0){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+             }
-     /* fclose(ficlog); */
+             for(j=1; j<=nlstate+ndeath;j++) {
- /*     exit(1); */
+               kk1=0.;kk2=0;
-   }
+               for(i=1; i<=nlstate;i++) {
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
- /*     perror("mkdir"); */
+               }
- /*   } */
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+             }
-   /*-------- arguments in the command line --------*/
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* Log file */
+         }
-   strcat(filelog, optionfilefiname);
+       }
-   strcat(filelog,".log");    /* */
+    }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+   }
-     printf("Problem with logfile %s\n",filelog);
-     goto end;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   }
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+   if (popforecast==1) {
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+     free_ivector(popage,0,AGESUP);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+     free_vector(popeffectif,0,AGESUP);
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+     free_vector(popcount,0,AGESUP);
-  path=%s \n\
+   }
-  optionfile=%s\n\
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  optionfilext=%s\n\
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   fclose(ficrespop);
+ } /* End of popforecast */
-   printf("Local time (at start):%s",strstart);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+ int fileappend(FILE *fichier, char *optionfich)
-   fflush(ficlog);
+ {
- /*   (void) gettimeofday(&curr_time,&tzp); */
+   if((fichier=fopen(optionfich,"a"))==NULL) {
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+     printf("Problem with file: %s\n", optionfich);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-   /* */
+     return (0);
-   strcpy(fileres,"r");
+   }
-   strcat(fileres, optionfilefiname);
+   fflush(fichier);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+   return (1);
+ }
-   /*---------arguments file --------*/
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+ /**************** function prwizard **********************/
-     printf("Problem with optionfile %s\n",optionfile);
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+ {
-     fflush(ficlog);
-     goto end;
+   /* Wizard to print covariance matrix template */
-   }
+   char ca[32], cb[32], cc[32];
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
-   strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("Problem with Output resultfile: %s\n", filereso);
+   for(i=1; i <=nlstate; i++){
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     jj=0;
-     fflush(ficlog);
+     for(j=1; j <=nlstate+ndeath; j++){
-     goto end;
+       if(j==i) continue;
-   }
+       jj++;
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   /* Reads comments: lines beginning with '#' */
+       printf("%1d%1d",i,j);
-   numlinepar=0;
+       fprintf(ficparo,"%1d%1d",i,j);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       for(k=1; k<=ncovmodel;k++){
-     ungetc(c,ficpar);
+         /*        printf(" %lf",param[i][j][k]); */
-     fgets(line, MAXLINE, ficpar);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-     numlinepar++;
+         printf(" 0.");
-     puts(line);
+         fprintf(ficparo," 0.");
-     fputs(line,ficparo);
+       }
-     fputs(line,ficlog);
+       printf("\n");
-   }
+       fprintf(ficparo,"\n");
-   ungetc(c,ficpar);
+     }
+   }
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   printf("# Scales (for hessian or gradient estimation)\n");
-   numlinepar++;
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\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);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   for(i=1; i <=nlstate; i++){
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+     jj=0;
-   fflush(ficlog);
+     for(j=1; j <=nlstate+ndeath; j++){
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       if(j==i) continue;
-     ungetc(c,ficpar);
+       jj++;
-     fgets(line, MAXLINE, ficpar);
+       fprintf(ficparo,"%1d%1d",i,j);
-     numlinepar++;
+       printf("%1d%1d",i,j);
-     puts(line);
+       fflush(stdout);
-     fputs(line,ficparo);
+       for(k=1; k<=ncovmodel;k++){
-     fputs(line,ficlog);
+         /*      printf(" %le",delti3[i][j][k]); */
-   }
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   ungetc(c,ficpar);
+         printf(" 0.");
+         fprintf(ficparo," 0.");
+       }
-   covar=matrix(0,NCOVMAX,1,n);
+       numlinepar++;
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       printf("\n");
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       fprintf(ficparo,"\n");
+     }
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+   }
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+   printf("# Covariance matrix\n");
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-   delti=delti3[1][1];
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-     printf(" You choose mle=-1, 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=-1, look at file %s for a template of covariance matrix \n",filereso);
+   fflush(stdout);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   fprintf(ficparo,"# Covariance matrix\n");
-     fclose (ficparo);
+   /* # 121 Var(a12)\n\ */
-     fclose (ficlog);
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     goto end;
+   /* #   ...\n\ */
-     exit(0);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-   }
-   else if(mle==-3) {
+   for(itimes=1;itimes<=2;itimes++){
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     jj=0;
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     for(i=1; i <=nlstate; i++){
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       for(j=1; j <=nlstate+ndeath; j++){
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         if(j==i) continue;
-     matcov=matrix(1,npar,1,npar);
+         for(k=1; k<=ncovmodel;k++){
-   }
+           jj++;
-   else{
+           ca[0]= k+'a'-1;ca[1]='\0';
-     /* Read guess parameters */
+           if(itimes==1){
-     /* Reads comments: lines beginning with '#' */
+             printf("#%1d%1d%d",i,j,k);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-       ungetc(c,ficpar);
+           }else{
-       fgets(line, MAXLINE, ficpar);
+             printf("%1d%1d%d",i,j,k);
-       numlinepar++;
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-       puts(line);
+             /*  printf(" %.5le",matcov[i][j]); */
-       fputs(line,ficparo);
+           }
-       fputs(line,ficlog);
+           ll=0;
-     }
+           for(li=1;li <=nlstate; li++){
-     ungetc(c,ficpar);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+               for(lk=1;lk<=ncovmodel;lk++){
-     for(i=1; i <=nlstate; i++){
+                 ll++;
-       j=0;
+                 if(ll<=jj){
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-         if(jj==i) continue;
+                   if(ll<jj){
-         j++;
+                     if(itimes==1){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-         if ((i1 != i) && (j1 != j)){
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+                     }else{
- It might be a problem of design; if ncovcol and the model are correct\n \
+                       printf(" 0.");
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+                       fprintf(ficparo," 0.");
-           exit(1);
+                     }
-         }
+                   }else{
-         fprintf(ficparo,"%1d%1d",i1,j1);
+                     if(itimes==1){
-         if(mle==1)
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-           printf("%1d%1d",i,j);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+                     }else{
-         for(k=1; k<=ncovmodel;k++){
+                       printf(" 0.");
-           fscanf(ficpar," %lf",&param[i][j][k]);
+                       fprintf(ficparo," 0.");
-           if(mle==1){
+                     }
-             printf(" %lf",param[i][j][k]);
+                   }
-             fprintf(ficlog," %lf",param[i][j][k]);
+                 }
-           }
+               } /* end lk */
-           else
+             } /* end lj */
-             fprintf(ficlog," %lf",param[i][j][k]);
+           } /* end li */
-           fprintf(ficparo," %lf",param[i][j][k]);
+           printf("\n");
-         }
+           fprintf(ficparo,"\n");
-         fscanf(ficpar,"\n");
+           numlinepar++;
-         numlinepar++;
+         } /* end k*/
-         if(mle==1)
+       } /*end j */
-           printf("\n");
+     } /* end i */
-         fprintf(ficlog,"\n");
+   } /* end itimes */
-         fprintf(ficparo,"\n");
-       }
+ } /* end of prwizard */
-     }
+ /******************* Gompertz Likelihood ******************************/
-     fflush(ficlog);
+ double gompertz(double x[])
+ {
-     p=param[1][1];
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
-     /* Reads comments: lines beginning with '#' */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   for (i=0;i<=imx-1 ; i++) {
-       ungetc(c,ficpar);
+     sump=sump+weight[i];
-       fgets(line, MAXLINE, ficpar);
+     /*    sump=sump+1;*/
-       numlinepar++;
+     num=num+1;
-       puts(line);
+   }
-       fputs(line,ficparo);
-       fputs(line,ficlog);
-     }
+   /* for (i=0; i<=imx; i++)
-     ungetc(c,ficpar);
+      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 <=nlstate; i++){
+   for (i=1;i<=imx ; i++)
-       for(j=1; j <=nlstate+ndeath-1; j++){
+     {
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       if (cens[i] == 1 && wav[i]>1)
-         if ((i1-i)*(j1-j)!=0){
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-           exit(1);
+       if (cens[i] == 0 && wav[i]>1)
-         }
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-         printf("%1d%1d",i,j);
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-         for(k=1; k<=ncovmodel;k++){
+       if (wav[i] > 1 ) { /* ??? */
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+         L=L+A*weight[i];
-           printf(" %le",delti3[i][j][k]);
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-           fprintf(ficparo," %le",delti3[i][j][k]);
+       }
-           fprintf(ficlog," %le",delti3[i][j][k]);
+     }
-         }
-         fscanf(ficpar,"\n");
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-         numlinepar++;
-         printf("\n");
+   return -2*L*num/sump;
-         fprintf(ficparo,"\n");
+ }
-         fprintf(ficlog,"\n");
-       }
+ #ifdef GSL
-     }
+ /******************* Gompertz_f Likelihood ******************************/
-     fflush(ficlog);
+ double gompertz_f(const gsl_vector *v, void *params)
+ {
-     delti=delti3[1][1];
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+   for (i=0;i<=imx-1 ; i++) {
-     /* Reads comments: lines beginning with '#' */
+     sump=sump+weight[i];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /*    sump=sump+1;*/
-       ungetc(c,ficpar);
+     num=num+1;
-       fgets(line, MAXLINE, ficpar);
+   }
-       numlinepar++;
-       puts(line);
-       fputs(line,ficparo);
+   /* for (i=0; i<=imx; i++)
-       fputs(line,ficlog);
+      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("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     ungetc(c,ficpar);
+   for (i=1;i<=imx ; i++)
+     {
-     matcov=matrix(1,npar,1,npar);
+       if (cens[i] == 1 && wav[i]>1)
-     for(i=1; i <=npar; i++){
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       fscanf(ficpar,"%s",&str);
-       if(mle==1)
+       if (cens[i] == 0 && wav[i]>1)
-         printf("%s",str);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-       fprintf(ficlog,"%s",str);
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-       fprintf(ficparo,"%s",str);
-       for(j=1; j <=i; j++){
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-         fscanf(ficpar," %le",&matcov[i][j]);
+       if (wav[i] > 1 ) { /* ??? */
-         if(mle==1){
+         LL=LL+A*weight[i];
-           printf(" %.5le",matcov[i][j]);
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-         }
+       }
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     }
-         fprintf(ficparo," %.5le",matcov[i][j]);
-       }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       fscanf(ficpar,"\n");
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-       numlinepar++;
-       if(mle==1)
+   return -2*LL*num/sump;
-         printf("\n");
+ }
-       fprintf(ficlog,"\n");
+ #endif
-       fprintf(ficparo,"\n");
-     }
+ /******************* Printing html file ***********/
-     for(i=1; i <=npar; i++)
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-       for(j=i+1;j<=npar;j++)
+                   int lastpass, int stepm, int weightopt, char model[],\
-         matcov[i][j]=matcov[j][i];
+                   int imx,  double p[],double **matcov,double agemortsup){
+   int i,k;
-     if(mle==1)
-       printf("\n");
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     fprintf(ficlog,"\n");
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+   for (i=1;i<=2;i++)
-     fflush(ficlog);
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     /*-------- Rewriting parameter file ----------*/
+   fprintf(fichtm,"</ul>");
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
-     if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+  for (k=agegomp;k<(agemortsup-2);k++)
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+    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(ficres,"#%s\n",version);
-   }    /* End of mle != -3 */
+   fflush(fichtm);
+ }
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+ /******************* Gnuplot file **************/
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
-   }
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   n= lastobs;
+   int ng;
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
-   num=lvector(1,n);
+   /*#ifdef windows */
-   moisnais=vector(1,n);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   annais=vector(1,n);
+     /*#endif */
-   moisdc=vector(1,n);
-   andc=vector(1,n);
-   agedc=vector(1,n);
+   strcpy(dirfileres,optionfilefiname);
-   cod=ivector(1,n);
+   strcpy(optfileres,"vpl");
-   weight=vector(1,n);
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   mint=matrix(1,maxwav,1,n);
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-   anint=matrix(1,maxwav,1,n);
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-   s=imatrix(1,maxwav+1,1,n);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+ }
-   i=1;
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-   linei=0;
+ {
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     linei=linei+1;
+   /*-------- data file ----------*/
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+   FILE *fic;
-       if(line[j] == '\t')
+   char dummy[]="                         ";
-         line[j] = ' ';
+   int i, j, n;
-     }
+   int linei, month, year,iout;
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+   char line[MAXLINE], linetmp[MAXLINE];
-       ;
+   char stra[80], strb[80];
-     };
+   char *stratrunc;
-     line[j+1]=0;  /* Trims blanks at end of line */
+   int lstra;
-     if(line[0]=='#'){
-       fprintf(ficlog,"Comment line\n%s\n",line);
-       printf("Comment line\n%s\n",line);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-       continue;
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-     }
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+   }
-     for (j=maxwav;j>=1;j--){
-       cutv(stra, strb,line,' ');
+   i=1;
-       errno=0;
+   linei=0;
-       lval=strtol(strb,&endptr,10);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     linei=linei+1;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-         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);
+       if(line[j] == '\t')
-         exit(1);
+         line[j] = ' ';
-       }
+     }
-       s[j][i]=lval;
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
-       strcpy(line,stra);
+     };
-       cutv(stra, strb,line,' ');
+     line[j+1]=0;  /* Trims blanks at end of line */
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if(line[0]=='#'){
-       }
+       fprintf(ficlog,"Comment line\n%s\n",line);
-       else  if(iout=sscanf(strb,"%s.") != 0){
+       printf("Comment line\n%s\n",line);
-         month=99;
+       continue;
-         year=9999;
+     }
-       }else{
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
+     for (j=0; line[j]!='\0';j++){
-         exit(1);
+       line[j]=linetmp[j];
-       }
+     }
-       anint[j][i]= (double) year;
-       mint[j][i]= (double)month;
-       strcpy(line,stra);
+     for (j=maxwav;j>=1;j--){
-     } /* ENd Waves */
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
-     cutv(stra, strb,line,' ');
+         lval=-1;
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }else{
-     }
+         errno=0;
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+         lval=strtol(strb,&endptr,10);
-       month=99;
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       year=9999;
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     }else{
+           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);
-       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);
+           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);
-       exit(1);
+           return 1;
-     }
+         }
-     andc[i]=(double) year;
+       }
-     moisdc[i]=(double) month;
+       s[j][i]=lval;
-     strcpy(line,stra);
+       strcpy(line,stra);
-     cutv(stra, strb,line,' ');
+       cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     }
+       }
-     else  if(iout=sscanf(strb,"%s.") != 0){
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-       month=99;
+         month=99;
-       year=9999;
+         year=9999;
-     }else{
+       }else{
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-       exit(1);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
-     }
+         return 1;
-     annais[i]=(double)(year);
+       }
-     moisnais[i]=(double)(month);
+       anint[j][i]= (double) year;
-     strcpy(line,stra);
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
-     cutv(stra, strb,line,' ');
+     } /* ENd Waves */
-     errno=0;
-     dval=strtod(strb,&endptr);
+     cutv(stra, strb,line,' ');
-     if( strb[0]=='\0' || (*endptr != '\0')){
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 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);
+     }
-       exit(1);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     }
+       month=99;
-     weight[i]=dval;
+       year=9999;
-     strcpy(line,stra);
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-     for (j=ncovcol;j>=1;j--){
+         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);
-       cutv(stra, strb,line,' ');
+         return 1;
-       errno=0;
+     }
-       lval=strtol(strb,&endptr,10);
+     andc[i]=(double) year;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     moisdc[i]=(double) month;
-         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);
+     strcpy(line,stra);
-         exit(1);
-       }
+     cutv(stra, strb,line,' ');
-       if(lval <-1 || lval >1){
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+     }
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+       month=99;
-  For example, for multinomial values like 1, 2 and 3,\n \
+       year=9999;
-  build V1=0 V2=0 for the reference value (1),\n \
+     }else{
-         V1=1 V2=0 for (2) \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);
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+       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);
-  output of IMaCh is often meaningless.\n \
+         return 1;
-  Exiting.\n",lval,linei, i,line,j);
+     }
-         exit(1);
+     if (year==9999) {
-       }
+       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);
-       covar[j][i]=(double)(lval);
+       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);
-       strcpy(line,stra);
+         return 1;
-     }
-     lstra=strlen(stra);
+     }
+     annais[i]=(double)(year);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+     moisnais[i]=(double)(month);
-       stratrunc = &(stra[lstra-9]);
+     strcpy(line,stra);
-       num[i]=atol(stratrunc);
-     }
+     cutv(stra, strb,line,' ');
-     else
+     errno=0;
-       num[i]=atol(stra);
+     dval=strtod(strb,&endptr);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+     if( strb[0]=='\0' || (*endptr != '\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;}*/
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-     i=i+1;
+       fflush(ficlog);
-   } /* End loop reading  data */
+       return 1;
-   fclose(fic);
+     }
-   /* printf("ii=%d", ij);
+     weight[i]=dval;
-      scanf("%d",i);*/
+     strcpy(line,stra);
-   imx=i-1; /* Number of individuals */
+     for (j=ncovcol;j>=1;j--){
-   /* for (i=1; i<=imx; i++){
+       cutv(stra, strb,line,' ');
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+       if(strb[0]=='.') { /* Missing status */
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+         lval=-1;
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+       }else{
-     }*/
+         errno=0;
-    /*  for (i=1; i<=imx; i++){
+         lval=strtol(strb,&endptr,10);
-      if (s[4][i]==9)  s[4][i]=-1;
+         if( strb[0]=='\0' || (*endptr != '\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]));}*/
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
-   /* for (i=1; i<=imx; i++) */
+           return 1;
+         }
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+       }
-      else weight[i]=1;*/
+       if(lval <-1 || lval >1){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-   /* Calculation of the number of parameters from char model */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-   Tprod=ivector(1,15);
+  For example, for multinomial values like 1, 2 and 3,\n \
-   Tvaraff=ivector(1,15);
+  build V1=0 V2=0 for the reference value (1),\n \
-   Tvard=imatrix(1,15,1,2);
+         V1=1 V2=0 for (2) \n \
-   Tage=ivector(1,15);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+  output of IMaCh is often meaningless.\n \
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+  Exiting.\n",lval,linei, i,line,j);
-     j=0, j1=0, k1=1, k2=1;
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     j=nbocc(model,'+'); /* j=Number of '+' */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     cptcovn=j+1;
+  For example, for multinomial values like 1, 2 and 3,\n \
-     cptcovprod=j1; /*Number of products */
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
-     strcpy(modelsav,model);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+  output of IMaCh is often meaningless.\n \
-       printf("Error. Non available option model=%s ",model);
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+         return 1;
-       goto end;
+       }
-     }
+       covar[j][i]=(double)(lval);
+       strcpy(line,stra);
-     /* This loop fills the array Tvar from the string 'model'.*/
+     }
+     lstra=strlen(stra);
-     for(i=(j+1); i>=1;i--){
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       stratrunc = &(stra[lstra-9]);
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       num[i]=atol(stratrunc);
-       /*scanf("%d",i);*/
+     }
-       if (strchr(strb,'*')) {  /* Model includes a product */
+     else
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+       num[i]=atol(stra);
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-           cptcovprod--;
+       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;}*/
-           cutv(strb,stre,strd,'V');
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+     i=i+1;
-           cptcovage++;
+   } /* End loop reading  data */
-             Tage[cptcovage]=i;
-             /*printf("stre=%s ", stre);*/
+   *imax=i-1; /* Number of individuals */
-         }
+   fclose(fic);
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+   return (0);
-           cutv(strb,stre,strc,'V');
+   endread:
-           Tvar[i]=atoi(stre);
+     printf("Exiting readdata: ");
-           cptcovage++;
+     fclose(fic);
-           Tage[cptcovage]=i;
+     return (1);
-         }
-         else {  /* Age is not in the model */
-           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 */
+ void removespace(char *str) {
-           Tprod[k1]=i;
+   char *p1 = str, *p2 = str;
-           Tvard[k1][1]=atoi(strc); /* m*/
+   do
-           Tvard[k1][2]=atoi(stre); /* n */
+     while (*p2 == ' ')
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+       p2++;
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+   while (*p1++ = *p2++);
-           for (k=1; k<=lastobs;k++)
+ }
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
-           k1++;
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-           k2=k2+2;
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-         }
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-       }
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-       else { /* no more sum */
+    * - cptcovage number of covariates with age*products =2
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+    * - cptcovs number of simple covariates
-        /*  scanf("%d",i);*/
+    * - 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
-       cutv(strd,strc,strb,'V');
+    *     which is a new column after the 9 (ncovcol) variables.
-       Tvar[i]=atoi(strc);
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-       }
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-       strcpy(modelsav,stra);
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-         scanf("%d",i);*/
+  */
-     } /* end of loop + */
+ {
-   } /* end model */
+   int i, j, k, ks;
+   int i1, j1, k1, k2;
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+   char modelsav[80];
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   /*removespace(model);*/
-   printf("cptcovprod=%d ", cptcovprod);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-   scanf("%d ",i);*/
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     /*  if(mle==1){*/
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+                   /* including age products which are counted in cptcovage.
-     for(i=1;i<=n;i++) weight[i]=1.0;
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-   }
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-     /*-calculation of age at interview from date of interview and age at death -*/
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-   agev=matrix(1,maxwav,1,imx);
+     strcpy(modelsav,model);
+     if (strstr(model,"AGE") !=0){
-   for (i=1; i<=imx; i++) {
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-     for(m=2; (m<= maxwav); m++) {
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       return 1;
-         anint[m][i]=9999;
+     }
-         s[m][i]=-1;
+     if (strstr(model,"v") !=0){
-       }
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-         nberr++;
+       return 1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+     }
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-         s[m][i]=-1;
+     /*   Design
-       }
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+      *  <          ncovcol=8                >
-         nberr++;
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-         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]);
+      *   k=  1    2      3       4     5       6      7        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]);
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+      *  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
-   }
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+      *  Tage[++cptcovage]=k
-   for (i=1; i<=imx; i++)  {
+      *       if products, new covar are created after ncovcol with k1
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-     for(m=firstpass; (m<= lastpass); m++){
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+      *  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 (s[m][i] >= nlstate+1) {
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-           if(agedc[i]>0)
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-               agev[m][i]=agedc[i];
+      *  <          ncovcol=8                >
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-             else {
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-               if ((int)andc[i]!=9999){
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-                 nbwarn++;
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+      * p Tprod[1]@2={                         6, 5}
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-                 agev[m][i]=-1;
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-               }
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-             }
+      *How to reorganize?
-         }
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-                                  years but with the precision of a month */
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+      * Struct []
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+      */
-             agev[m][i]=1;
-           else if(agev[m][i] <agemin){
+     /* This loop fills the array Tvar from the string 'model'.*/
-             agemin=agev[m][i];
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-           }
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-           else if(agev[m][i] >agemax){
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-             agemax=agev[m][i];
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+     /*  k=1 Tvar[1]=2 (from V2) */
-           }
+     /*  k=5 Tvar[5] */
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+     /* for (k=1; k<=cptcovn;k++) { */
-           /*     agev[m][i] = age[i]+2*m;*/
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-         }
+     /*  } */
-         else { /* =9 */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           agev[m][i]=1;
+     /*
-           s[m][i]=-1;
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-         }
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-       }
+         Tvar[k]=0;
-       else /*= 0 Unknown */
+     cptcovage=0;
-         agev[m][i]=1;
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-     }
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-   }
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-   for (i=1; i<=imx; i++)  {
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-     for(m=firstpass; (m<=lastpass); m++){
+       /*scanf("%d",i);*/
-       if (s[m][i] > (nlstate+ndeath)) {
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-         nberr++;
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         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 (strcmp(strc,"age")==0) { /**< Model includes age: Vn*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);
+           /* covar is not filled and then is empty */
-         goto end;
+           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 */
-   }
+           cptcovage++; /* Sums the number of covariates which include age as a product */
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-   /*for (i=1; i<=imx; i++){
+           /*printf("stre=%s ", stre);*/
-   for (m=firstpass; (m<lastpass); m++){
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+           cptcovprod--;
- }
+           cutl(stre,strb,strc,'V');
+           Tvar[k]=atoi(stre);
- }*/
+           cptcovage++;
+           Tage[cptcovage]=k;
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           cptcovn++;
+           cptcovprodnoage++;k1++;
-   agegomp=(int)agemin;
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   free_vector(severity,1,maxwav);
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-   free_imatrix(outcome,1,maxwav+1,1,n);
+                                   because this model-covariate is a construction we invent a new column
-   free_vector(moisnais,1,n);
+                                   ncovcol + k1
-   free_vector(annais,1,n);
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-   /* free_matrix(mint,1,maxwav,1,n);
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-      free_matrix(anint,1,maxwav,1,n);*/
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-   free_vector(moisdc,1,n);
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-   free_vector(andc,1,n);
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+           k2=k2+2;
-   wav=ivector(1,imx);
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+           for (i=1; i<=lastobs;i++){
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+             /* Computes the new covariate which is a product of
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-   /* Concatenates waves */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+           }
+         } /* End age is not in the model */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+       } /* End if model includes a product */
+       else { /* no more sum */
-   Tcode=ivector(1,100);
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+        /*  scanf("%d",i);*/
-   ncodemax[1]=1;
+         cutl(strd,strc,strb,'V');
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+         ks++; /**< Number of simple covariates */
+         cptcovn++;
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+         Tvar[k]=atoi(strd);
-                                  the estimations*/
+       }
-   h=0;
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   m=pow(2,cptcoveff);
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         scanf("%d",i);*/
-   for(k=1;k<=cptcoveff; k++){
+     } /* end of loop + */
-     for(i=1; i <=(m/pow(2,k));i++){
+   } /* end model */
-       for(j=1; j <= ncodemax[k]; j++){
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-           h++;
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   /* 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);
-     }
-   }
+   scanf("%d ",i);*/
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-      codtab[1][2]=1;codtab[2][2]=2; */
-   /* for(i=1; i <=m ;i++){
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-      for(k=1; k <=cptcovn; k++){
+   endread:
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+     printf("Exiting decodemodel: ");
-      }
+     return (1);
-      printf("\n");
+ }
-      }
-      scanf("%d",i);*/
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
-   /*------------ gnuplot -------------*/
+   int i, m;
-   strcpy(optionfilegnuplot,optionfilefiname);
-   if(mle==-3)
+   for (i=1; i<=imx; i++) {
-     strcat(optionfilegnuplot,"-mort");
+     for(m=2; (m<= maxwav); m++) {
-   strcat(optionfilegnuplot,".gp");
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+         s[m][i]=-1;
-     printf("Problem with file %s",optionfilegnuplot);
+       }
-   }
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-   else{
+         *nberr++;
-     fprintf(ficgp,"\n# %s\n", version);
+         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(ficgp,"# %s\n", optionfilegnuplot);
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-     fprintf(ficgp,"set missing 'NaNq'\n");
+         s[m][i]=-1;
-   }
+       }
-   /*  fclose(ficgp);*/
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-   /*--------- index.htm --------*/
+         *nberr++;
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-   if(mle==-3)
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-     strcat(optionfilehtm,"-mort");
+       }
-   strcat(optionfilehtm,".htm");
+     }
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+   }
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+     for(m=firstpass; (m<= lastpass); m++){
-   strcat(optionfilehtmcov,"-cov.htm");
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+         if (s[m][i] >= nlstate+1) {
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+           if(agedc[i]>0)
-   }
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-   else{
+               agev[m][i]=agedc[i];
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+             else {
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+               if ((int)andc[i]!=9999){
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+                 nbwarn++;
-   }
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+                 agev[m][i]=-1;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+               }
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+             }
- \n\
+         }
- <hr  size=\"2\" color=\"#EC5E5E\">\
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-  <ul><li><h4>Parameter files</h4>\n\
+                                  years but with the precision of a month */
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+             agev[m][i]=1;
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+           else if(agev[m][i] < *agemin){
-  - Date and time at start: %s</ul>\n",\
+             *agemin=agev[m][i];
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           }
-           fileres,fileres,\
+           else if(agev[m][i] >*agemax){
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+             *agemax=agev[m][i];
-   fflush(fichtm);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
+           }
-   strcpy(pathr,path);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-   strcat(pathr,optionfilefiname);
+           /*     agev[m][i] = age[i]+2*m;*/
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+         }
+         else { /* =9 */
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+           agev[m][i]=1;
-      and prints on file fileres'p'. */
+           s[m][i]=-1;
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+         }
+       }
-   fprintf(fichtm,"\n");
+       else /*= 0 Unknown */
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         agev[m][i]=1;
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+     }
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-           imx,agemin,agemax,jmin,jmax,jmean);
+   }
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   for (i=1; i<=imx; i++)  {
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     for(m=firstpass; (m<=lastpass); m++){
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       if (s[m][i] > (nlstate+ndeath)) {
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         *nberr++;
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         return 1;
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       }
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+     }
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   }
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /*for (i=1; i<=imx; i++){
+   for (m=firstpass; (m<lastpass); m++){
-   if (mle==-3){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-     ximort=matrix(1,NDIM,1,NDIM);
+ }
-     cens=ivector(1,n);
-     ageexmed=vector(1,n);
+ }*/
-     agecens=vector(1,n);
-     dcwave=ivector(1,n);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     for (i=1; i<=imx; i++){
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-       dcwave[i]=-1;
-       for (m=firstpass; m<=lastpass; m++)
+   return (0);
-         if (s[m][i]>nlstate) {
+   endread:
-           dcwave[i]=m;
+     printf("Exiting calandcheckages: ");
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+     return (1);
-           break;
+ }
-         }
-     }
+ /***********************************************/
-     for (i=1; i<=imx; i++) {
+ /**************** Main Program *****************/
-       if (wav[i]>0){
+ /***********************************************/
-         ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];
+ int main(int argc, char *argv[])
-         agecens[i]=1.;
+ {
+ #ifdef GSL
-         if (ageexmed[i]> 1 && wav[i] > 0){
+   const gsl_multimin_fminimizer_type *T;
-           agecens[i]=agev[mw[j][i]][i];
+   size_t iteri = 0, it;
-           cens[i]= 1;
+   int rval = GSL_CONTINUE;
-         }else if (ageexmed[i]< 1)
+   int status = GSL_SUCCESS;
-           cens[i]= -1;
+   double ssval;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+ #endif
-           cens[i]=0 ;
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-       }
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-       else cens[i]=-1;
+   int linei, month, year,iout;
-     }
+   int jj, ll, li, lj, lk, imk;
+   int numlinepar=0; /* Current linenumber of parameter file */
-     for (i=1;i<=NDIM;i++) {
+   int itimes;
-       for (j=1;j<=NDIM;j++)
+   int NDIM=2;
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   int vpopbased=0;
-     }
+   char ca[32], cb[32], cc[32];
-     p[1]=0.0268; p[NDIM]=0.083;
+   /*  FILE *fichtm; *//* Html File */
-     /*printf("%lf %lf", p[1], p[2]);*/
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
+   double agedeb, agefin,hf;
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
+   double fret;
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   double **xi,tmp,delta;
-       printf("Problem with resultfile: %s\n", filerespow);
-       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++)
+   int *indx;
-         for(j=1;j<=nlstate+ndeath;j++)
+   char line[MAXLINE], linepar[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 **bp, *tok, *val; /* pathtot */
+   int firstobs=1, lastobs=10;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+   int sdeb, sfin; /* Status at beginning and end */
-     fclose(ficrespow);
+   int c,  h , cpt,l;
+   int ju,jl, mi;
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   int i1,j1, jk,aa,bb, stepsize, ij;
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-     for(i=1; i <=NDIM; i++)
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-       for(j=i+1;j<=NDIM;j++)
+   int mobilav=0,popforecast=0;
-         matcov[i][j]=matcov[j][i];
+   int hstepm, nhstepm;
+   int agemortsup;
-     printf("\nCovariance matrix\n ");
+   float  sumlpop=0.;
-     for(i=1; i <=NDIM; i++) {
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-       for(j=1;j<=NDIM;j++){
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-         printf("%f ",matcov[i][j]);
-       }
+   double bage, fage, age, agelim, agebase;
-       printf("\n ");
+   double ftolpl=FTOL;
-     }
+   double **prlim;
+   double ***param; /* Matrix of parameters */
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+   double  *p;
-     for (i=1;i<=NDIM;i++)
+   double **matcov; /* Matrix of covariance */
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   double ***delti3; /* Scale */
+   double *delti; /* Scale */
-     lsurv=vector(1,AGESUP);
+   double ***eij, ***vareij;
-     lpop=vector(1,AGESUP);
+   double **varpl; /* Variances of prevalence limits by age */
-     tpop=vector(1,AGESUP);
+   double *epj, vepp;
-     lsurv[agegomp]=100000;
+   double kk1, kk2;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-     for (k=agegomp;k<=AGESUP;k++) {
+   double **ximort;
-       agemortsup=k;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+   int *dcwave;
-     }
+   char z[1]="c", occ;
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   /*char  *strt;*/
+   char strtend[80];
-     for (k=agegomp;k<agemortsup;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   long total_usecs;
-       sumlpop=sumlpop+lpop[k];
-     }
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     tpop[agegomp]=sumlpop;
+ /*   textdomain (PACKAGE); */
-     for (k=agegomp;k<(agemortsup-3);k++){
+ /*   setlocale (LC_CTYPE, ""); */
-       /*  tpop[k+1]=2;*/
+ /*   setlocale (LC_MESSAGES, ""); */
-       tpop[k+1]=tpop[k]-lpop[k];
-     }
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   start_time = *localtime(&rstart_time);
-     for (k=agegomp;k<(agemortsup-2);k++)
+   curr_time=start_time;
-       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]);
+   /*tml = *localtime(&start_time.tm_sec);*/
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+ /*  tm = *localtime(&start_time.tm_sec); */
-                      stepm, weightopt,\
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-                      model,imx,p,matcov,agemortsup);
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-     free_vector(lsurv,1,AGESUP);
+ /*   tp.tm_sec = mktime(&tmg); */
-     free_vector(lpop,1,AGESUP);
+ /*   strt=asctime(&tmg); */
-     free_vector(tpop,1,AGESUP);
+ /*   printf("Time(after) =%s",strstart);  */
-   } /* Endof if mle==-3 */
+ /*  (void) time (&time_value);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-   else{ /* For mle >=1 */
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-     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]);
+   nberr=0; /* Number of errors and warnings */
-     printf("\n");
+   nbwarn=0;
-     globpr=1; /* to print the contributions */
+   getcwd(pathcd, size);
-     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);
+   printf("\n%s\n%s",version,fullversion);
-     for (k=1; k<=npar;k++)
+   if(argc <=1){
-       printf(" %d %8.5f",k,p[k]);
+     printf("\nEnter the parameter file name: ");
-     printf("\n");
+     fgets(pathr,FILENAMELENGTH,stdin);
-     if(mle>=1){ /* Could be 1 or 2 */
+     i=strlen(pathr);
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     if(pathr[i-1]=='\n')
-     }
+       pathr[i-1]='\0';
+     i=strlen(pathr);
-     /*--------- results files --------------*/
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-     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);
+       pathr[i-1]='\0';
+    for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       printf("val= |%s| pathr=%s\n",val,pathr);
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       strcpy (pathtot, val);
-     for(i=1,jk=1; i <=nlstate; i++){
+       if(pathr[0] == '\0') break; /* Dirty */
-       for(k=1; k <=(nlstate+ndeath); k++){
+     }
-         if (k != i) {
+   }
-           printf("%d%d ",i,k);
+   else{
-           fprintf(ficlog,"%d%d ",i,k);
+     strcpy(pathtot,argv[1]);
-           fprintf(ficres,"%1d%1d ",i,k);
+   }
-           for(j=1; j <=ncovmodel; j++){
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-             printf("%lf ",p[jk]);
+   /*cygwin_split_path(pathtot,path,optionfile);
-             fprintf(ficlog,"%lf ",p[jk]);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-             fprintf(ficres,"%lf ",p[jk]);
+   /* cutv(path,optionfile,pathtot,'\\');*/
-             jk++;
-           }
+   /* Split argv[0], imach program to get pathimach */
-           printf("\n");
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-           fprintf(ficlog,"\n");
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           fprintf(ficres,"\n");
+   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);
-     if(mle!=0){
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-       /* Computing hessian and covariance matrix */
+   chdir(path); /* Can be a relative path */
-       ftolhess=ftol; /* Usually correct */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+     printf("Current directory %s!\n",pathcd);
-     }
+   strcpy(command,"mkdir ");
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   strcat(command,optionfilefiname);
-     printf("# Scales (for hessian or gradient estimation)\n");
+   if((outcmd=system(command)) != 0){
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     for(i=1,jk=1; i <=nlstate; i++){
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-       for(j=1; j <=nlstate+ndeath; j++){
+     /* fclose(ficlog); */
-         if (j!=i) {
+ /*     exit(1); */
-           fprintf(ficres,"%1d%1d",i,j);
+   }
-           printf("%1d%1d",i,j);
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-           fprintf(ficlog,"%1d%1d",i,j);
+ /*     perror("mkdir"); */
-           for(k=1; k<=ncovmodel;k++){
+ /*   } */
-             printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
+   /*-------- arguments in the command line --------*/
-             fprintf(ficres," %.5e",delti[jk]);
-             jk++;
+   /* Log file */
-           }
+   strcat(filelog, optionfilefiname);
-           printf("\n");
+   strcat(filelog,".log");    /* */
-           fprintf(ficlog,"\n");
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-           fprintf(ficres,"\n");
+     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(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");
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-     if(mle>=1)
+   fprintf(ficlog,"pathimach=%s\npathtot=%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");
+  path=%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");
+  optionfile=%s\n\
-     /* # 121 Var(a12)\n\ */
+  optionfilext=%s\n\
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   printf("Local time (at start):%s",strstart);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   fflush(ficlog);
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
+   /* */
-     /* Just to have a covariance matrix which will be more understandable
+   strcpy(fileres,"r");
-        even is we still don't want to manage dictionary of variables
+   strcat(fileres, optionfilefiname);
-     */
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     for(itimes=1;itimes<=2;itimes++){
-       jj=0;
+   /*---------arguments file --------*/
-       for(i=1; i <=nlstate; i++){
-         for(j=1; j <=nlstate+ndeath; j++){
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-           if(j==i) continue;
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-           for(k=1; k<=ncovmodel;k++){
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-             jj++;
+     fflush(ficlog);
-             ca[0]= k+'a'-1;ca[1]='\0';
+     /* goto end; */
-             if(itimes==1){
+     exit(70);
-               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{
+   strcpy(filereso,"o");
-               if(mle>=1)
+   strcat(filereso,fileres);
-                 printf("%1d%1d%d",i,j,k);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+     printf("Problem with Output resultfile: %s\n", filereso);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-             }
+     fflush(ficlog);
-             ll=0;
+     goto end;
-             for(li=1;li <=nlstate; li++){
+   }
-               for(lj=1;lj <=nlstate+ndeath; lj++){
-                 if(lj==li) continue;
+   /* Reads comments: lines beginning with '#' */
-                 for(lk=1;lk<=ncovmodel;lk++){
+   numlinepar=0;
-                   ll++;
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                   if(ll<=jj){
+     ungetc(c,ficpar);
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+     fgets(line, MAXLINE, ficpar);
-                     if(ll<jj){
+     numlinepar++;
-                       if(itimes==1){
+     fputs(line,stdout);
-                         if(mle>=1)
+     fputs(line,ficparo);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     fputs(line,ficlog);
-                         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);
+   ungetc(c,ficpar);
-                       }else{
-                         if(mle>=1)
+   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(" %.5e",matcov[jj][ll]);
+   numlinepar++;
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   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(ficres," %.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,"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);
-                     }else{
+   fflush(ficlog);
-                       if(itimes==1){
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                         if(mle>=1)
+     ungetc(c,ficpar);
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+     fgets(line, MAXLINE, ficpar);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+     numlinepar++;
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     fputs(line, stdout);
-                       }else{
+     //puts(line);
-                         if(mle>=1)
+     fputs(line,ficparo);
-                           printf(" %.5e",matcov[jj][ll]);
+     fputs(line,ficlog);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   }
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   ungetc(c,ficpar);
-                       }
-                     }
-                   }
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-                 } /* end lk */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-               } /* end lj */
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-             } /* end li */
+      v1+v2*age+v2*v3 makes cptcovn = 3
-             if(mle>=1)
+   */
-               printf("\n");
+   if (strlen(model)>1)
-             fprintf(ficlog,"\n");
+     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*/
-             fprintf(ficres,"\n");
+   else
-             numlinepar++;
+     ncovmodel=2;
-           } /* end k*/
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-         } /*end j */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-       } /* end i */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-     } /* end itimes */
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-     fflush(ficlog);
+     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(ficres);
+     fflush(stdout);
+     fclose (ficlog);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     goto end;
-       ungetc(c,ficpar);
+   }
-       fgets(line, MAXLINE, ficpar);
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       puts(line);
+   delti=delti3[1][1];
-       fputs(line,ficparo);
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     }
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     ungetc(c,ficpar);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     estepm=0;
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+     fclose (ficparo);
-     if (fage <= 2) {
+     fclose (ficlog);
-       bage = ageminpar;
+     goto end;
-       fage = agemaxpar;
+     exit(0);
-     }
+   }
+   else if(mle==-3) {
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     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);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     matcov=matrix(1,npar,1,npar);
-       ungetc(c,ficpar);
+   }
-       fgets(line, MAXLINE, ficpar);
+   else{
-       puts(line);
+     /* Read guessed parameters */
-       fputs(line,ficparo);
+     /* Reads comments: lines beginning with '#' */
-     }
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, 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);
+       numlinepar++;
-     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,stdout);
-     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);
+       fputs(line,ficparo);
-     printf("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(ficlog,"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);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       fgets(line, MAXLINE, ficpar);
+     for(i=1; i <=nlstate; i++){
-       puts(line);
+       j=0;
-       fputs(line,ficparo);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-     }
+         if(jj==i) continue;
-     ungetc(c,ficpar);
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) && (j1 != j)){
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+ It might be a problem of design; if ncovcol and the model are correct\n \
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+           exit(1);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+         }
-     fprintf(ficres,"pop_based=%d\n",popbased);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           printf("%1d%1d",i,j);
-       ungetc(c,ficpar);
+         fprintf(ficlog,"%1d%1d",i,j);
-       fgets(line, MAXLINE, ficpar);
+         for(k=1; k<=ncovmodel;k++){
-       puts(line);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-       fputs(line,ficparo);
+           if(mle==1){
-     }
+             printf(" %lf",param[i][j][k]);
-     ungetc(c,ficpar);
+             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);
+           else
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+             fprintf(ficlog," %lf",param[i][j][k]);
-     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(ficparo," %lf",param[i][j][k]);
-     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);
+         fscanf(ficpar,"\n");
-     /* day and month of proj2 are not used but only year anproj2.*/
+         numlinepar++;
+         if(mle==1)
+           printf("\n");
+         fprintf(ficlog,"\n");
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+         fprintf(ficparo,"\n");
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       }
+     }
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     fflush(ficlog);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     /* Reads scales values */
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     p=param[1][1];
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-    /*------------ free_vector  -------------*/
+       ungetc(c,ficpar);
-    /*  chdir(path); */
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
-     free_ivector(wav,1,imx);
+       fputs(line,stdout);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+       fputs(line,ficparo);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+       fputs(line,ficlog);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     }
-     free_lvector(num,1,n);
+     ungetc(c,ficpar);
-     free_vector(agedc,1,n);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     for(i=1; i <=nlstate; i++){
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     fclose(ficparo);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     fclose(ficres);
+         if ((i1-i)*(j1-j)!=0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+         }
+         printf("%1d%1d",i,j);
-     strcpy(filerespl,"pl");
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     strcat(filerespl,fileres);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+         for(k=1; k<=ncovmodel;k++){
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+           printf(" %le",delti3[i][j][k]);
-     }
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+         }
-     pstamp(ficrespl);
+         fscanf(ficpar,"\n");
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+         numlinepar++;
-     fprintf(ficrespl,"#Age ");
+         printf("\n");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+         fprintf(ficparo,"\n");
-     fprintf(ficrespl,"\n");
+         fprintf(ficlog,"\n");
+       }
-     prlim=matrix(1,nlstate,1,nlstate);
+     }
+     fflush(ficlog);
-     agebase=ageminpar;
-     agelim=agemaxpar;
+     /* Reads covariance matrix */
-     ftolpl=1.e-10;
+     delti=delti3[1][1];
-     i1=cptcoveff;
-     if (cptcovn < 1){i1=1;}
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     /* Reads comments: lines beginning with '#' */
-         k=k+1;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+       ungetc(c,ficpar);
-         fprintf(ficrespl,"\n#******");
+       fgets(line, MAXLINE, ficpar);
-         printf("\n#******");
+       numlinepar++;
-         fprintf(ficlog,"\n#******");
+       fputs(line,stdout);
-         for(j=1;j<=cptcoveff;j++) {
+       fputs(line,ficparo);
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fputs(line,ficlog);
-           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]]);
+     ungetc(c,ficpar);
-         }
-         fprintf(ficrespl,"******\n");
+     matcov=matrix(1,npar,1,npar);
-         printf("******\n");
+     for(i=1; i <=npar; i++)
-         fprintf(ficlog,"******\n");
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-         for (age=agebase; age<=agelim; age++){
+     for(i=1; i <=npar; i++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       fscanf(ficpar,"%s",str);
-           fprintf(ficrespl,"%.0f ",age );
+       if(mle==1)
-           for(j=1;j<=cptcoveff;j++)
+         printf("%s",str);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficlog,"%s",str);
-           for(i=1; i<=nlstate;i++)
+       fprintf(ficparo,"%s",str);
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       for(j=1; j <=i; j++){
-           fprintf(ficrespl,"\n");
+         fscanf(ficpar," %le",&matcov[i][j]);
-         }
+         if(mle==1){
-       }
+           printf(" %.5le",matcov[i][j]);
-     }
+         }
-     fclose(ficrespl);
+         fprintf(ficlog," %.5le",matcov[i][j]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-     /*------------- h Pij x at various ages ------------*/
+       }
+       fscanf(ficpar,"\n");
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+       numlinepar++;
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       if(mle==1)
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+         printf("\n");
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"\n");
-     }
+       fprintf(ficparo,"\n");
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     }
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+         matcov[i][j]=matcov[j][i];
-     /*if (stepm<=24) stepsize=2;*/
+     if(mle==1)
-     agelim=AGESUP;
+       printf("\n");
-     hstepm=stepsize*YEARM; /* Every year of age */
+     fprintf(ficlog,"\n");
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     fflush(ficlog);
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
+     /*-------- Rewriting parameter file ----------*/
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     strcat(rfileres,".");    /* */
-         k=k+1;
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-         fprintf(ficrespij,"\n#****** ");
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-         for(j=1;j<=cptcoveff;j++)
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-         fprintf(ficrespij,"******\n");
+     }
+     fprintf(ficres,"#%s\n",version);
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+   }    /* End of mle != -3 */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   n= lastobs;
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   num=lvector(1,n);
+   moisnais=vector(1,n);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   annais=vector(1,n);
-           oldm=oldms;savm=savms;
+   moisdc=vector(1,n);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   andc=vector(1,n);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+   agedc=vector(1,n);
-           for(i=1; i<=nlstate;i++)
+   cod=ivector(1,n);
-             for(j=1; j<=nlstate+ndeath;j++)
+   weight=vector(1,n);
-               fprintf(ficrespij," %1d-%1d",i,j);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-           fprintf(ficrespij,"\n");
+   mint=matrix(1,maxwav,1,n);
-           for (h=0; h<=nhstepm; h++){
+   anint=matrix(1,maxwav,1,n);
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-             for(i=1; i<=nlstate;i++)
+   tab=ivector(1,NCOVMAX);
-               for(j=1; j<=nlstate+ndeath;j++)
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
+   /* Reads data from file datafile */
-           }
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     goto end;
-           fprintf(ficrespij,"\n");
-         }
+   /* Calculation of the number of parameters from char model */
-       }
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-     }
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+         k=2 V1 Tvar[k=2]= 1 (from V1)
+         k=1 Tvar[1]=2 (from V2)
-     fclose(ficrespij);
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-     for(i=1;i<=AGESUP;i++)
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
-       for(j=1;j<=NCOVMAX;j++)
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
-         for(k=1;k<=NCOVMAX;k++)
+   */
-           probs[i][j][k]=0.;
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
-     /*---------- Forecasting ------------------*/
+     ncovcol + k1
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     if(prevfcast==1){
+     Tvar[3=V1*V4]=4+1 etc */
-       /*    if(stepm ==1){*/
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-       /*      }  */
+   */
-       /*      else{ */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-       /*        erreur=108; */
+   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
-       /*        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); */
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-       /*        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); */
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-       /*      } */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-     }
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
-     /*---------- Health expectancies and variances ------------*/
+   if(decodemodel(model, lastobs) == 1)
-     strcpy(filerest,"t");
+     goto end;
-     strcat(filerest,fileres);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     nbwarn++;
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-     }
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-     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);
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-     strcpy(filerese,"e");
+   }
-     strcat(filerese,fileres);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+     /*-calculation of age at interview from date of interview and age at death -*/
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   agev=matrix(1,maxwav,1,imx);
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
-     }
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     goto end;
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-     strcpy(fileresstde,"stde");
+   agegomp=(int)agemin;
-     strcat(fileresstde,fileres);
+   free_vector(moisnais,1,n);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   free_vector(annais,1,n);
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   /* free_matrix(mint,1,maxwav,1,n);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+      free_matrix(anint,1,maxwav,1,n);*/
-     }
+   free_vector(moisdc,1,n);
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   free_vector(andc,1,n);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   /* */
-     strcpy(filerescve,"cve");
+   wav=ivector(1,imx);
-     strcat(filerescve,fileres);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
-     }
+   /* Concatenates waves */
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   /* */
-     strcpy(fileresv,"v");
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     strcat(fileresv,fileres);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+   ncodemax[1]=1;
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+   Ndum =ivector(-1,NCOVMAX);
-     }
+   if (ncovmodel > 2)
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-     fprintf(ficlog,"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) */
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   h=0;
-     /*  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 (cptcovn > 0) */
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   m=pow(2,cptcoveff);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       }
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-     }
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
+           h++;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+           if (h>m)
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+             h=1;
-         k=k+1;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-         fprintf(ficrest,"\n#****** ");
+            *     h     1     2     3     4
-         for(j=1;j<=cptcoveff;j++)
+            *______________________________
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-         fprintf(ficrest,"******\n");
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
-         fprintf(ficreseij,"\n#****** ");
+            *     4     2     2     1     1
-         fprintf(ficresstdeij,"\n#****** ");
+            *     5 i=3 1 i=2 1     2     1
-         fprintf(ficrescveij,"\n#****** ");
+            *     6     2     1     2     1
-         for(j=1;j<=cptcoveff;j++) {
+            *     7 i=4 1     2     2     1
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     8     2     2     2     1
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     9 i=5 1 i=3 1 i=2 1     1
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    10     2     1     1     1
-         }
+            *    11 i=6 1     2     1     1
-         fprintf(ficreseij,"******\n");
+            *    12     2     2     1     1
-         fprintf(ficresstdeij,"******\n");
+            *    13 i=7 1 i=4 1     2     1
-         fprintf(ficrescveij,"******\n");
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
-         fprintf(ficresvij,"\n#****** ");
+            *    16     2     2     2     1
-         for(j=1;j<=cptcoveff;j++)
+            */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           codtab[h][k]=j;
-         fprintf(ficresvij,"******\n");
+           /*codtab[h][Tvar[k]]=j;*/
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
-         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);
+     }
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+   }
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+      codtab[1][2]=1;codtab[2][2]=2; */
-         oldm=oldms;savm=savms;
+   /* for(i=1; i <=m ;i++){
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+      for(k=1; k <=cptcovn; k++){
-         if(popbased==1){
+        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,popbased,mobilav, strstart);
+      }
-         }
+      printf("\n");
+      }
-         pstamp(ficrest);
+      scanf("%d",i);*/
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+  free_ivector(Ndum,-1,NCOVMAX);
-         fprintf(ficrest,"\n");
-         epj=vector(1,nlstate+1);
-         for(age=bage; age <=fage ;age++){
+   /*------------ gnuplot -------------*/
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   strcpy(optionfilegnuplot,optionfilefiname);
-           if (popbased==1) {
+   if(mle==-3)
-             if(mobilav ==0){
+     strcat(optionfilegnuplot,"-mort");
-               for(i=1; i<=nlstate;i++)
+   strcat(optionfilegnuplot,".gp");
-                 prlim[i][i]=probs[(int)age][i][k];
-             }else{ /* mobilav */
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-               for(i=1; i<=nlstate;i++)
+     printf("Problem with file %s",optionfilegnuplot);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+   }
-             }
+   else{
-           }
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-           fprintf(ficrest," %4.0f",age);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   }
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+   /*  fclose(ficgp);*/
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+   /*--------- index.htm --------*/
-             }
-             epj[nlstate+1] +=epj[j];
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-           }
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   strcat(optionfilehtm,".htm");
-             for(j=1;j <=nlstate;j++)
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-               vepp += vareij[i][j][(int)age];
+     printf("Problem with %s \n",optionfilehtm);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     exit(0);
-           for(j=1;j <=nlstate;j++){
+   }
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-           }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-           fprintf(ficrest,"\n");
+   strcat(optionfilehtmcov,"-cov.htm");
-         }
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   }
-         free_vector(epj,1,nlstate+1);
+   else{
-       }
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     }
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     free_vector(weight,1,n);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-     free_imatrix(Tvard,1,15,1,2);
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-     free_imatrix(s,1,maxwav+1,1,n);
+   }
-     free_matrix(anint,1,maxwav,1,n);
-     free_matrix(mint,1,maxwav,1,n);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     free_ivector(cod,1,n);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     free_ivector(tab,1,NCOVMAX);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     fclose(ficreseij);
+ \n\
-     fclose(ficresstdeij);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-     fclose(ficrescveij);
+  <ul><li><h4>Parameter files</h4>\n\
-     fclose(ficresvij);
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-     fclose(ficrest);
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-     fclose(ficpar);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-     /*------- Variance of period (stable) prevalence------*/
+  - Date and time at start: %s</ul>\n",\
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     strcpy(fileresvpl,"vpl");
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-     strcat(fileresvpl,fileres);
+           fileres,fileres,\
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+   fflush(fichtm);
-       exit(0);
-     }
+   strcpy(pathr,path);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-         k=k+1;
+      and prints on file fileres'p'. */
-         fprintf(ficresvpl,"\n#****** ");
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   fprintf(fichtm,"\n");
-         fprintf(ficresvpl,"******\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-         oldm=oldms;savm=savms;
+           imx,agemin,agemax,jmin,jmax,jmean);
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       }
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     }
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     fclose(ficresvpl);
-     /*---------- End : free ----------------*/
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-   }  /* mle==-3 arrives here for freeing */
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-   free_matrix(prlim,1,nlstate,1,nlstate);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+   if (mle==-3){
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     ximort=matrix(1,NDIM,1,NDIM);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     cens=ivector(1,n);
-     free_matrix(covar,0,NCOVMAX,1,n);
+     ageexmed=vector(1,n);
-     free_matrix(matcov,1,npar,1,npar);
+     agecens=vector(1,n);
-     /*free_vector(delti,1,npar);*/
+     dcwave=ivector(1,n);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_matrix(agev,1,maxwav,1,imx);
+     for (i=1; i<=imx; i++){
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
-     free_ivector(ncodemax,1,8);
+         if (s[m][i]>nlstate) {
-     free_ivector(Tvar,1,15);
+           dcwave[i]=m;
-     free_ivector(Tprod,1,15);
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     free_ivector(Tvaraff,1,15);
+           break;
-     free_ivector(Tage,1,15);
+         }
-     free_ivector(Tcode,1,100);
+     }
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     for (i=1; i<=imx; i++) {
-     free_imatrix(codtab,1,100,1,10);
+       if (wav[i]>0){
-   fflush(fichtm);
+         ageexmed[i]=agev[mw[1][i]][i];
-   fflush(ficgp);
+         j=wav[i];
+         agecens[i]=1.;
-   if((nberr >0) || (nbwarn>0)){
+         if (ageexmed[i]> 1 && wav[i] > 0){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+           agecens[i]=agev[mw[j][i]][i];
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+           cens[i]= 1;
-   }else{
+         }else if (ageexmed[i]< 1)
-     printf("End of Imach\n");
+           cens[i]= -1;
-     fprintf(ficlog,"End of Imach\n");
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-   }
+           cens[i]=0 ;
-   printf("See log file on %s\n",filelog);
+       }
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+       else cens[i]=-1;
-   (void) gettimeofday(&end_time,&tzp);
+     }
-   tm = *localtime(&end_time.tv_sec);
-   tmg = *gmtime(&end_time.tv_sec);
+     for (i=1;i<=NDIM;i++) {
-   strcpy(strtend,asctime(&tm));
+       for (j=1;j<=NDIM;j++)
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     }
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     /*printf("%lf %lf", p[1], p[2]);*/
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ #ifdef GSL
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     printf("GSL optimization\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);
+ #else
-   fclose(fichtm);
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+ #endif
-   fclose(fichtmcov);
+     strcpy(filerespow,"pow-mort");
-   fclose(ficgp);
+     strcat(filerespow,fileres);
-   fclose(ficlog);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   /*------ End -----------*/
+       printf("Problem with resultfile: %s\n", filerespow);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+     }
-    printf("Before Current directory %s!\n",pathcd);
+ #ifdef GSL
-    if(chdir(pathcd) != 0)
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-     printf("Can't move to directory %s!\n",path);
+ #else
-   if(getcwd(pathcd,MAXLINE) > 0)
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     printf("Current directory %s!\n",pathcd);
+ #endif
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     /*  for (i=1;i<=nlstate;i++)
-   sprintf(plotcmd,"gnuplot");
+         for(j=1;j<=nlstate+ndeath;j++)
- #ifndef UNIX
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+     */
- #endif
+     fprintf(ficrespow,"\n");
-   if(!stat(plotcmd,&info)){
+ #ifdef GSL
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     /* gsl starts here */
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     T = gsl_multimin_fminimizer_nmsimplex;
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     gsl_multimin_fminimizer *sfm = NULL;
-     }else
+     gsl_vector *ss, *x;
-       strcpy(pplotcmd,plotcmd);
+     gsl_multimin_function minex_func;
- #ifdef UNIX
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     /* Initial vertex size vector */
-     if(!stat(plotcmd,&info)){
+     ss = gsl_vector_alloc (NDIM);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
-     }else
+     if (ss == NULL){
-       strcpy(pplotcmd,plotcmd);
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
- #endif
+     }
-   }else
+     /* Set all step sizes to 1 */
-     strcpy(pplotcmd,plotcmd);
+     gsl_vector_set_all (ss, 0.001);
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     /* Starting point */
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     x = gsl_vector_alloc (NDIM);
-   if((outcmd=system(plotcmd)) != 0){
-     printf("\n Problem with gnuplot\n");
+     if (x == NULL){
-   }
+       gsl_vector_free(ss);
-   printf(" Wait...");
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-   while (z[0] != 'q') {
+     }
-     /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     /* Initialize method and iterate */
-     scanf("%s",z);
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
- /*     if (z[0] == 'c') system("./imach"); */
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     if (z[0] == 'e') {
+ /*     gsl_vector_set(x, 1, 0.083); */
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+     gsl_vector_set(x, 0, p[1]);
-       system(optionfilehtm);
+     gsl_vector_set(x, 1, p[2]);
-     }
-     else if (z[0] == 'g') system(plotcmd);
+     minex_func.f = &gompertz_f;
-     else if (z[0] == 'q') exit(0);
+     minex_func.n = NDIM;
-   }
+     minex_func.params = (void *)&p; /* ??? */
-   end:
-   while (z[0] != 'q') {
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-     printf("\nType  q for exiting: ");
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-     scanf("%s",z);
-   }
+     printf("Iterations beginning .....\n\n");
- }
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+ #include "hpijx.h"
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           oldm=oldms;savm=savms; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f",age);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  endfree:
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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Removed from v.1.125
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	Added in v.1.163