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Diff for /imach/src/imach.c between versions 1.125 and 1.162

-version 1.125, 2006/04/04 15:20:31
+version 1.162, 2014/09/25 11:43:39
  Line 1
  /* $Id$
    $State$
    $Log$
+   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;
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
-       k[0]=1;
+       fu=(*func)(u);
-       k[1]=-1;
+       if (fu < *fc) {
-       printf("Max: %.12e",(*func)(p));
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+           SHFT(*fb,*fc,fu,(*func)(u))
-       for (j=1;j<=n;j++) {
+           }
-         printf(" %.12e",p[j]);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
-         fprintf(ficlog," %.12e",p[j]);
+       u=ulim;
-       }
+       fu=(*func)(u);
-       printf("\n");
+     } else {
-       fprintf(ficlog,"\n");
+       u=(*cx)+GOLD*(*cx-*bx);
-       for(l=0;l<=1;l++) {
+       fu=(*func)(u);
-         for (j=1;j<=n;j++) {
+     }
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+     SHFT(*ax,*bx,*cx,u)
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       SHFT(*fa,*fb,*fc,fu)
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       }
-         }
+ }
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ /*************** linmin ************************/
-       }
+ /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
- #endif
+ resets p to where the function func(p) takes on a minimum along the direction xi from p ,
+ and replaces xi by the actual vector displacement that p was moved. Also returns as fret
+ the value of func at the returned location p . This is actually all accomplished by calling the
-       free_vector(xit,1,n);
+ routines mnbrak and brent .*/
-       free_vector(xits,1,n);
+ int ncom;
-       free_vector(ptt,1,n);
+ double *pcom,*xicom;
-       free_vector(pt,1,n);
+ double (*nrfunc)(double []);
-       return;
-     }
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ {
-     for (j=1;j<=n;j++) {
+   double brent(double ax, double bx, double cx,
-       ptt[j]=2.0*p[j]-pt[j];
+                double (*f)(double), double tol, double *xmin);
-       xit[j]=p[j]-pt[j];
+   double f1dim(double x);
-       pt[j]=p[j];
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-     }
+               double *fc, double (*func)(double));
-     fptt=(*func)(ptt);
+   int j;
-     if (fptt < fp) {
+   double xx,xmin,bx,ax;
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+   double fx,fb,fa;
-       if (t < 0.0) {
-         linmin(p,xit,n,fret,func);
+   ncom=n;
-         for (j=1;j<=n;j++) {
+   pcom=vector(1,n);
-           xi[j][ibig]=xi[j][n];
+   xicom=vector(1,n);
-           xi[j][n]=xit[j];
+   nrfunc=func;
-         }
+   for (j=1;j<=n;j++) {
- #ifdef DEBUG
+     pcom[j]=p[j];
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     xicom[j]=xi[j];
-         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++){
+   ax=0.0;
-           printf(" %.12e",xit[j]);
+   xx=1.0;
-           fprintf(ficlog," %.12e",xit[j]);
+   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 */
-         printf("\n");
+ #ifdef DEBUG
-         fprintf(ficlog,"\n");
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- #endif
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       }
+ #endif
-     }
+   for (j=1;j<=n;j++) {
-   }
+     xi[j] *= xmin;
- }
+     p[j] += xi[j];
+   }
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   free_vector(xicom,1,n);
+   free_vector(pcom,1,n);
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+ }
- {
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-      matrix by transitions matrix until convergence is reached */
+ /*************** powell ************************/
+ /*
-   int i, ii,j,k;
+ Minimization of a function func of n variables. Input consists of an initial starting point
-   double min, max, maxmin, maxmax,sumnew=0.;
+ p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
-   double **matprod2();
+ rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
-   double **out, cov[NCOVMAX], **pmij();
+ such that failure to decrease by more than this amount on one iteration signals doneness. On
-   double **newm;
+ output, p is set to the best point found, xi is the then-current direction set, fret is the returned
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+ function value at p , and iter is the number of iterations taken. The routine linmin is used.
+  */
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-     for (j=1;j<=nlstate+ndeath;j++){
+             double (*func)(double []))
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ {
-     }
+   void linmin(double p[], double xi[], int n, double *fret,
+               double (*func)(double []));
-    cov[1]=1.;
+   int i,ibig,j;
+   double del,t,*pt,*ptt,*xit;
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   double fp,fptt;
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+   double *xits;
-     newm=savm;
+   int niterf, itmp;
-     /* Covariates have to be included here again */
-      cov[2]=agefin;
+   pt=vector(1,n);
+   ptt=vector(1,n);
-       for (k=1; k<=cptcovn;k++) {
+   xit=vector(1,n);
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   xits=vector(1,n);
-         /*      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]]);*/
+   *fret=(*func)(p);
-       }
+   for (j=1;j<=n;j++) pt[j]=p[j];
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     rcurr_time = time(NULL);
-       for (k=1; k<=cptcovprod;k++)
+   for (*iter=1;;++(*iter)) {
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     fp=(*fret);
+     ibig=0;
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     del=0.0;
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     rlast_time=rcurr_time;
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /* (void) gettimeofday(&curr_time,&tzp); */
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     rcurr_time = time(NULL);
+     curr_time = *localtime(&rcurr_time);
-     savm=oldm;
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-     oldm=newm;
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-     maxmax=0.;
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-     for(j=1;j<=nlstate;j++){
+    for (i=1;i<=n;i++) {
-       min=1.;
+       printf(" %d %.12f",i, p[i]);
-       max=0.;
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-       for(i=1; i<=nlstate; i++) {
+       fprintf(ficrespow," %.12lf", p[i]);
-         sumnew=0;
+     }
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+     printf("\n");
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+     fprintf(ficlog,"\n");
-         max=FMAX(max,prlim[i][j]);
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-         min=FMIN(min,prlim[i][j]);
+     if(*iter <=3){
-       }
+       tml = *localtime(&rcurr_time);
-       maxmin=max-min;
+       strcpy(strcurr,asctime(&tml));
-       maxmax=FMAX(maxmax,maxmin);
+       rforecast_time=rcurr_time;
-     }
+       itmp = strlen(strcurr);
-     if(maxmax < ftolpl){
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       return prlim;
+         strcurr[itmp-1]='\0';
-     }
+       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-   }
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
- }
+       for(niterf=10;niterf<=30;niterf+=10){
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
- /*************** transition probabilities ***************/
+         forecast_time = *localtime(&rforecast_time);
+         strcpy(strfor,asctime(&forecast_time));
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+         itmp = strlen(strfor);
- {
+         if(strfor[itmp-1]=='\n')
-   double s1, s2;
+         strfor[itmp-1]='\0';
-   /*double t34;*/
+         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);
-   int i,j,j1, nc, ii, jj;
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+       }
-     for(i=1; i<= nlstate; i++){
+     }
-       for(j=1; j<i;j++){
+     for (i=1;i<=n;i++) {
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       fptt=(*fret);
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ #ifdef DEBUG
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+       printf("fret=%lf \n",*fret);
-         }
+       fprintf(ficlog,"fret=%lf \n",*fret);
-         ps[i][j]=s2;
+ #endif
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       printf("%d",i);fflush(stdout);
-       }
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       linmin(p,xit,n,fret,func);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       if (fabs(fptt-(*fret)) > del) {
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+         del=fabs(fptt-(*fret));
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+         ibig=i;
-         }
+       }
-         ps[i][j]=s2;
+ #ifdef DEBUG
-       }
+       printf("%d %.12e",i,(*fret));
-     }
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-     /*ps[3][2]=1;*/
+       for (j=1;j<=n;j++) {
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-     for(i=1; i<= nlstate; i++){
+         printf(" x(%d)=%.12e",j,xit[j]);
-       s1=0;
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       for(j=1; j<i; j++)
+       }
-         s1+=exp(ps[i][j]);
+       for(j=1;j<=n;j++) {
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         printf(" p(%d)=%.12e",j,p[j]);
-         s1+=exp(ps[i][j]);
+         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
-       ps[i][i]=1./(s1+1.);
+       }
-       for(j=1; j<i; j++)
+       printf("\n");
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       fprintf(ficlog,"\n");
-       for(j=i+1; j<=nlstate+ndeath; j++)
+ #endif
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     } /* end i */
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-     } /* end i */
+ #ifdef DEBUG
+       int k[2],l;
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       k[0]=1;
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       k[1]=-1;
-         ps[ii][jj]=0;
+       printf("Max: %.12e",(*func)(p));
-         ps[ii][ii]=1;
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-       }
+       for (j=1;j<=n;j++) {
-     }
+         printf(" %.12e",p[j]);
+         fprintf(ficlog," %.12e",p[j]);
+       }
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       printf("\n");
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+       fprintf(ficlog,"\n");
- /*         printf("ddd %lf ",ps[ii][jj]); */
+       for(l=0;l<=1;l++) {
- /*       } */
+         for (j=1;j<=n;j++) {
- /*       printf("\n "); */
+           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]);
- /*        printf("\n ");printf("%lf ",cov[2]); */
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-        /*
+         }
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       goto end;*/
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-     return ps;
+       }
- }
+ #endif
- /**************** Product of 2 matrices ******************/
+       free_vector(xit,1,n);
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+       free_vector(xits,1,n);
- {
+       free_vector(ptt,1,n);
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+       free_vector(pt,1,n);
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+       return;
-   /* in, b, out are matrice of pointers which should have been initialized
+     }
-      before: only the contents of out is modified. The function returns
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-      a pointer to pointers identical to out */
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
-   long i, j, k;
+       ptt[j]=2.0*p[j]-pt[j];
-   for(i=nrl; i<= nrh; i++)
+       xit[j]=p[j]-pt[j];
-     for(k=ncolol; k<=ncoloh; k++)
+       pt[j]=p[j];
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+     }
-         out[i][k] +=in[i][j]*b[j][k];
+     fptt=(*func)(ptt);
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-   return out;
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
- }
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
- /************* Higher Matrix Product ***************/
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+       /* Thus we compare delta(2h) with observed f1-f3 */
- {
+       /* or best gain on one ancient line 'del' with total  */
-   /* Computes the transition matrix starting at age 'age' over
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
-      'nhstepm*hstepm*stepm' months (i.e. until
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-      nhstepm*hstepm matrices.
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+       t= t- del*SQR(fp-fptt);
-      (typically every 2 years instead of every month which is too big
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-      for the memory).
+       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);
-      Model is determined by parameters x and covariates have to be
+ #ifdef DEBUG
-      included manually here.
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-      */
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-   int i, j, d, h, k;
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
-   double **out, cov[NCOVMAX];
+       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);
-   double **newm;
+ #endif
+       if (t < 0.0) { /* Then we use it for last direction */
-   /* Hstepm could be zero and should return the unit matrix */
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
-   for (i=1;i<=nlstate+ndeath;i++)
+         for (j=1;j<=n;j++) {
-     for (j=1;j<=nlstate+ndeath;j++){
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+         }
-     }
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
-   for(h=1; h <=nhstepm; h++){
-     for(d=1; d <=hstepm; d++){
+ #ifdef DEBUG
-       newm=savm;
+         for(j=1;j<=n;j++){
-       /* Covariates have to be included here again */
+           printf(" %.12e",xit[j]);
-       cov[1]=1.;
+           fprintf(ficlog," %.12e",xit[j]);
-       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("\n");
-       for (k=1; k<=cptcovage;k++)
+         fprintf(ficlog,"\n");
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ #endif
-       for (k=1; k<=cptcovprod;k++)
+       } /* end of t negative */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     } /* end if (fptt < fp)  */
+   }
+ }
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-       savm=oldm;
+ {
-       oldm=newm;
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-     }
+      matrix by transitions matrix until convergence is reached */
-     for(i=1; i<=nlstate+ndeath; i++)
-       for(j=1;j<=nlstate+ndeath;j++) {
+   int i, ii,j,k;
-         po[i][j][h]=newm[i][j];
+   double min, max, maxmin, maxmax,sumnew=0.;
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   /* double **matprod2(); */ /* test */
-          */
+   double **out, cov[NCOVMAX+1], **pmij();
-       }
+   double **newm;
-   } /* end h */
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-   return po;
- }
+   for (ii=1;ii<=nlstate+ndeath;ii++)
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- /*************** log-likelihood *************/
+     }
- double func( double *x)
- {
+    cov[1]=1.;
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   double **out;
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-   double sw; /* Sum of weights */
+     newm=savm;
-   double lli; /* Individual log likelihood */
+     /* Covariates have to be included here again */
-   int s1, s2;
+     cov[2]=agefin;
-   double bbh, survp;
-   long ipmx;
+     for (k=1; k<=cptcovn;k++) {
-   /*extern weight */
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-   /* We are differentiating ll according to initial status */
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+     }
-   /*for(i=1;i<imx;i++)
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     printf(" %d\n",s[4][i]);
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-   */
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-   cov[1]=1.;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-   if(mle==1){
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     savm=oldm;
-           for (j=1;j<=nlstate+ndeath;j++){
+     oldm=newm;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     maxmax=0.;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for(j=1;j<=nlstate;j++){
-           }
+       min=1.;
-         for(d=0; d<dh[mi][i]; d++){
+       max=0.;
-           newm=savm;
+       for(i=1; i<=nlstate; i++) {
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         sumnew=0;
-           for (kk=1; kk<=cptcovage;kk++) {
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-           }
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         max=FMAX(max,prlim[i][j]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         min=FMIN(min,prlim[i][j]);
-           savm=oldm;
+       }
-           oldm=newm;
+       maxmin=max-min;
-         } /* end mult */
+       maxmax=FMAX(maxmax,maxmin);
+     }
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     if(maxmax < ftolpl){
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       return prlim;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     }
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+   }
-          * 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
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+ /*************** transition probabilities ***************/
-          * 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
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-          * -stepm/2 to stepm/2 .
+ {
-          * For stepm=1 the results are the same as for previous versions of Imach.
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-          * For stepm > 1 the results are less biased than in previous versions.
+      computes the probability to be observed in state j being in state i by appying the
-          */
+      model to the ncovmodel covariates (including constant and age).
-         s1=s[mw[mi][i]][i];
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         s2=s[mw[mi+1][i]][i];
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         bbh=(double)bh[mi][i]/(double)stepm;
+      ncth covariate in the global vector x is given by the formula:
-         /* bias bh is positive if real duration
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-          * is higher than the multiple of stepm and negative otherwise.
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-          */
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         if( s2 > nlstate){
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-           /* i.e. if s2 is a death state and if the date of death is known
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-              then the contribution to the likelihood is the probability to
+   */
-              die between last step unit time and current  step unit time,
+   double s1, lnpijopii;
-              which is also equal to probability to die before dh
+   /*double t34;*/
-              minus probability to die before dh-stepm .
+   int i,j,j1, nc, ii, jj;
-              In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
+     for(i=1; i<= nlstate; i++){
-         health state: the date of the interview describes the actual state
+       for(j=1; j<i;j++){
-         and not the date of a change in health state. The former idea was
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         to consider that at each interview the state was recorded
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-         (healthy, disable or death) and IMaCh was corrected; but when we
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-         introduced the exact date of death then we should have modified
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         the contribution of an exact death to the likelihood. This new
+         }
-         contribution is smaller and very dependent of the step unit
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         stepm. It is no more the probability to die between last interview
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         and month of death but the probability to survive from last
+       }
-         interview up to one month before death multiplied by the
+       for(j=i+1; j<=nlstate+ndeath;j++){
-         probability to die within a month. Thanks to Chris
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-         Jackson for correcting this bug.  Former versions increased
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-         mortality artificially. The bad side is that we add another loop
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         which slows down the processing. The difference can be up to 10%
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-         lower mortality.
+         }
-           */
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       }
+     }
-         } else if  (s2==-2) {
+     for(i=1; i<= nlstate; i++){
-           for (j=1,survp=0. ; j<=nlstate; j++)
+       s1=0;
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for(j=1; j<i; j++){
-           /*survp += out[s1][j]; */
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           lli= log(survp);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         }
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
-         else if  (s2==-4) {
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           for (j=3,survp=0. ; j<=nlstate; j++)
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       }
-           lli= log(survp);
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         }
+       ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
-         else if  (s2==-5) {
+       for(j=1; j<i; j++)
-           for (j=1,survp=0. ; j<=2; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for(j=i+1; j<=nlstate+ndeath; j++)
-           lli= log(survp);
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         }
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
-         else{
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-           /*  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(jj=1; jj<= nlstate+ndeath; jj++){
-         }
+         ps[ii][jj]=0;
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         ps[ii][ii]=1;
-         /*if(lli ==000.0)*/
+       }
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
+     }
-         ipmx +=1;
-         sw += weight[i];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-       } /* end of wave */
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-     } /* end of individual */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-   }  else if(mle==2){
+     /*   } */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /*   printf("\n "); */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     /* } */
-       for(mi=1; mi<= wav[i]-1; mi++){
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+     /*
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       goto end;*/
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     return ps;
-           }
+ }
-         for(d=0; d<=dh[mi][i]; d++){
-           newm=savm;
+ /**************** Product of 2 matrices ******************/
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ {
-           }
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   /* in, b, out are matrice of pointers which should have been initialized
-           savm=oldm;
+      before: only the contents of out is modified. The function returns
-           oldm=newm;
+      a pointer to pointers identical to out */
-         } /* end mult */
+   int i, j, k;
+   for(i=nrl; i<= nrh; i++)
-         s1=s[mw[mi][i]][i];
+     for(k=ncolol; k<=ncoloh; k++){
-         s2=s[mw[mi+1][i]][i];
+       out[i][k]=0.;
-         bbh=(double)bh[mi][i]/(double)stepm;
+       for(j=ncl; j<=nch; j++)
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         out[i][k] +=in[i][j]*b[j][k];
-         ipmx +=1;
+     }
-         sw += weight[i];
+   return out;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ }
-       } /* end of wave */
-     } /* end of individual */
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+ /************* Higher Matrix Product ***************/
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-       for(mi=1; mi<= wav[i]-1; mi++){
+ {
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* Computes the transition matrix starting at age 'age' over
-           for (j=1;j<=nlstate+ndeath;j++){
+      'nhstepm*hstepm*stepm' months (i.e. until
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+      nhstepm*hstepm matrices.
-           }
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-         for(d=0; d<dh[mi][i]; d++){
+      (typically every 2 years instead of every month which is too big
-           newm=savm;
+      for the memory).
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+      Model is determined by parameters x and covariates have to be
-           for (kk=1; kk<=cptcovage;kk++) {
+      included manually here.
-             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));
+   int i, j, d, h, k;
-           savm=oldm;
+   double **out, cov[NCOVMAX+1];
-           oldm=newm;
+   double **newm;
-         } /* end mult */
+   /* Hstepm could be zero and should return the unit matrix */
-         s1=s[mw[mi][i]][i];
+   for (i=1;i<=nlstate+ndeath;i++)
-         s2=s[mw[mi+1][i]][i];
+     for (j=1;j<=nlstate+ndeath;j++){
-         bbh=(double)bh[mi][i]/(double)stepm;
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-         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 */
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         ipmx +=1;
+     }
-         sw += weight[i];
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   for(h=1; h <=nhstepm; h++){
-       } /* end of wave */
+     for(d=1; d <=hstepm; d++){
-     } /* end of individual */
+       newm=savm;
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+       /* Covariates have to be included here again */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       cov[1]=1.;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for(mi=1; mi<= wav[i]-1; mi++){
+       for (k=1; k<=cptcovn;k++)
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           for (j=1;j<=nlstate+ndeath;j++){
+       for (k=1; k<=cptcovage;k++)
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-           }
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         for(d=0; d<dh[mi][i]; d++){
-           newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-           for (kk=1; kk<=cptcovage;kk++) {
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-           }
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+       savm=oldm;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       oldm=newm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     }
-           savm=oldm;
+     for(i=1; i<=nlstate+ndeath; i++)
-           oldm=newm;
+       for(j=1;j<=nlstate+ndeath;j++) {
-         } /* end mult */
+         po[i][j][h]=newm[i][j];
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-         s1=s[mw[mi][i]][i];
+       }
-         s2=s[mw[mi+1][i]][i];
+     /*printf("h=%d ",h);*/
-         if( s2 > nlstate){
+   } /* end h */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ /*     printf("\n H=%d \n",h); */
-         }else{
+   return po;
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+ }
-         }
-         ipmx +=1;
+ #ifdef NLOPT
-         sw += weight[i];
+   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   double fret;
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+   double *xt;
-       } /* end of wave */
+   int j;
-     } /* end of individual */
+   myfunc_data *d2 = (myfunc_data *) pd;
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+ /* xt = (p1-1); */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   xt=vector(1,n);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
-           for (j=1;j<=nlstate+ndeath;j++){
+   /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   printf("Function = %.12lf ",fret);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
-           }
+   printf("\n");
-         for(d=0; d<dh[mi][i]; d++){
+  free_vector(xt,1,n);
-           newm=savm;
+   return fret;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ }
-           for (kk=1; kk<=cptcovage;kk++) {
+ #endif
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+ /*************** log-likelihood *************/
+ double func( double *x)
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ {
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   int i, ii, j, k, mi, d, kk;
-           savm=oldm;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-           oldm=newm;
+   double **out;
-         } /* end mult */
+   double sw; /* Sum of weights */
+   double lli; /* Individual log likelihood */
-         s1=s[mw[mi][i]][i];
+   int s1, s2;
-         s2=s[mw[mi+1][i]][i];
+   double bbh, survp;
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+   long ipmx;
-         ipmx +=1;
+   /*extern weight */
-         sw += weight[i];
+   /* We are differentiating ll according to initial status */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+   /*for(i=1;i<imx;i++)
-       } /* end of wave */
+     printf(" %d\n",s[4][i]);
-     } /* end of individual */
+   */
-   } /* End of if */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   ++countcallfunc;
-   /* 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 */
+   cov[1]=1.;
-   return -l;
- }
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
- /*************** log-likelihood *************/
+   if(mle==1){
- double funcone( double *x)
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- {
+       /* Computes the values of the ncovmodel covariates of the model
-   /* Same as likeli but slower because of a lot of printf and if */
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-   int i, ii, j, k, mi, d, kk;
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+          to be observed in j being in i according to the model.
-   double **out;
+        */
-   double lli; /* Individual log likelihood */
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-   double llt;
+         cov[2+k]=covar[Tvar[k]][i];
-   int s1, s2;
+       }
-   double bbh, survp;
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-   /*extern weight */
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-   /* We are differentiating ll according to initial status */
+          has been calculated etc */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+       for(mi=1; mi<= wav[i]-1; mi++){
-   /*for(i=1;i<imx;i++)
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     printf(" %d\n",s[4][i]);
+           for (j=1;j<=nlstate+ndeath;j++){
-   */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   cov[1]=1.;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+           for (kk=1; kk<=cptcovage;kk++) {
-     for(mi=1; mi<= wav[i]-1; mi++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+           }
-         for (j=1;j<=nlstate+ndeath;j++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm=oldm;
-         }
+           oldm=newm;
-       for(d=0; d<dh[mi][i]; d++){
+         } /* end mult */
-         newm=savm;
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         for (kk=1; kk<=cptcovage;kk++) {
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         }
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         savm=oldm;
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         oldm=newm;
+          * probability in order to take into account the bias as a fraction of the way
-       } /* end mult */
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+          * -stepm/2 to stepm/2 .
-       s1=s[mw[mi][i]][i];
+          * For stepm=1 the results are the same as for previous versions of Imach.
-       s2=s[mw[mi+1][i]][i];
+          * For stepm > 1 the results are less biased than in previous versions.
-       bbh=(double)bh[mi][i]/(double)stepm;
+          */
-       /* bias is positive if real duration
+         s1=s[mw[mi][i]][i];
-        * is higher than the multiple of stepm and negative otherwise.
+         s2=s[mw[mi+1][i]][i];
-        */
+         bbh=(double)bh[mi][i]/(double)stepm;
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         /* bias bh is positive if real duration
-         lli=log(out[s1][s2] - savm[s1][s2]);
+          * is higher than the multiple of stepm and negative otherwise.
-       } else if  (s2==-2) {
+          */
-         for (j=1,survp=0. ; j<=nlstate; j++)
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         if( s2 > nlstate){
-         lli= log(survp);
+           /* i.e. if s2 is a death state and if the date of death is known
-       }else if (mle==1){
+              then the contribution to the likelihood is the probability to
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+              die between last step unit time and current  step unit time,
-       } else if(mle==2){
+              which is also equal to probability to die before dh
-         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 */
+              minus probability to die before dh-stepm .
-       } else if(mle==3){  /* exponential inter-extrapolation */
+              In version up to 0.92 likelihood was computed
-         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 */
+         as if date of death was unknown. Death was treated as any other
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         health state: the date of the interview describes the actual state
-         lli=log(out[s1][s2]); /* Original formula */
+         and not the date of a change in health state. The former idea was
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         to consider that at each interview the state was recorded
-         lli=log(out[s1][s2]); /* Original formula */
+         (healthy, disable or death) and IMaCh was corrected; but when we
-       } /* End of if */
+         introduced the exact date of death then we should have modified
-       ipmx +=1;
+         the contribution of an exact death to the likelihood. This new
-       sw += weight[i];
+         contribution is smaller and very dependent of the step unit
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         stepm. It is no more the probability to die between last interview
- /*       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]); */
+         and month of death but the probability to survive from last
-       if(globpr){
+         interview up to one month before death multiplied by the
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         probability to die within a month. Thanks to Chris
-  %11.6f %11.6f %11.6f ", \
+         Jackson for correcting this bug.  Former versions increased
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+         mortality artificially. The bad side is that we add another loop
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         which slows down the processing. The difference can be up to 10%
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         lower mortality.
-           llt +=ll[k]*gipmx/gsw;
+           */
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         }
-         fprintf(ficresilk," %10.6f\n", -llt);
-       }
+         } else if  (s2==-2) {
-     } /* end of wave */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   } /* end of individual */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+           /*survp += out[s1][j]; */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           lli= log(survp);
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         }
-   if(globpr==0){ /* First time we count the contributions and weights */
-     gipmx=ipmx;
+         else if  (s2==-4) {
-     gsw=sw;
+           for (j=3,survp=0. ; j<=nlstate; j++)
-   }
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   return -l;
+           lli= log(survp);
- }
+         }
+         else if  (s2==-5) {
- /*************** function likelione ***********/
+           for (j=1,survp=0. ; j<=2; j++)
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- {
+           lli= log(survp);
-   /* This routine should help understanding what is done with
+         }
-      the selection of individuals/waves and
-      to check the exact contribution to the likelihood.
+         else{
-      Plotting could be done.
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-    */
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-   int k;
+         }
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+         /*if(lli ==000.0)*/
-     strcpy(fileresilk,"ilk");
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-     strcat(fileresilk,fileres);
+         ipmx +=1;
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+         sw += weight[i];
-       printf("Problem with resultfile: %s\n", fileresilk);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+       } /* end of wave */
-     }
+     } /* end of individual */
-     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");
+   }  else if(mle==2){
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     for(k=1; k<=nlstate; k++)
+       for(mi=1; mi<= wav[i]-1; mi++){
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+           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);
-   *fretone=(*funcone)(p);
+           }
-   if(*globpri !=0){
+         for(d=0; d<=dh[mi][i]; d++){
-     fclose(ficresilk);
+           newm=savm;
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     fflush(fichtm);
+           for (kk=1; kk<=cptcovage;kk++) {
-   }
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   return;
+           }
- }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
- /*********** Maximum Likelihood Estimation ***************/
+           oldm=newm;
+         } /* end mult */
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
- {
+         s1=s[mw[mi][i]][i];
-   int i,j, iter;
+         s2=s[mw[mi+1][i]][i];
-   double **xi;
+         bbh=(double)bh[mi][i]/(double)stepm;
-   double fret;
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   double fretone; /* Only one call to likelihood */
+         ipmx +=1;
-   /*  char filerespow[FILENAMELENGTH];*/
+         sw += weight[i];
-   xi=matrix(1,npar,1,npar);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   for (i=1;i<=npar;i++)
+       } /* end of wave */
-     for (j=1;j<=npar;j++)
+     } /* end of individual */
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   strcpy(filerespow,"pow");
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   strcat(filerespow,fileres);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     printf("Problem with resultfile: %s\n", filerespow);
+           for (j=1;j<=nlstate+ndeath;j++){
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+           }
-   for (i=1;i<=nlstate;i++)
+         for(d=0; d<dh[mi][i]; d++){
-     for(j=1;j<=nlstate+ndeath;j++)
+           newm=savm;
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   fprintf(ficrespow,"\n");
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+           }
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   free_matrix(xi,1,npar,1,npar);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   fclose(ficrespow);
+           savm=oldm;
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+           oldm=newm;
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+         } /* end mult */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+         s1=s[mw[mi][i]][i];
- }
+         s2=s[mw[mi+1][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
- /**** Computes Hessian and covariance matrix ***/
+         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 */
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+         ipmx +=1;
- {
+         sw += weight[i];
-   double  **a,**y,*x,pd;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double **hess;
+       } /* end of wave */
-   int i, j,jk;
+     } /* end of individual */
-   int *indx;
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+           for (j=1;j<=nlstate+ndeath;j++){
-   double gompertz(double p[]);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   hess=matrix(1,npar,1,npar);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+         for(d=0; d<dh[mi][i]; d++){
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+           newm=savm;
-   for (i=1;i<=npar;i++){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     printf("%d",i);fflush(stdout);
+           for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           }
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     /*  printf(" %f ",p[i]);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+           savm=oldm;
-   }
+           oldm=newm;
+         } /* end mult */
-   for (i=1;i<=npar;i++) {
-     for (j=1;j<=npar;j++)  {
+         s1=s[mw[mi][i]][i];
-       if (j>i) {
+         s2=s[mw[mi+1][i]][i];
-         printf(".%d%d",i,j);fflush(stdout);
+         if( s2 > nlstate){
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+         }else{
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         hess[j][i]=hess[i][j];
+         }
-         /*printf(" %lf ",hess[i][j]);*/
+         ipmx +=1;
-       }
+         sw += weight[i];
-     }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   }
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-   printf("\n");
+       } /* end of wave */
-   fprintf(ficlog,"\n");
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-   a=matrix(1,npar,1,npar);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   y=matrix(1,npar,1,npar);
+           for (j=1;j<=nlstate+ndeath;j++){
-   x=vector(1,npar);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   indx=ivector(1,npar);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   for (i=1;i<=npar;i++)
+           }
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+         for(d=0; d<dh[mi][i]; d++){
-   ludcmp(a,npar,indx,&pd);
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   for (j=1;j<=npar;j++) {
+           for (kk=1; kk<=cptcovage;kk++) {
-     for (i=1;i<=npar;i++) x[i]=0;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     x[j]=1;
+           }
-     lubksb(a,npar,indx,x);
-     for (i=1;i<=npar;i++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       matcov[i][j]=x[i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     }
+           savm=oldm;
-   }
+           oldm=newm;
+         } /* end mult */
-   printf("\n#Hessian matrix#\n");
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+         s1=s[mw[mi][i]][i];
-   for (i=1;i<=npar;i++) {
+         s2=s[mw[mi+1][i]][i];
-     for (j=1;j<=npar;j++) {
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       printf("%.3e ",hess[i][j]);
+         ipmx +=1;
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+         sw += weight[i];
-     }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     printf("\n");
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-     fprintf(ficlog,"\n");
+       } /* end of wave */
-   }
+     } /* end of individual */
+   } /* End of if */
-   /* Recompute Inverse */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   for (i=1;i<=npar;i++)
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   ludcmp(a,npar,indx,&pd);
+   return -l;
+ }
-   /*  printf("\n#Hessian matrix recomputed#\n");
+ /*************** log-likelihood *************/
-   for (j=1;j<=npar;j++) {
+ double funcone( double *x)
-     for (i=1;i<=npar;i++) x[i]=0;
+ {
-     x[j]=1;
+   /* Same as likeli but slower because of a lot of printf and if */
-     lubksb(a,npar,indx,x);
+   int i, ii, j, k, mi, d, kk;
-     for (i=1;i<=npar;i++){
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-       y[i][j]=x[i];
+   double **out;
-       printf("%.3e ",y[i][j]);
+   double lli; /* Individual log likelihood */
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   double llt;
-     }
+   int s1, s2;
-     printf("\n");
+   double bbh, survp;
-     fprintf(ficlog,"\n");
+   /*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++)
-   free_matrix(a,1,npar,1,npar);
+     printf(" %d\n",s[4][i]);
-   free_matrix(y,1,npar,1,npar);
+   */
-   free_vector(x,1,npar);
+   cov[1]=1.;
-   free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- }
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for(mi=1; mi<= wav[i]-1; mi++){
- /*************** hessian matrix ****************/
+       for (ii=1;ii<=nlstate+ndeath;ii++)
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+         for (j=1;j<=nlstate+ndeath;j++){
- {
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int i;
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int l=1, lmax=20;
+         }
-   double k1,k2;
+       for(d=0; d<dh[mi][i]; d++){
-   double p2[NPARMAX+1];
+         newm=savm;
-   double res;
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+         for (kk=1; kk<=cptcovage;kk++) {
-   double fx;
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   int k=0,kmax=10;
+         }
-   double l1;
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   fx=func(x);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-   for(l=0 ; l <=lmax; l++){
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-     l1=pow(10,l);
+         savm=oldm;
-     delts=delt;
+         oldm=newm;
-     for(k=1 ; k <kmax; k=k+1){
+       } /* end mult */
-       delt = delta*(l1*k);
-       p2[theta]=x[theta] +delt;
+       s1=s[mw[mi][i]][i];
-       k1=func(p2)-fx;
+       s2=s[mw[mi+1][i]][i];
-       p2[theta]=x[theta]-delt;
+       bbh=(double)bh[mi][i]/(double)stepm;
-       k2=func(p2)-fx;
+       /* bias is positive if real duration
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+        * is higher than the multiple of stepm and negative otherwise.
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
- #ifdef DEBUG
+         lli=log(out[s1][s2] - savm[s1][s2]);
-       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);
+       } else if  (s2==-2) {
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+         for (j=1,survp=0. ; j<=nlstate; j++)
- #endif
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+         lli= log(survp);
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+       }else if (mle==1){
-         k=kmax;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       }
+       } else if(mle==2){
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+         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 */
-         k=kmax; l=lmax*10.;
+       } 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((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-         delts=delt;
+         lli=log(out[s1][s2]); /* Original formula */
-       }
+       } else{  /* mle=0 back to 1 */
-     }
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   }
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   delti[theta]=delts;
+       } /* End of if */
-   return res;
+       ipmx +=1;
+       sw += weight[i];
- }
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+       if(globpr){
- {
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-   int i;
+  %11.6f %11.6f %11.6f ", \
-   int l=1, l1, lmax=20;
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-   double k1,k2,k3,k4,res,fx;
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-   double p2[NPARMAX+1];
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   int k;
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   fx=func(x);
+         }
-   for (k=1; k<=2; k++) {
+         fprintf(ficresilk," %10.6f\n", -llt);
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+       }
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     } /* end of wave */
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   } /* end of individual */
-     k1=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 */
-     k2=func(p2)-fx;
+     gipmx=ipmx;
+     gsw=sw;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   }
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   return -l;
-     k3=func(p2)-fx;
+ }
-     p2[thetai]=x[thetai]-delti[thetai]/k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ /*************** function likelione ***********/
-     k4=func(p2)-fx;
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+ {
- #ifdef DEBUG
+   /* This routine should help understanding what is done with
-     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);
+      the selection of individuals/waves and
-     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);
+      to check the exact contribution to the likelihood.
- #endif
+      Plotting could be done.
-   }
+    */
-   return res;
+   int k;
- }
+   if(*globpri !=0){ /* Just counts and sums, no printings */
- /************** Inverse of matrix **************/
+     strcpy(fileresilk,"ilk");
- void ludcmp(double **a, int n, int *indx, double *d)
+     strcat(fileresilk,fileres);
- {
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-   int i,imax,j,k;
+       printf("Problem with resultfile: %s\n", fileresilk);
-   double big,dum,sum,temp;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   double *vv;
+     }
+     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");
-   vv=vector(1,n);
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-   *d=1.0;
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-   for (i=1;i<=n;i++) {
+     for(k=1; k<=nlstate; k++)
-     big=0.0;
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-     for (j=1;j<=n;j++)
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+   }
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     vv[i]=1.0/big;
+   *fretone=(*funcone)(p);
-   }
+   if(*globpri !=0){
-   for (j=1;j<=n;j++) {
+     fclose(ficresilk);
-     for (i=1;i<j;i++) {
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-       sum=a[i][j];
+     fflush(fichtm);
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   }
-       a[i][j]=sum;
+   return;
-     }
+ }
-     big=0.0;
-     for (i=j;i<=n;i++) {
-       sum=a[i][j];
+ /*********** Maximum Likelihood Estimation ***************/
-       for (k=1;k<j;k++)
-         sum -= a[i][k]*a[k][j];
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-       a[i][j]=sum;
+ {
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   int i,j, iter;
-         big=dum;
+   double **xi;
-         imax=i;
+   double fret;
-       }
+   double fretone; /* Only one call to likelihood */
-     }
+   /*  char filerespow[FILENAMELENGTH];*/
-     if (j != imax) {
-       for (k=1;k<=n;k++) {
+ #ifdef NLOPT
-         dum=a[imax][k];
+   int creturn;
-         a[imax][k]=a[j][k];
+   nlopt_opt opt;
-         a[j][k]=dum;
+   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
-       }
+   double *lb;
-       *d = -(*d);
+   double minf; /* the minimum objective value, upon return */
-       vv[imax]=vv[j];
+   double * p1; /* Shifted parameters from 0 instead of 1 */
-     }
+   myfunc_data dinst, *d = &dinst;
-     indx[j]=imax;
+ #endif
-     if (a[j][j] == 0.0) a[j][j]=TINY;
-     if (j != n) {
-       dum=1.0/(a[j][j]);
+   xi=matrix(1,npar,1,npar);
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   for (i=1;i<=npar;i++)
-     }
+     for (j=1;j<=npar;j++)
-   }
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-   free_vector(vv,1,n);  /* Doesn't work */
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
- ;
+   strcpy(filerespow,"pow");
- }
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
- void lubksb(double **a, int n, int *indx, double b[])
+     printf("Problem with resultfile: %s\n", filerespow);
- {
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   int i,ii=0,ip,j;
+   }
-   double sum;
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   for (i=1;i<=nlstate;i++)
-   for (i=1;i<=n;i++) {
+     for(j=1;j<=nlstate+ndeath;j++)
-     ip=indx[i];
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     sum=b[ip];
+   fprintf(ficrespow,"\n");
-     b[ip]=b[i];
+ #ifdef POWELL
-     if (ii)
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+ #endif
-     else if (sum) ii=i;
-     b[i]=sum;
+ #ifdef NLOPT
-   }
+ #ifdef NEWUOA
-   for (i=n;i>=1;i--) {
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
-     sum=b[i];
+ #else
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
-     b[i]=sum/a[i][i];
+ #endif
-   }
+   lb=vector(0,npar-1);
- }
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
- void pstamp(FILE *fichier)
+   nlopt_set_initial_step1(opt, 0.1);
- {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
- }
+   d->function = func;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
- /************ Frequencies ********************/
+   nlopt_set_min_objective(opt, myfunc, d);
- 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[])
+   nlopt_set_xtol_rel(opt, ftol);
- {  /* Some frequencies */
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+     printf("nlopt failed! %d\n",creturn);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   }
-   int first;
+   else {
-   double ***freq; /* Frequencies */
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
-   double *pp, **prop;
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+     iter=1; /* not equal */
-   char fileresp[FILENAMELENGTH];
+   }
+   nlopt_destroy(opt);
-   pp=vector(1,nlstate);
+ #endif
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   free_matrix(xi,1,npar,1,npar);
-   strcpy(fileresp,"p");
+   fclose(ficrespow);
-   strcat(fileresp,fileres);
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-     exit(0);
+ }
-   }
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+ /**** Computes Hessian and covariance matrix ***/
-   j1=0;
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ {
-   j=cptcoveff;
+   double  **a,**y,*x,pd;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   double **hess;
+   int i, j,jk;
-   first=1;
+   int *indx;
-   for(k1=1; k1<=j;k1++){
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-       j1++;
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-         scanf("%d", i);*/
+   double gompertz(double p[]);
-       for (i=-5; i<=nlstate+ndeath; i++)
+   hess=matrix(1,npar,1,npar);
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           for(m=iagemin; m <= iagemax+3; m++)
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-             freq[i][jk][m]=0;
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+   for (i=1;i<=npar;i++){
-     for (i=1; i<=nlstate; i++)
+     printf("%d",i);fflush(stdout);
-       for(m=iagemin; m <= iagemax+3; m++)
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-         prop[i][m]=0;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-       dateintsum=0;
-       k2cpt=0;
+     /*  printf(" %f ",p[i]);
-       for (i=1; i<=imx; i++) {
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-         bool=1;
+   }
-         if  (cptcovn>0) {
-           for (z1=1; z1<=cptcoveff; z1++)
+   for (i=1;i<=npar;i++) {
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     for (j=1;j<=npar;j++)  {
-               bool=0;
+       if (j>i) {
-         }
+         printf(".%d%d",i,j);fflush(stdout);
-         if (bool==1){
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-           for(m=firstpass; m<=lastpass; m++){
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-             k2=anint[m][i]+(mint[m][i]/12.);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+         hess[j][i]=hess[i][j];
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+         /*printf(" %lf ",hess[i][j]);*/
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+       }
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     }
-               if (m<lastpass) {
+   }
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+   printf("\n");
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+   fprintf(ficlog,"\n");
-               }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-                 dateintsum=dateintsum+k2;
-                 k2cpt++;
+   a=matrix(1,npar,1,npar);
-               }
+   y=matrix(1,npar,1,npar);
-               /*}*/
+   x=vector(1,npar);
-           }
+   indx=ivector(1,npar);
-         }
+   for (i=1;i<=npar;i++)
-       }
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+   ludcmp(a,npar,indx,&pd);
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       pstamp(ficresp);
+   for (j=1;j<=npar;j++) {
-       if  (cptcovn>0) {
+     for (i=1;i<=npar;i++) x[i]=0;
-         fprintf(ficresp, "\n#********** Variable ");
+     x[j]=1;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     lubksb(a,npar,indx,x);
-         fprintf(ficresp, "**********\n#");
+     for (i=1;i<=npar;i++){
-       }
+       matcov[i][j]=x[i];
-       for(i=1; i<=nlstate;i++)
+     }
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   }
-       fprintf(ficresp, "\n");
+   printf("\n#Hessian matrix#\n");
-       for(i=iagemin; i <= iagemax+3; i++){
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-         if(i==iagemax+3){
+   for (i=1;i<=npar;i++) {
-           fprintf(ficlog,"Total");
+     for (j=1;j<=npar;j++) {
-         }else{
+       printf("%.3e ",hess[i][j]);
-           if(first==1){
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-             first=0;
+     }
-             printf("See log file for details...\n");
+     printf("\n");
-           }
+     fprintf(ficlog,"\n");
-           fprintf(ficlog,"Age %d", i);
+   }
-         }
-         for(jk=1; jk <=nlstate ; jk++){
+   /* Recompute Inverse */
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   for (i=1;i<=npar;i++)
-             pp[jk] += freq[jk][m][i];
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-         }
+   ludcmp(a,npar,indx,&pd);
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pos=0; m <=0 ; m++)
+   /*  printf("\n#Hessian matrix recomputed#\n");
-             pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10){
+   for (j=1;j<=npar;j++) {
-             if(first==1){
+     for (i=1;i<=npar;i++) x[i]=0;
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     x[j]=1;
-             }
+     lubksb(a,npar,indx,x);
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     for (i=1;i<=npar;i++){
-           }else{
+       y[i][j]=x[i];
-             if(first==1)
+       printf("%.3e ",y[i][j]);
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       fprintf(ficlog,"%.3e ",y[i][j]);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     }
-           }
+     printf("\n");
-         }
+     fprintf(ficlog,"\n");
+   }
-         for(jk=1; jk <=nlstate ; jk++){
+   */
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
+   free_matrix(a,1,npar,1,npar);
-         }
+   free_matrix(y,1,npar,1,npar);
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+   free_vector(x,1,npar);
-           pos += pp[jk];
+   free_ivector(indx,1,npar);
-           posprop += prop[jk][i];
+   free_matrix(hess,1,npar,1,npar);
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
+ }
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ /*************** hessian matrix ****************/
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-           }else{
+ {
-             if(first==1)
+   int i;
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   int l=1, lmax=20;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double k1,k2;
-           }
+   double p2[MAXPARM+1]; /* identical to x */
-           if( i <= iagemax){
+   double res;
-             if(pos>=1.e-5){
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   double fx;
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+   int k=0,kmax=10;
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+   double l1;
-             }
-             else
+   fx=func(x);
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-           }
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-         }
+     l1=pow(10,l);
+     delts=delt;
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+     for(k=1 ; k <kmax; k=k+1){
-           for(m=-1; m <=nlstate+ndeath; m++)
+       delt = delta*(l1*k);
-             if(freq[jk][m][i] !=0 ) {
+       p2[theta]=x[theta] +delt;
-             if(first==1)
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+       p2[theta]=x[theta]-delt;
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+       k2=func(p2)-fx;
-             }
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-         if(i <= iagemax)
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-           fprintf(ficresp,"\n");
-         if(first==1)
+ #ifdef DEBUGHESS
-           printf("Others in log...\n");
+       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);
-         fprintf(ficlog,"\n");
+       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-       }
+ #endif
-     }
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   }
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   dateintmean=dateintsum/k2cpt;
+         k=kmax;
+       }
-   fclose(ficresp);
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+         k=kmax; l=lmax*10.;
-   free_vector(pp,1,nlstate);
+       }
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   /* End of Freq */
+         delts=delt;
- }
+       }
+     }
- /************ 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)
+   delti[theta]=delts;
- {
+   return res;
-   /* 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).
+ }
-      We still use firstpass and lastpass as another selection.
-   */
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ {
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   int i;
-   double ***freq; /* Frequencies */
+   int l=1, l1, lmax=20;
-   double *pp, **prop;
+   double k1,k2,k3,k4,res,fx;
-   double pos,posprop;
+   double p2[MAXPARM+1];
-   double  y2; /* in fractional years */
+   int k;
-   int iagemin, iagemax;
+   fx=func(x);
-   iagemin= (int) agemin;
+   for (k=1; k<=2; k++) {
-   iagemax= (int) agemax;
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-   /*pp=vector(1,nlstate);*/
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+     k1=func(p2)-fx;
-   j1=0;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   j=cptcoveff;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+     k2=func(p2)-fx;
-   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++;
+     k3=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;
+     k4=func(p2)-fx;
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-       for (i=1; i<=imx; i++) { /* Each individual */
+ #ifdef DEBUG
-         bool=1;
+     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  (cptcovn>0) {
+     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);
-           for (z1=1; z1<=cptcoveff; z1++)
+ #endif
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   }
-               bool=0;
+   return res;
-         }
+ }
-         if (bool==1) {
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+ /************** Inverse of matrix **************/
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+ void ludcmp(double **a, int n, int *indx, double *d)
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+ {
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   int i,imax,j,k;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   double big,dum,sum,temp;
-               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);
+   double *vv;
-               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]]);*/
+   vv=vector(1,n);
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   *d=1.0;
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   for (i=1;i<=n;i++) {
-               }
+     big=0.0;
-             }
+     for (j=1;j<=n;j++)
-           } /* end selection of waves */
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-         }
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-       }
+     vv[i]=1.0/big;
-       for(i=iagemin; i <= iagemax+3; i++){
+   }
+   for (j=1;j<=n;j++) {
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     for (i=1;i<j;i++) {
-           posprop += prop[jk][i];
+       sum=a[i][j];
-         }
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+       a[i][j]=sum;
-         for(jk=1; jk <=nlstate ; jk++){
+     }
-           if( i <=  iagemax){
+     big=0.0;
-             if(posprop>=1.e-5){
+     for (i=j;i<=n;i++) {
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+       sum=a[i][j];
-             }
+       for (k=1;k<j;k++)
-           }
+         sum -= a[i][k]*a[k][j];
-         }/* end jk */
+       a[i][j]=sum;
-       }/* end i */
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-     } /* end i1 */
+         big=dum;
-   } /* end k1 */
+         imax=i;
+       }
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+     }
-   /*free_vector(pp,1,nlstate);*/
+     if (j != imax) {
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+       for (k=1;k<=n;k++) {
- }  /* End of prevalence */
+         dum=a[imax][k];
+         a[imax][k]=a[j][k];
- /************* Waves Concatenation ***************/
+         a[j][k]=dum;
+       }
- 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)
+       *d = -(*d);
- {
+       vv[imax]=vv[j];
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+     }
-      Death is a valid wave (if date is known).
+     indx[j]=imax;
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+     if (j != n) {
-      and mw[mi+1][i]. dh depends on stepm.
+       dum=1.0/(a[j][j]);
-      */
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+     }
-   int i, mi, m;
+   }
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   free_vector(vv,1,n);  /* Doesn't work */
-      double sum=0., jmean=0.;*/
+ ;
-   int first;
+ }
-   int j, k=0,jk, ju, jl;
-   double sum=0.;
+ void lubksb(double **a, int n, int *indx, double b[])
-   first=0;
+ {
-   jmin=1e+5;
+   int i,ii=0,ip,j;
-   jmax=-1;
+   double sum;
-   jmean=0.;
-   for(i=1; i<=imx; i++){
+   for (i=1;i<=n;i++) {
-     mi=0;
+     ip=indx[i];
-     m=firstpass;
+     sum=b[ip];
-     while(s[m][i] <= nlstate){
+     b[ip]=b[i];
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+     if (ii)
-         mw[++mi][i]=m;
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-       if(m >=lastpass)
+     else if (sum) ii=i;
-         break;
+     b[i]=sum;
-       else
+   }
-         m++;
+   for (i=n;i>=1;i--) {
-     }/* end while */
+     sum=b[i];
-     if (s[m][i] > nlstate){
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       mi++;     /* Death is another wave */
+     b[i]=sum/a[i][i];
-       /* if(mi==0)  never been interviewed correctly before death */
+   }
-          /* Only death is a correct wave */
+ }
-       mw[mi][i]=m;
-     }
+ void pstamp(FILE *fichier)
+ {
-     wav[i]=mi;
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-     if(mi==0){
+ }
-       nbwarn++;
-       if(first==0){
+ /************ Frequencies ********************/
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-         first=1;
+ {  /* Some frequencies */
-       }
-       if(first==1){
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+   int first;
-       }
+   double ***freq; /* Frequencies */
-     } /* end mi==0 */
+   double *pp, **prop;
-   } /* End individuals */
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   char fileresp[FILENAMELENGTH];
-   for(i=1; i<=imx; i++){
-     for(mi=1; mi<wav[i];mi++){
+   pp=vector(1,nlstate);
-       if (stepm <=0)
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-         dh[mi][i]=1;
+   strcpy(fileresp,"p");
-       else{
+   strcat(fileresp,fileres);
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-           if (agedc[i] < 2*AGESUP) {
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-             if(j==0) j=1;  /* Survives at least one month after exam */
+     exit(0);
-             else if(j<0){
+   }
-               nberr++;
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,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]);
+   j1=0;
-               j=1; /* Temporary Dangerous patch */
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+   j=cptcoveff;
-               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]);
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-               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);
-             }
+   first=1;
-             k=k+1;
-             if (j >= jmax){
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-               jmax=j;
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-               ijmax=i;
+   /*    j1++;
-             }
+ */
-             if (j <= jmin){
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-               jmin=j;
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-               ijmin=i;
+         scanf("%d", i);*/
-             }
+       for (i=-5; i<=nlstate+ndeath; i++)
-             sum=sum+j;
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+           for(m=iagemin; m <= iagemax+3; m++)
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+             freq[i][jk][m]=0;
-           }
-         }
+       for (i=1; i<=nlstate; i++)
-         else{
+         for(m=iagemin; m <= iagemax+3; m++)
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+           prop[i][m]=0;
- /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
+       dateintsum=0;
-           k=k+1;
+       k2cpt=0;
-           if (j >= jmax) {
+       for (i=1; i<=imx; i++) {
-             jmax=j;
+         bool=1;
-             ijmax=i;
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-           }
+           for (z1=1; z1<=cptcoveff; z1++)
-           else if (j <= jmin){
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-             jmin=j;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-             ijmin=i;
+               bool=0;
-           }
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-           /*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]);*/
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-           if(j<0){
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-             nberr++;
+             }
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         }
-             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]);
-           }
+         if (bool==1){
-           sum=sum+j;
+           for(m=firstpass; m<=lastpass; m++){
-         }
+             k2=anint[m][i]+(mint[m][i]/12.);
-         jk= j/stepm;
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-         jl= j -jk*stepm;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-         ju= j -(jk+1)*stepm;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-           if(jl==0){
+               if (m<lastpass) {
-             dh[mi][i]=jk;
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-             bh[mi][i]=0;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-           }else{ /* We want a negative bias in order to only have interpolation ie
+               }
-                   * at the price of an extra matrix product in likelihood */
-             dh[mi][i]=jk+1;
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-             bh[mi][i]=ju;
+                 dateintsum=dateintsum+k2;
-           }
+                 k2cpt++;
-         }else{
+               }
-           if(jl <= -ju){
+               /*}*/
-             dh[mi][i]=jk;
+           }
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         }
-                                  * is higher than the multiple of stepm and negative otherwise.
+       } /* end i */
-                                  */
-           }
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-           else{
+       pstamp(ficresp);
-             dh[mi][i]=jk+1;
+       if  (cptcovn>0) {
-             bh[mi][i]=ju;
+         fprintf(ficresp, "\n#********** Variable ");
-           }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-           if(dh[mi][i]==0){
+         fprintf(ficresp, "**********\n#");
-             dh[mi][i]=1; /* At least one step */
+         fprintf(ficlog, "\n#********** Variable ");
-             bh[mi][i]=ju; /* At least one step */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-             /*  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(ficlog, "**********\n#");
-           }
+       }
-         } /* end if mle */
+       for(i=1; i<=nlstate;i++)
-       }
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-     } /* end wave */
+       fprintf(ficresp, "\n");
-   }
-   jmean=sum/k;
+       for(i=iagemin; i <= iagemax+3; i++){
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+         if(i==iagemax+3){
-   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,"Total");
-  }
+         }else{
+           if(first==1){
- /*********** Tricode ****************************/
+             first=0;
- void tricode(int *Tvar, int **nbcode, int imx)
+             printf("See log file for details...\n");
- {
+           }
+           fprintf(ficlog,"Age %d", i);
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+         }
-   int cptcode=0;
+         for(jk=1; jk <=nlstate ; jk++){
-   cptcoveff=0;
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+         }
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+             pos += freq[jk][m][i];
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+           if(pp[jk]>=1.e-10){
-                                modality*/
+             if(first==1){
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       Ndum[ij]++; /*store the modality */
+             }
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+           }else{
-                                        Tvar[j]. If V=sex and male is 0 and
+             if(first==1)
-                                        female is 1, then  cptcode=1.*/
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     }
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
-     for (i=0; i<=cptcode; i++) {
+         }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
-     }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-     ij=1;
+             pp[jk] += freq[jk][m][i];
-     for (i=1; i<=ncodemax[j]; i++) {
+         }
-       for (k=0; k<= maxncov; k++) {
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-         if (Ndum[k] != 0) {
+           pos += pp[jk];
-           nbcode[Tvar[j]][ij]=k;
+           posprop += prop[jk][i];
-           /* 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++;
+           if(pos>=1.e-5){
-         }
+             if(first==1)
-         if (ij > ncodemax[j]) break;
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-       }
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-     }
+           }else{
-   }
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           }
-  for (i=1; i<=ncovmodel-2; i++) {
+           if( i <= iagemax){
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+             if(pos>=1.e-5){
-    ij=Tvar[i];
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-    Ndum[ij]++;
+               /*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]);*/
+             }
-  ij=1;
+             else
-  for (i=1; i<= maxncov; i++) {
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+           }
-      Tvaraff[ij]=i; /*For printing */
+         }
-      ij++;
-    }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-  }
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) {
-  cptcoveff=ij-1; /*Number of simple covariates*/
+             if(first==1)
- }
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
- /*********** Health Expectancies ****************/
+             }
+         if(i <= iagemax)
- 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[] )
+           fprintf(ficresp,"\n");
+         if(first==1)
- {
+           printf("Others in log...\n");
-   /* Health expectancies, no variances */
+         fprintf(ficlog,"\n");
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+       }
-   double age, agelim, hf;
+       /*}*/
-   double ***p3mat;
+   }
-   double eip;
+   dateintmean=dateintsum/k2cpt;
-   pstamp(ficreseij);
+   fclose(ficresp);
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   fprintf(ficreseij,"# Age");
+   free_vector(pp,1,nlstate);
-   for(i=1; i<=nlstate;i++){
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-     for(j=1; j<=nlstate;j++){
+   /* End of Freq */
-       fprintf(ficreseij," e%1d%1d ",i,j);
+ }
-     }
-     fprintf(ficreseij," e%1d. ",i);
+ /************ 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)
-   fprintf(ficreseij,"\n");
+ {
+   /* 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).
-   if(estepm < stepm){
+      We still use firstpass and lastpass as another selection.
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   */
-   }
-   else  hstepm=estepm;
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   double ***freq; /* Frequencies */
-    * This is mainly to measure the difference between two models: for example
+   double *pp, **prop;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   double pos,posprop;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   double  y2; /* in fractional years */
-    * progression in between and thus overestimating or underestimating according
+   int iagemin, iagemax;
-    * to the curvature of the survival function. If, for the same date, we
+   int first; /** to stop verbosity which is redirected to log file */
-    * 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
+   iagemin= (int) agemin;
-    * hypothesis. A more precise result, taking into account a more precise
+   iagemax= (int) agemax;
-    * curvature will be obtained if estepm is as small as stepm. */
+   /*pp=vector(1,nlstate);*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   j1=0;
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+   /*j=cptcoveff;*/
-      Look at hpijx to understand the reason of that which relies in memory size
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-      and note for a fixed period like estepm months */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   first=1;
-      survival function given by stepm (the optimization length). Unfortunately it
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-      means that if the survival funtion is printed only each two years of age and if
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+       j1++;*/
-      results. So we changed our mind and took the option of the best precision.
-   */
+       for (i=1; i<=nlstate; i++)
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+         for(m=iagemin; m <= iagemax+3; m++)
+           prop[i][m]=0.0;
-   agelim=AGESUP;
-   /* If stepm=6 months */
+       for (i=1; i<=imx; i++) { /* Each individual */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+         bool=1;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         if  (cptcovn>0) {
+           for (z1=1; z1<=cptcoveff; z1++)
- /* nhstepm age range expressed in number of stepm */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+               bool=0;
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         }
-   /* if (stepm >= YEARM) hstepm=1;*/
+         if (bool==1) {
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   for (age=bage; age<=fage; age ++){
+               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);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+               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]]);*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-     printf("%d|",(int)age);fflush(stdout);
+               }
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+             }
+           } /* end selection of waves */
+         }
-     /* Computing expectancies */
+       }
-     for(i=1; i<=nlstate;i++)
+       for(i=iagemin; i <= iagemax+3; i++){
-       for(j=1; j<=nlstate;j++)
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           posprop += prop[jk][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]);*/
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <=  iagemax){
-         }
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-     fprintf(ficreseij,"%3.0f",age );
+             } else{
-     for(i=1; i<=nlstate;i++){
+               if(first==1){
-       eip=0;
+                 first=0;
-       for(j=1; j<=nlstate;j++){
+                 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]);
-         eip +=eij[i][j][(int)age];
+               }
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+             }
-       }
+           }
-       fprintf(ficreseij,"%9.4f", eip );
+         }/* end jk */
-     }
+       }/* end i */
-     fprintf(ficreseij,"\n");
+     /*} *//* end i1 */
+   } /* end j1 */
-   }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-   printf("\n");
+   /*free_vector(pp,1,nlstate);*/
-   fprintf(ficlog,"\n");
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+ }  /* End of prevalence */
- }
+ /************* Waves Concatenation ***************/
- 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[] )
+ 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)
  {
-   /* Covariances of health expectancies eij and of total life expectancies according
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-    to initial status i, ei. .
+      Death is a valid wave (if date is known).
-   */
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   double age, agelim, hf;
+      and mw[mi+1][i]. dh depends on stepm.
-   double ***p3matp, ***p3matm, ***varhe;
+      */
-   double **dnewm,**doldm;
-   double *xp, *xm;
+   int i, mi, m;
-   double **gp, **gm;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   double ***gradg, ***trgradg;
+      double sum=0., jmean=0.;*/
-   int theta;
+   int first;
+   int j, k=0,jk, ju, jl;
-   double eip, vip;
+   double sum=0.;
+   first=0;
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   jmin=1e+5;
-   xp=vector(1,npar);
+   jmax=-1;
-   xm=vector(1,npar);
+   jmean=0.;
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   for(i=1; i<=imx; i++){
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+     mi=0;
+     m=firstpass;
-   pstamp(ficresstdeij);
+     while(s[m][i] <= nlstate){
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-   fprintf(ficresstdeij,"# Age");
+         mw[++mi][i]=m;
-   for(i=1; i<=nlstate;i++){
+       if(m >=lastpass)
-     for(j=1; j<=nlstate;j++)
+         break;
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+       else
-     fprintf(ficresstdeij," e%1d. ",i);
+         m++;
-   }
+     }/* end while */
-   fprintf(ficresstdeij,"\n");
+     if (s[m][i] > nlstate){
+       mi++;     /* Death is another wave */
-   pstamp(ficrescveij);
+       /* if(mi==0)  never been interviewed correctly before death */
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+          /* Only death is a correct wave */
-   fprintf(ficrescveij,"# Age");
+       mw[mi][i]=m;
-   for(i=1; i<=nlstate;i++)
+     }
-     for(j=1; j<=nlstate;j++){
-       cptj= (j-1)*nlstate+i;
+     wav[i]=mi;
-       for(i2=1; i2<=nlstate;i2++)
+     if(mi==0){
-         for(j2=1; j2<=nlstate;j2++){
+       nbwarn++;
-           cptj2= (j2-1)*nlstate+i2;
+       if(first==0){
-           if(cptj2 <= cptj)
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+         first=1;
-         }
+       }
-     }
+       if(first==1){
-   fprintf(ficrescveij,"\n");
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+       }
-   if(estepm < stepm){
+     } /* end mi==0 */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   } /* End individuals */
-   }
-   else  hstepm=estepm;
+   for(i=1; i<=imx; i++){
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     for(mi=1; mi<wav[i];mi++){
-    * This is mainly to measure the difference between two models: for example
+       if (stepm <=0)
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+         dh[mi][i]=1;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       else{
-    * progression in between and thus overestimating or underestimating according
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-    * to the curvature of the survival function. If, for the same date, we
+           if (agedc[i] < 2*AGESUP) {
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-    * to compare the new estimate of Life expectancy with the same linear
+             if(j==0) j=1;  /* Survives at least one month after exam */
-    * hypothesis. A more precise result, taking into account a more precise
+             else if(j<0){
-    * curvature will be obtained if estepm is as small as stepm. */
+               nberr++;
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+               j=1; /* Temporary Dangerous patch */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-      nhstepm is the number of hstepm from age to agelim
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-      nstepm is the number of stepm from age to agelin.
+               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);
-      Look at hpijx to understand the reason of that which relies in memory size
+             }
-      and note for a fixed period like estepm months */
+             k=k+1;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+             if (j >= jmax){
-      survival function given by stepm (the optimization length). Unfortunately it
+               jmax=j;
-      means that if the survival funtion is printed only each two years of age and if
+               ijmax=i;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+             }
-      results. So we changed our mind and took the option of the best precision.
+             if (j <= jmin){
-   */
+               jmin=j;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+               ijmin=i;
+             }
-   /* If stepm=6 months */
+             sum=sum+j;
-   /* nhstepm age range expressed in number of stepm */
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-   agelim=AGESUP;
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+           }
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         }
-   /* if (stepm >= YEARM) hstepm=1;*/
+         else{
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           k=k+1;
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+           if (j >= jmax) {
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+             jmax=j;
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+             ijmax=i;
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+           }
+           else if (j <= jmin){
-   for (age=bage; age<=fage; age ++){
+             jmin=j;
+             ijmin=i;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           }
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           if(j<0){
+             nberr++;
-     /* Computing  Variances of health expectancies */
+             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]);
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+             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]);
-        decrease memory allocation */
+           }
-     for(theta=1; theta <=npar; theta++){
+           sum=sum+j;
-       for(i=1; i<=npar; i++){
+         }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+         jk= j/stepm;
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+         jl= j -jk*stepm;
-       }
+         ju= j -(jk+1)*stepm;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+           if(jl==0){
+             dh[mi][i]=jk;
-       for(j=1; j<= nlstate; j++){
+             bh[mi][i]=0;
-         for(i=1; i<=nlstate; i++){
+           }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 */
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             dh[mi][i]=jk+1;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+             bh[mi][i]=ju;
            }
-         }
+         }else{
-       }
+           if(jl <= -ju){
+             dh[mi][i]=jk;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+             bh[mi][i]=jl;       /* bias is positive if real duration
-         for(h=0; h<=nhstepm-1; h++){
+                                  * is higher than the multiple of stepm and negative otherwise.
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+                                  */
-         }
+           }
-     }/* End theta */
+           else{
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
-     for(h=0; h<=nhstepm-1; h++)
+           }
-       for(j=1; j<=nlstate*nlstate;j++)
+           if(dh[mi][i]==0){
-         for(theta=1; theta <=npar; theta++)
+             dh[mi][i]=1; /* At least one step */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+             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);*/
+           }
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+         } /* end if mle */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+       }
-         varhe[ij][ji][(int)age] =0.;
+     } /* end wave */
+   }
-      printf("%d|",(int)age);fflush(stdout);
+   jmean=sum/k;
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-      for(h=0;h<=nhstepm-1;h++){
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-       for(k=0;k<=nhstepm-1;k++){
+  }
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+ /*********** Tricode ****************************/
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+ {
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-       }
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-     }
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-     /* Computing expectancies */
+   /* nbcode[Tvar[j]][1]=
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   */
-     for(i=1; i<=nlstate;i++)
-       for(j=1; j<=nlstate;j++)
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   int modmaxcovj=0; /* Modality max of covariates j */
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+   int cptcode=0; /* Modality max of covariates j */
+   int modmincovj=0; /* Modality min of covariates j */
-           /* 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]);*/
-         }
+   cptcoveff=0;
-     fprintf(ficresstdeij,"%3.0f",age );
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-     for(i=1; i<=nlstate;i++){
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-       eip=0.;
-       vip=0.;
+   /* Loop on covariates without age and products */
-       for(j=1; j<=nlstate;j++){
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-         eip += eij[i][j][(int)age];
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+                                modality of this covariate Vj*/
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+                                     * If product of Vn*Vm, still boolean *:
-       }
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-     }
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-     fprintf(ficresstdeij,"\n");
+                                       modality of the nth covariate of individual i. */
+       if (ij > modmaxcovj)
-     fprintf(ficrescveij,"%3.0f",age );
+         modmaxcovj=ij;
-     for(i=1; i<=nlstate;i++)
+       else if (ij < modmincovj)
-       for(j=1; j<=nlstate;j++){
+         modmincovj=ij;
-         cptj= (j-1)*nlstate+i;
+       if ((ij < -1) && (ij > NCOVMAX)){
-         for(i2=1; i2<=nlstate;i2++)
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-           for(j2=1; j2<=nlstate;j2++){
+         exit(1);
-             cptj2= (j2-1)*nlstate+i2;
+       }else
-             if(cptj2 <= cptj)
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-           }
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       }
+       /* getting the maximum value of the modality of the covariate
-     fprintf(ficrescveij,"\n");
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+          female is 1, then modmaxcovj=1.*/
-   }
+     }
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+     cptcode=modmaxcovj;
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+    /*for (i=0; i<=cptcode; i++) {*/
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-   printf("\n");
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-   fprintf(ficlog,"\n");
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
+       }
-   free_vector(xm,1,npar);
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   free_vector(xp,1,npar);
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+     } /* Ndum[-1] number of undefined modalities */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
- }
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
- /************ Variance ******************/
+        modmincovj=3; modmaxcovj = 7;
- 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[])
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
- {
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-   /* Variance of health expectancies */
+        variables V1_1 and V1_2.
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+        nbcode[Tvar[j]][ij]=k;
-   /* double **newm;*/
+        nbcode[Tvar[j]][1]=0;
-   double **dnewm,**doldm;
+        nbcode[Tvar[j]][2]=1;
-   double **dnewmp,**doldmp;
+        nbcode[Tvar[j]][3]=2;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+     */
-   int k, cptcode;
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   double *xp;
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   double **gp, **gm;  /* for var eij */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-   double ***gradg, ***trgradg; /*for var eij */
+         /*recode from 0 */
-   double **gradgp, **trgradgp; /* for var p point j */
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-   double *gpp, *gmp; /* for var p point j */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+                                      k is a modality. If we have model=V1+V1*sex
-   double ***p3mat;
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-   double age,agelim, hf;
+           ij++;
-   double ***mobaverage;
+         }
-   int theta;
+         if (ij > ncodemax[j]) break;
-   char digit[4];
+       }  /* end of loop on */
-   char digitp[25];
+     } /* end of loop on modality */
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   char fileresprobmorprev[FILENAMELENGTH];
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   if(popbased==1){
-     if(mobilav!=0)
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-       strcpy(digitp,"-populbased-mobilav-");
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     else strcpy(digitp,"-populbased-nomobil-");
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-   }
+    Ndum[ij]++;
-   else
+  }
-     strcpy(digitp,"-stablbased-");
+  ij=1;
-   if (mobilav!=0) {
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+      Tvaraff[ij]=i; /*For printing (unclear) */
-     }
+      ij++;
-   }
+    }else
+        Tvaraff[ij]=0;
-   strcpy(fileresprobmorprev,"prmorprev");
+  }
-   sprintf(digit,"%-d",ij);
+  ij--;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+  cptcoveff=ij; /*Number of total covariates*/
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+ }
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+ /*********** Health Expectancies ****************/
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ {
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   /* Health expectancies, no variances */
-   pstamp(ficresprobmorprev);
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-   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);
+   int nhstepma, nstepma; /* Decreasing with age */
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   double age, agelim, hf;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   double ***p3mat;
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   double eip;
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   pstamp(ficreseij);
-   }
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   fprintf(ficresprobmorprev,"\n");
+   fprintf(ficreseij,"# Age");
-   fprintf(ficgp,"\n# Routine varevsij");
+   for(i=1; i<=nlstate;i++){
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+     for(j=1; j<=nlstate;j++){
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+       fprintf(ficreseij," e%1d%1d ",i,j);
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+     }
- /*   } */
+     fprintf(ficreseij," e%1d. ",i);
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   }
-   pstamp(ficresvij);
+   fprintf(ficreseij,"\n");
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+   if(estepm < stepm){
-   else
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   }
-   fprintf(ficresvij,"# Age");
+   else  hstepm=estepm;
-   for(i=1; i<=nlstate;i++)
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     for(j=1; j<=nlstate;j++)
+    * This is mainly to measure the difference between two models: for example
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-   fprintf(ficresvij,"\n");
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
-   xp=vector(1,npar);
+    * to the curvature of the survival function. If, for the same date, we
-   dnewm=matrix(1,nlstate,1,npar);
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   doldm=matrix(1,nlstate,1,nlstate);
+    * to compare the new estimate of Life expectancy with the same linear
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    * hypothesis. A more precise result, taking into account a more precise
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    * curvature will be obtained if estepm is as small as stepm. */
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   gmp=vector(nlstate+1,nlstate+ndeath);
+      nhstepm is the number of hstepm from age to agelim
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
-   if(estepm < stepm){
+      and note for a fixed period like estepm months */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   /* 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
-   else  hstepm=estepm;
+      means that if the survival funtion is printed only each two years of age and if
-   /* For example we decided to compute the life expectancy with the smallest unit */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      results. So we changed our mind and took the option of the best precision.
-      nhstepm is the number of hstepm from age to agelim
+   */
-      nstepm is the number of stepm from age to agelin.
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like k years */
+   agelim=AGESUP;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   /* If stepm=6 months */
-      survival function given by stepm (the optimization length). Unfortunately it
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-      means that if the survival funtion is printed every two years of age and if
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-      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.
+ /* nhstepm age range expressed in number of stepm */
-   */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   agelim = AGESUP;
+   /* if (stepm >= YEARM) hstepm=1;*/
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   for (age=bage; age<=fage; age ++){
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     gp=matrix(0,nhstepm,1,nlstate);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     gm=matrix(0,nhstepm,1,nlstate);
+     /* if (stepm >= YEARM) hstepm=1;*/
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     for(theta=1; theta <=npar; theta++){
+     /* If stepm=6 months */
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       if (popbased==1) {
-         if(mobilav ==0){
+     printf("%d|",(int)age);fflush(stdout);
-           for(i=1; i<=nlstate;i++)
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
+     /* Computing expectancies */
-           for(i=1; i<=nlstate;i++)
+     for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+       for(j=1; j<=nlstate;j++)
-         }
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-       }
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-       for(j=1; j<= nlstate; j++){
+           /* 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(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+         }
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
+     fprintf(ficreseij,"%3.0f",age );
-       }
+     for(i=1; i<=nlstate;i++){
-       /* This for computing probability of death (h=1 means
+       eip=0;
-          computed over hstepm matrices product = hstepm*stepm months)
+       for(j=1; j<=nlstate;j++){
-          as a weighted average of prlim.
+         eip +=eij[i][j][(int)age];
-       */
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       }
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+       fprintf(ficreseij,"%9.4f", eip );
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
-       }
+     fprintf(ficreseij,"\n");
-       /* end probability of death */
+   }
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   printf("\n");
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   fprintf(ficlog,"\n");
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ }
-       if (popbased==1) {
-         if(mobilav ==0){
+ 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(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+ {
-         }else{ /* mobilav */
+   /* Covariances of health expectancies eij and of total life expectancies according
-           for(i=1; i<=nlstate;i++)
+    to initial status i, ei. .
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   */
-         }
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-       }
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
-       for(j=1; j<= nlstate; j++){
+   double ***p3matp, ***p3matm, ***varhe;
-         for(h=0; h<=nhstepm; h++){
+   double **dnewm,**doldm;
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+   double *xp, *xm;
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+   double **gp, **gm;
-         }
+   double ***gradg, ***trgradg;
-       }
+   int theta;
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+   double eip, vip;
-          as a weighted average of prlim.
-       */
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   xp=vector(1,npar);
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+   xm=vector(1,npar);
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-       }
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-       /* end probability of death */
+   pstamp(ficresstdeij);
-       for(j=1; j<= nlstate; j++) /* vareij */
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-         for(h=0; h<=nhstepm; h++){
+   fprintf(ficresstdeij,"# Age");
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   for(i=1; i<=nlstate;i++){
-         }
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+     fprintf(ficresstdeij," e%1d. ",i);
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   }
-       }
+   fprintf(ficresstdeij,"\n");
-     } /* End theta */
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   fprintf(ficrescveij,"# Age");
+   for(i=1; i<=nlstate;i++)
-     for(h=0; h<=nhstepm; h++) /* veij */
+     for(j=1; j<=nlstate;j++){
-       for(j=1; j<=nlstate;j++)
+       cptj= (j-1)*nlstate+i;
-         for(theta=1; theta <=npar; theta++)
+       for(i2=1; i2<=nlstate;i2++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+           if(cptj2 <= cptj)
-       for(theta=1; theta <=npar; theta++)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-         trgradgp[j][theta]=gradgp[theta][j];
+         }
+     }
+   fprintf(ficrescveij,"\n");
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     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] =0.;
+   }
+   else  hstepm=estepm;
-     for(h=0;h<=nhstepm;h++){
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-       for(k=0;k<=nhstepm;k++){
+    * This is mainly to measure the difference between two models: for example
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-         for(i=1;i<=nlstate;i++)
+    * progression in between and thus overestimating or underestimating according
-           for(j=1;j<=nlstate;j++)
+    * to the curvature of the survival function. If, for the same date, we
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-       }
+    * to compare the new estimate of Life expectancy with the same linear
-     }
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
-     /* pptj */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+      nhstepm is the number of hstepm from age to agelim
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+      nstepm is the number of stepm from age to agelin.
-         varppt[j][i]=doldmp[j][i];
+      Look at hpijx to understand the reason of that which relies in memory size
-     /* end ppptj */
+      and note for a fixed period like estepm months */
-     /*  x centered again */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+      survival function given by stepm (the optimization length). Unfortunately it
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,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
-     if (popbased==1) {
+      results. So we changed our mind and took the option of the best precision.
-       if(mobilav ==0){
+   */
-         for(i=1; i<=nlstate;i++)
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-           prlim[i][i]=probs[(int)age][i][ij];
-       }else{ /* mobilav */
+   /* If stepm=6 months */
-         for(i=1; i<=nlstate;i++)
+   /* nhstepm age range expressed in number of stepm */
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+   agelim=AGESUP;
-       }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     }
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
-     /* This for computing probability of death (h=1 means
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-        as a weighted average of prlim.
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     */
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     }
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     /* end probability of death */
+   for (age=bage; age<=fage; age ++){
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+     /* if (stepm >= YEARM) hstepm=1;*/
-       for(i=1; i<=nlstate;i++){
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       }
+     /* If stepm=6 months */
-     }
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-     fprintf(ficresprobmorprev,"\n");
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     fprintf(ficresvij,"%.0f ",age );
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     for(i=1; i<=nlstate;i++)
-       for(j=1; j<=nlstate;j++){
+     /* Computing  Variances of health expectancies */
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-       }
+        decrease memory allocation */
-     fprintf(ficresvij,"\n");
+     for(theta=1; theta <=npar; theta++){
-     free_matrix(gp,0,nhstepm,1,nlstate);
+       for(i=1; i<=npar; i++){
-     free_matrix(gm,0,nhstepm,1,nlstate);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+       }
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   } /* End age */
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+       for(j=1; j<= nlstate; j++){
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+         for(i=1; i<=nlstate; i++){
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+           for(h=0; h<=nhstepm-1; h++){
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+           }
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+         }
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       }
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-   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));
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+         }
-   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);
+     }/* End theta */
-   /*  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); */
+     for(h=0; h<=nhstepm-1; h++)
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       for(j=1; j<=nlstate*nlstate;j++)
+         for(theta=1; theta <=npar; theta++)
-   free_vector(xp,1,npar);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         varhe[ij][ji][(int)age] =0.;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
+      printf("%d|",(int)age);fflush(stdout);
-   fflush(ficgp);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   fflush(fichtm);
+      for(h=0;h<=nhstepm-1;h++){
- }  /* end varevsij */
+       for(k=0;k<=nhstepm-1;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
- /************ Variance of prevlim ******************/
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+         for(ij=1;ij<=nlstate*nlstate;ij++)
- {
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   /* Variance of prevalence limit */
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+       }
-   double **newm;
+     }
-   double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm;
+     /* Computing expectancies */
-   int k, cptcode;
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   double *xp;
+     for(i=1; i<=nlstate;i++)
-   double *gp, *gm;
+       for(j=1; j<=nlstate;j++)
-   double **gradg, **trgradg;
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   double age,agelim;
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   int theta;
+           /* 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]);*/
-   pstamp(ficresvpl);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+         }
-   fprintf(ficresvpl,"# Age");
-   for(i=1; i<=nlstate;i++)
+     fprintf(ficresstdeij,"%3.0f",age );
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     for(i=1; i<=nlstate;i++){
-   fprintf(ficresvpl,"\n");
+       eip=0.;
+       vip=0.;
-   xp=vector(1,npar);
+       for(j=1; j<=nlstate;j++){
-   dnewm=matrix(1,nlstate,1,npar);
+         eip += eij[i][j][(int)age];
-   doldm=matrix(1,nlstate,1,nlstate);
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-   hstepm=1*YEARM; /* Every year of age */
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+       }
-   agelim = AGESUP;
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     }
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     fprintf(ficresstdeij,"\n");
-     if (stepm >= YEARM) hstepm=1;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     fprintf(ficrescveij,"%3.0f",age );
-     gradg=matrix(1,npar,1,nlstate);
+     for(i=1; i<=nlstate;i++)
-     gp=vector(1,nlstate);
+       for(j=1; j<=nlstate;j++){
-     gm=vector(1,nlstate);
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-     for(theta=1; theta <=npar; theta++){
+           for(j2=1; j2<=nlstate;j2++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+             cptj2= (j2-1)*nlstate+i2;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+             if(cptj2 <= cptj)
-       }
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+           }
-       for(i=1;i<=nlstate;i++)
+       }
-         gp[i] = prlim[i][i];
+     fprintf(ficrescveij,"\n");
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   }
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-       for(i=1;i<=nlstate;i++)
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-         gm[i] = prlim[i][i];
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(i=1;i<=nlstate;i++)
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   printf("\n");
-     } /* End theta */
+   fprintf(ficlog,"\n");
-     trgradg =matrix(1,nlstate,1,npar);
+   free_vector(xm,1,npar);
+   free_vector(xp,1,npar);
-     for(j=1; j<=nlstate;j++)
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-       for(theta=1; theta <=npar; theta++)
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-         trgradg[j][theta]=gradg[theta][j];
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+ }
-     for(i=1;i<=nlstate;i++)
-       varpl[i][(int)age] =0.;
+ /************ Variance ******************/
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ 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[])
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ {
-     for(i=1;i<=nlstate;i++)
+   /* Variance of health expectancies */
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /* double **newm;*/
-     fprintf(ficresvpl,"%.0f ",age );
+   double **dnewm,**doldm;
-     for(i=1; i<=nlstate;i++)
+   double **dnewmp,**doldmp;
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   int i, j, nhstepm, hstepm, h, nstepm ;
-     fprintf(ficresvpl,"\n");
+   int k, cptcode;
-     free_vector(gp,1,nlstate);
+   double *xp;
-     free_vector(gm,1,nlstate);
+   double **gp, **gm;  /* for var eij */
-     free_matrix(gradg,1,npar,1,nlstate);
+   double ***gradg, ***trgradg; /*for var eij */
-     free_matrix(trgradg,1,nlstate,1,npar);
+   double **gradgp, **trgradgp; /* for var p point j */
-   } /* End age */
+   double *gpp, *gmp; /* for var p point j */
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   free_vector(xp,1,npar);
+   double ***p3mat;
-   free_matrix(doldm,1,nlstate,1,npar);
+   double age,agelim, hf;
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   double ***mobaverage;
+   int theta;
- }
+   char digit[4];
+   char digitp[25];
- /************ 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[])
+   char fileresprobmorprev[FILENAMELENGTH];
- {
-   int i, j=0,  i1, k1, l1, t, tj;
+   if(popbased==1){
-   int k2, l2, j1,  z1;
+     if(mobilav!=0)
-   int k=0,l, cptcode;
+       strcpy(digitp,"-populbased-mobilav-");
-   int first=1, first1;
+     else strcpy(digitp,"-populbased-nomobil-");
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   }
-   double **dnewm,**doldm;
+   else
-   double *xp;
+     strcpy(digitp,"-stablbased-");
-   double *gp, *gm;
-   double **gradg, **trgradg;
+   if (mobilav!=0) {
-   double **mu;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double age,agelim, cov[NCOVMAX];
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   int theta;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   char fileresprob[FILENAMELENGTH];
+     }
-   char fileresprobcov[FILENAMELENGTH];
+   }
-   char fileresprobcor[FILENAMELENGTH];
+   strcpy(fileresprobmorprev,"prmorprev");
-   double ***varpij;
+   sprintf(digit,"%-d",ij);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   strcpy(fileresprob,"prob");
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   strcat(fileresprob,fileres);
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   strcat(fileresprobmorprev,fileres);
-     printf("Problem with resultfile: %s\n", fileresprob);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   strcpy(fileresprobcov,"probcov");
+   }
-   strcat(fileresprobcov,fileres);
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   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);
-   strcpy(fileresprobcor,"probcor");
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   strcat(fileresprobcor,fileres);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+     for(i=1; i<=nlstate;i++)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficgp,"\n# Routine varevsij");
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   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");
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+ /*   } */
-   pstamp(ficresprob);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   pstamp(ficresvij);
-   fprintf(ficresprob,"# Age");
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   pstamp(ficresprobcov);
+   if(popbased==1)
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   fprintf(ficresprobcov,"# Age");
+   else
-   pstamp(ficresprobcor);
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresvij,"# Age");
-   fprintf(ficresprobcor,"# Age");
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   for(i=1; i<=nlstate;i++)
+   fprintf(ficresvij,"\n");
-     for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   xp=vector(1,npar);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   dnewm=matrix(1,nlstate,1,npar);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   doldm=matrix(1,nlstate,1,nlstate);
-     }
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-  /* fprintf(ficresprob,"\n");
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   fprintf(ficresprobcov,"\n");
-   fprintf(ficresprobcor,"\n");
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-  */
+   gpp=vector(nlstate+1,nlstate+ndeath);
-  xp=vector(1,npar);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+   if(estepm < stepm){
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   first=1;
+   }
-   fprintf(ficgp,"\n# Routine varprob");
+   else  hstepm=estepm;
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   fprintf(fichtm,"\n");
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+      nhstepm is the number of hstepm from age to agelim
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+      nstepm is the number of stepm from age to agelin.
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-   file %s<br>\n",optionfilehtmcov);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+      survival function given by stepm (the optimization length). Unfortunately it
- and drawn. It helps understanding how is the covariance between two incidences.\
+      means that if the survival funtion is printed every two years of age and if
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   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. \
+      results. So we changed our mind and took the option of the best precision.
- 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 \
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
- standard deviations wide on each axis. <br>\
+   agelim = AGESUP;
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   cov[1]=1;
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-   tj=cptcoveff;
+     gp=matrix(0,nhstepm,1,nlstate);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     gm=matrix(0,nhstepm,1,nlstate);
-   j1=0;
-   for(t=1; t<=tj;t++){
-     for(i1=1; i1<=ncodemax[t];i1++){
+     for(theta=1; theta <=npar; theta++){
-       j1++;
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-       if  (cptcovn>0) {
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         fprintf(ficresprob, "\n#********** Variable ");
+       }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         fprintf(ficresprob, "**********\n#\n");
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         fprintf(ficresprobcov, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       if (popbased==1) {
-         fprintf(ficresprobcov, "**********\n#\n");
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-         fprintf(ficgp, "\n#********** Variable ");
+             prlim[i][i]=probs[(int)age][i][ij];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         }else{ /* mobilav */
-         fprintf(ficgp, "**********\n#\n");
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+       }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+       for(j=1; j<= nlstate; j++){
+         for(h=0; h<=nhstepm; h++){
-         fprintf(ficresprobcor, "\n#********** Variable ");
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         fprintf(ficresprobcor, "**********\n#");
+         }
        }
+       /* This for computing probability of death (h=1 means
-       for (age=bage; age<=fage; age ++){
+          computed over hstepm matrices product = hstepm*stepm months)
-         cov[2]=age;
+          as a weighted average of prlim.
-         for (k=1; k<=cptcovn;k++) {
+       */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         }
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-         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]]];
+       /* end probability of death */
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         for(theta=1; theta <=npar; theta++){
+       if (popbased==1) {
-           for(i=1; i<=npar; i++)
+         if(mobilav ==0){
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
-           k=0;
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-           for(i=1; i<= (nlstate); i++){
+         }
-             for(j=1; j<=(nlstate+ndeath);j++){
+       }
-               k=k+1;
-               gp[k]=pmmij[i][j];
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-             }
+         for(h=0; h<=nhstepm; h++){
-           }
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-           for(i=1; i<=npar; i++)
+         }
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+       }
+       /* This for computing probability of death (h=1 means
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+          computed over hstepm matrices product = hstepm*stepm months)
-           k=0;
+          as a weighted average of prlim.
-           for(i=1; i<=(nlstate); i++){
+       */
-             for(j=1; j<=(nlstate+ndeath);j++){
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-               k=k+1;
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-               gm[k]=pmmij[i][j];
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-             }
+       }
-           }
+       /* end probability of death */
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+       for(j=1; j<= nlstate; j++) /* vareij */
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         for(h=0; h<=nhstepm; h++){
-         }
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-           for(theta=1; theta <=npar; theta++)
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-             trgradg[j][theta]=gradg[theta][j];
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       }
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+     } /* End theta */
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+     for(h=0; h<=nhstepm; h++) /* veij */
+       for(j=1; j<=nlstate;j++)
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
-         k=0;
-         for(i=1; i<=(nlstate); i++){
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-           for(j=1; j<=(nlstate+ndeath);j++){
+       for(theta=1; theta <=npar; theta++)
-             k=k+1;
+         trgradgp[j][theta]=gradgp[theta][j];
-             mu[k][(int) age]=pmmij[i][j];
-           }
-         }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+     for(i=1;i<=nlstate;i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+       for(j=1;j<=nlstate;j++)
-             varpij[i][j][(int)age] = doldm[i][j];
+         vareij[i][j][(int)age] =0.;
-         /*printf("\n%d ",(int)age);
+     for(h=0;h<=nhstepm;h++){
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+       for(k=0;k<=nhstepm;k++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-           }*/
+         for(i=1;i<=nlstate;i++)
+           for(j=1;j<=nlstate;j++)
-         fprintf(ficresprob,"\n%d ",(int)age);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+       }
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+     }
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+     /* pptj */
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-         }
+         varppt[j][i]=doldmp[j][i];
-         i=0;
+     /* end ppptj */
-         for (k=1; k<=(nlstate);k++){
+     /*  x centered again */
-           for (l=1; l<=(nlstate+ndeath);l++){
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-             i=i++;
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     if (popbased==1) {
-             for (j=1; j<=i;j++){
+       if(mobilav ==0){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+         for(i=1; i<=nlstate;i++)
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+           prlim[i][i]=probs[(int)age][i][ij];
-             }
+       }else{ /* mobilav */
-           }
+         for(i=1; i<=nlstate;i++)
-         }/* end of loop for state */
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-       } /* end of loop for age */
+       }
+     }
-       /* Confidence intervalle of pij  */
-       /*
+     /* This for computing probability of death (h=1 means
-         fprintf(ficgp,"\nset noparametric;unset label");
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+        as a weighted average of prlim.
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     */
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+     }
-       */
+     /* end probability of death */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-       first1=1;
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       for (k2=1; k2<=(nlstate);k2++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+       for(i=1; i<=nlstate;i++){
-           if(l2==k2) continue;
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-           j=(k2-1)*(nlstate+ndeath)+l2;
+       }
-           for (k1=1; k1<=(nlstate);k1++){
+     }
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+     fprintf(ficresprobmorprev,"\n");
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+     fprintf(ficresvij,"%.0f ",age );
-               if(i<=j) continue;
+     for(i=1; i<=nlstate;i++)
-               for (age=bage; age<=fage; age ++){
+       for(j=1; j<=nlstate;j++){
-                 if ((int)age %5==0){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+       }
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     fprintf(ficresvij,"\n");
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+     free_matrix(gp,0,nhstepm,1,nlstate);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+     free_matrix(gm,0,nhstepm,1,nlstate);
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-                   c12=cv12/sqrt(v1*v2);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-                   /* Computing eigen value of matrix of covariance */
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   } /* End age */
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-                   /* Eigen vectors */
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-                   v21=(lc1-v1)/cv12*v11;
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-                   v12=-v21;
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-                   v22=v11;
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-                   tnalp=v21/v11;
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-                   if(first1==1){
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                     first1=0;
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-                   }
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-                   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,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-                   /*printf(fignu*/
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+   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);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+   /*  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);
-                   if(first==1){
+ */
-                     first=0;
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-                     fprintf(ficgp,"\nset parametric;unset label");
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   free_vector(xp,1,npar);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+   free_matrix(doldm,1,nlstate,1,nlstate);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+   free_matrix(dnewm,1,nlstate,1,npar);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   fclose(ficresprobmorprev);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fflush(ficgp);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   fflush(fichtm);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ }  /* end varevsij */
-                     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",\
-                             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[])
-                   }else{
+ {
-                     first=0;
+   /* Variance of prevalence limit */
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   double **newm;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   double **dnewm,**doldm;
-                     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",\
+   int i, j, nhstepm, hstepm;
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   int k, cptcode;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   double *xp;
-                   }/* if first */
+   double *gp, *gm;
-                 } /* age mod 5 */
+   double **gradg, **trgradg;
-               } /* end loop age */
+   double age,agelim;
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   int theta;
-               first=1;
-             } /*l12 */
+   pstamp(ficresvpl);
-           } /* k12 */
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-         } /*l1 */
+   fprintf(ficresvpl,"# Age");
-       }/* k1 */
+   for(i=1; i<=nlstate;i++)
-     } /* loop covariates */
+       fprintf(ficresvpl," %1d-%1d",i,i);
-   }
+   fprintf(ficresvpl,"\n");
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   xp=vector(1,npar);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   dnewm=matrix(1,nlstate,1,npar);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
-   free_vector(xp,1,npar);
-   fclose(ficresprob);
+   hstepm=1*YEARM; /* Every year of age */
-   fclose(ficresprobcov);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   fclose(ficresprobcor);
+   agelim = AGESUP;
-   fflush(ficgp);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   fflush(fichtmcov);
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- }
+     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     gradg=matrix(1,npar,1,nlstate);
- /******************* Printing html file ***********/
+     gp=vector(1,nlstate);
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+     gm=vector(1,nlstate);
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     for(theta=1; theta <=npar; theta++){
-                   int popforecast, int estepm ,\
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-                   double jprev1, double mprev1,double anprev1, \
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-                   double jprev2, double mprev2,double anprev2){
+       }
-   int jj1, k1, i1, cpt;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       for(i=1;i<=nlstate;i++)
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+         gp[i] = prlim[i][i];
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
- </ul>");
+       for(i=1; i<=npar; i++) /* Computes gradient */
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+       for(i=1;i<=nlstate;i++)
-    fprintf(fichtm,"\
+         gm[i] = prlim[i][i];
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+       for(i=1;i<=nlstate;i++)
-    fprintf(fichtm,"\
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+     } /* End theta */
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-    fprintf(fichtm,"\
+     trgradg =matrix(1,nlstate,1,npar);
-  - (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): \
-    <a href=\"%s\">%s</a> <br>\n",
+     for(j=1; j<=nlstate;j++)
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+       for(theta=1; theta <=npar; theta++)
-    fprintf(fichtm,"\
+         trgradg[j][theta]=gradg[theta][j];
-  - Population projections by age and states: \
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+     for(i=1;i<=nlstate;i++)
+       varpl[i][(int)age] =0.;
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-  m=cptcoveff;
+     for(i=1;i<=nlstate;i++)
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-  jj1=0;
+     fprintf(ficresvpl,"%.0f ",age );
-  for(k1=1; k1<=m;k1++){
+     for(i=1; i<=nlstate;i++)
-    for(i1=1; i1<=ncodemax[k1];i1++){
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-      jj1++;
+     fprintf(ficresvpl,"\n");
-      if (cptcovn > 0) {
+     free_vector(gp,1,nlstate);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+     free_vector(gm,1,nlstate);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+     free_matrix(gradg,1,npar,1,nlstate);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     free_matrix(trgradg,1,nlstate,1,npar);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   } /* End age */
-      }
-      /* Pij */
+   free_vector(xp,1,npar);
-      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> \
+   free_matrix(doldm,1,nlstate,1,npar);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-      /* Quasi-incidences */
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+ }
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ /************ Variance of one-step probabilities  ******************/
-        /* Period (stable) prevalence in each health state */
+ 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[])
-        for(cpt=1; cpt<nlstate;cpt++){
+ {
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+   int i, j=0,  i1, k1, l1, t, tj;
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+   int k2, l2, j1,  z1;
-        }
+   int k=0,l, cptcode;
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   int first=1, first1, first2;
-         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> \
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+   double **dnewm,**doldm;
-      }
+   double *xp;
-    } /* end i1 */
+   double *gp, *gm;
-  }/* End k1 */
+   double **gradg, **trgradg;
-  fprintf(fichtm,"</ul>");
+   double **mu;
+   double age,agelim, cov[NCOVMAX+1];
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-  fprintf(fichtm,"\
+   int theta;
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+   char fileresprob[FILENAMELENGTH];
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   double ***varpij;
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  fprintf(fichtm,"\
+   strcpy(fileresprob,"prob");
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   strcat(fileresprob,fileres);
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprob);
-  fprintf(fichtm,"\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+   }
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+   strcpy(fileresprobcov,"probcov");
-  fprintf(fichtm,"\
+   strcat(fileresprobcov,fileres);
-  - 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): \
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-    <a href=\"%s\">%s</a> <br>\n</li>",
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  fprintf(fichtm,"\
+   }
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+   strcpy(fileresprobcor,"probcor");
-    <a href=\"%s\">%s</a> <br>\n</li>",
+   strcat(fileresprobcor,fileres);
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-  fprintf(fichtm,"\
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-  - 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",
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+   }
-  fprintf(fichtm,"\
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-  - 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",
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-  fprintf(fichtm,"\
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   fprintf(ficresprob,"# Age");
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   pstamp(ficresprobcov);
- /*      <br>",fileres,fileres,fileres,fileres); */
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- /*  else  */
+   fprintf(ficresprobcov,"# Age");
- /*    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); */
+   pstamp(ficresprobcor);
-  fflush(fichtm);
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   fprintf(ficresprobcor,"# Age");
-  m=cptcoveff;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
-  jj1=0;
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-  for(k1=1; k1<=m;k1++){
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-      jj1++;
+     }
-      if (cptcovn > 0) {
+  /* fprintf(ficresprob,"\n");
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   fprintf(ficresprobcov,"\n");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   fprintf(ficresprobcor,"\n");
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+  */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   xp=vector(1,npar);
-      }
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+   first=1;
-      }
+   fprintf(ficgp,"\n# Routine varprob");
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
- health expectancies in states (1) and (2): %s%d.png<br>\
+   fprintf(fichtm,"\n");
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-    } /* end i1 */
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-  }/* End k1 */
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-  fprintf(fichtm,"</ul>");
+   file %s<br>\n",optionfilehtmcov);
-  fflush(fichtm);
+   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.\
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- /******************* Gnuplot file **************/
+   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. \
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ 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 \
-   char dirfileres[132],optfileres[132];
+ standard deviations wide on each axis. <br>\
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-   int ng;
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
- /*     printf("Problem with file %s",optionfilegnuplot); */
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+   cov[1]=1;
- /*   } */
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
-   /*#ifdef windows */
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+   j1=0;
-     /*#endif */
+   for(j1=1; j1<=tj;j1++){
-   m=pow(2,cptcoveff);
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+     /*j1++;*/
-   strcpy(dirfileres,optionfilefiname);
+       if  (cptcovn>0) {
-   strcpy(optfileres,"vpl");
+         fprintf(ficresprob, "\n#********** Variable ");
-  /* 1eme*/
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficresprob, "**********\n#\n");
-    for (k1=1; k1<= m ; k1 ++) {
+         fprintf(ficresprobcov, "\n#********** Variable ");
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+         fprintf(ficresprobcov, "**********\n#\n");
-      fprintf(ficgp,"set xlabel \"Age\" \n\
- set ylabel \"Probability\" \n\
+         fprintf(ficgp, "\n#********** Variable ");
- set ter png small\n\
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- set size 0.65,0.65\n\
+         fprintf(ficgp, "**********\n#\n");
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-      for (i=1; i<= nlstate ; i ++) {
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-      }
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+         fprintf(ficresprobcor, "\n#********** Variable ");
-      for (i=1; i<= nlstate ; i ++) {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficresprobcor, "**********\n#");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-      }
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-      for (i=1; i<= nlstate ; i ++) {
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-      }
+       for (age=bage; age<=fage; age ++){
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+         cov[2]=age;
-    }
+         for (k=1; k<=cptcovn;k++) {
-   }
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-   /*2 eme*/
+                                                          * 1  1 1 1 1
+                                                          * 2  2 1 1 1
-   for (k1=1; k1<= m ; k1 ++) {
+                                                          * 3  1 2 1 1
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+                                                          */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+         }
-     for (i=1; i<= nlstate+1 ; i ++) {
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       k=2*i;
+         for (k=1; k<=cptcovprod;k++)
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for(theta=1; theta <=npar; theta++){
-       }
+           for(i=1; i<=npar; i++)
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           k=0;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+           for(i=1; i<= (nlstate); i++){
-       }
+             for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficgp,"\" t\"\" w l 0,");
+               k=k+1;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+               gp[k]=pmmij[i][j];
-       for (j=1; j<= nlstate+1 ; j ++) {
+             }
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+           }
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       }
+           for(i=1; i<=npar; i++)
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-       else fprintf(ficgp,"\" t\"\" w l 0,");
-     }
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-   }
+           k=0;
+           for(i=1; i<=(nlstate); i++){
-   /*3eme*/
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
-   for (k1=1; k1<= m ; k1 ++) {
+               gm[k]=pmmij[i][j];
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+             }
-       /*       k=2+nlstate*(2*cpt-2); */
+           }
-       k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-       fprintf(ficgp,"set ter png small\n\
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
- set size 0.65,0.65\n\
+         }
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           for(theta=1; theta <=npar; theta++)
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+             trgradg[j][theta]=gradg[theta][j];
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-       */
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-       for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+         k=0;
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
-       }
+             k=k+1;
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+             mu[k][(int) age]=pmmij[i][j];
-     }
+           }
-   }
+         }
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-   /* CV preval stable (period) */
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-   for (k1=1; k1<= m ; k1 ++) {
+             varpij[i][j][(int)age] = doldm[i][j];
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
-       k=3;
+         /*printf("\n%d ",(int)age);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- set ter png small\nset size 0.65,0.65\n\
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- unset log y\n\
+           }*/
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+         fprintf(ficresprob,"\n%d ",(int)age);
-       for (i=1; i< nlstate ; i ++)
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficgp,"+$%d",k+i+1);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-       l=3+(nlstate+ndeath)*cpt;
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-       for (i=1; i< nlstate ; i ++) {
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-         l=3+(nlstate+ndeath)*cpt;
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         fprintf(ficgp,"+$%d",l+i+1);
+         }
-       }
+         i=0;
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+         for (k=1; k<=(nlstate);k++){
-     }
+           for (l=1; l<=(nlstate+ndeath);l++){
-   }
+             i++;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-   /* proba elementaires */
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   for(i=1,jk=1; i <=nlstate; i++){
+             for (j=1; j<=i;j++){
-     for(k=1; k <=(nlstate+ndeath); k++){
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-       if (k != i) {
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-         for(j=1; j <=ncovmodel; j++){
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+             }
-           jk++;
+           }
-           fprintf(ficgp,"\n");
+         }/* end of loop for state */
-         }
+       } /* end of loop for age */
-       }
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-     }
+       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(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-      for(jk=1; jk <=m; jk++) {
+       /* Confidence intervalle of pij  */
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+       /*
-        if (ng==2)
+         fprintf(ficgp,"\nunset parametric;unset label");
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-        else
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-        i=1;
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-        for(k2=1; k2<=nlstate; k2++) {
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-          k3=i;
+       */
-          for(k=1; k<=(nlstate+ndeath); k++) {
-            if (k != k2){
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-              if(ng==2)
+       first1=1;first2=2;
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+       for (k2=1; k2<=(nlstate);k2++){
-              else
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+           if(l2==k2) continue;
-              ij=1;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-              for(j=3; j <=ncovmodel; j++) {
+           for (k1=1; k1<=(nlstate);k1++){
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+               if(l1==k1) continue;
-                  ij++;
+               i=(k1-1)*(nlstate+ndeath)+l1;
-                }
+               if(i<=j) continue;
-                else
+               for (age=bage; age<=fage; age ++){
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                 if ((int)age %5==0){
-              }
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-              fprintf(ficgp,")/(1");
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-              for(k1=1; k1 <=nlstate; k1++){
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-                ij=1;
+                   c12=cv12/sqrt(v1*v2);
-                for(j=3; j <=ncovmodel; j++){
+                   /* Computing eigen value of matrix of covariance */
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                    ij++;
+                   if ((lc2 <0) || (lc1 <0) ){
-                  }
+                     if(first2==1){
-                  else
+                       first1=0;
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-                }
+                     }
-                fprintf(ficgp,")");
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-              }
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+                     /* lc2=fabs(lc2); */
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+                   }
-              i=i+ncovmodel;
-            }
+                   /* Eigen vectors */
-          } /* end k */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-        } /* end k2 */
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-      } /* end jk */
+                   v21=(lc1-v1)/cv12*v11;
-    } /* end ng */
+                   v12=-v21;
-    fflush(ficgp);
+                   v22=v11;
- }  /* end gnuplot */
+                   tnalp=v21/v11;
+                   if(first1==1){
+                     first1=0;
- /*************** Moving average **************/
+                     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);
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+                   }
+                   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);
-   int i, cpt, cptcod;
+                   /*printf(fignu*/
-   int modcovmax =1;
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-   int mobilavrange, mob;
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-   double age;
+                   if(first==1){
+                     first=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+                     fprintf(ficgp,"\nset parametric;unset label");
-                            a covariate has 2 modalities */
+                     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);
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-     if(mobilav==1) mobilavrange=5; /* default */
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-     else mobilavrange=mobilav;
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-     for (age=bage; age<=fage; age++)
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       for (i=1; i<=nlstate;i++)
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-     /* We keep the original values on the extreme ages bage, fage and for
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-        we use a 5 terms etc. until the borders are no more concerned.
+                     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",\
-     */
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+                   }else{
-         for (i=1; i<=nlstate;i++){
+                     first=0;
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                     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",\
-                 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;
+                   }/* if first */
-           }
+                 } /* age mod 5 */
-         }
+               } /* end loop age */
-       }/* end age */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-     }/* end mob */
+               first=1;
-   }else return -1;
+             } /*l12 */
-   return 0;
+           } /* k12 */
- }/* End movingaverage */
+         } /*l1 */
+       }/* k1 */
+       /* } /* loop covariates */
- /************** 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){
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   /* proj1, year, month, day of starting projection
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-      agemin, agemax range of age
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-      anproj2 year of en of projection (same day and month as proj1).
+   free_vector(xp,1,npar);
-   */
+   fclose(ficresprob);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+   fclose(ficresprobcov);
-   int *popage;
+   fclose(ficresprobcor);
-   double agec; /* generic age */
+   fflush(ficgp);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   fflush(fichtmcov);
-   double *popeffectif,*popcount;
+ }
-   double ***p3mat;
-   double ***mobaverage;
-   char fileresf[FILENAMELENGTH];
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   agelim=AGESUP;
+                   int lastpass, int stepm, int weightopt, char model[],\
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   int popforecast, int estepm ,\
-   strcpy(fileresf,"f");
+                   double jprev1, double mprev1,double anprev1, \
-   strcat(fileresf,fileres);
+                   double jprev2, double mprev2,double anprev2){
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+   int jj1, k1, i1, cpt;
-     printf("Problem with forecast resultfile: %s\n", fileresf);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-   }
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+ </ul>");
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+    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 ",
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+    fprintf(fichtm,"\
-   if (mobilav!=0) {
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+    fprintf(fichtm,"\
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-     }
+    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): \
+    <a href=\"%s\">%s</a> <br>\n",
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-   if (stepm<=12) stepsize=1;
+    fprintf(fichtm,"\
-   if(estepm < stepm){
+  - Population projections by age and states: \
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   }
-   else  hstepm=estepm;
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   hstepm=hstepm/stepm;
+  m=pow(2,cptcoveff);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-                                fractional in yp1 */
-   anprojmean=yp;
+  jj1=0;
-   yp2=modf((yp1*12),&yp);
+  for(k1=1; k1<=m;k1++){
-   mprojmean=yp;
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   yp1=modf((yp2*30.5),&yp);
+      jj1++;
-   jprojmean=yp;
+      if (cptcovn > 0) {
-   if(jprojmean==0) jprojmean=1;
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   if(mprojmean==0) jprojmean=1;
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   i1=cptcoveff;
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   if (cptcovn < 1){i1=1;}
+      }
+      /* Pij */
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+      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> \
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+      /* Quasi-incidences */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- /*            if (h==(int)(YEARM*yearp)){ */
+  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> \
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+        /* Period (stable) prevalence in each health state */
-       k=k+1;
+        for(cpt=1; cpt<=nlstate;cpt++){
-       fprintf(ficresf,"\n#******");
+          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> \
-       for(j=1;j<=cptcoveff;j++) {
+ <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,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]]);
+        }
-       }
+      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,"# Covariate valuofcovar yearproj age");
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-       for(j=1; j<=nlstate+ndeath;j++){
+      }
-         for(i=1; i<=nlstate;i++)
+    } /* end i1 */
-           fprintf(ficresf," p%d%d",i,j);
+  }/* End k1 */
-         fprintf(ficresf," p.%d",j);
+  fprintf(fichtm,"</ul>");
-       }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-         fprintf(ficresf,"\n");
+  fprintf(fichtm,"\
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-           nhstepm = nhstepm/hstepm;
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  fprintf(fichtm,"\
-           oldm=oldms;savm=savms;
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-           for (h=0; h<=nhstepm; h++){
+  fprintf(fichtm,"\
-             if (h*hstepm/YEARM*stepm ==yearp) {
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-               fprintf(ficresf,"\n");
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-               for(j=1;j<=cptcoveff;j++)
+  fprintf(fichtm,"\
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+  - 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): \
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+    <a href=\"%s\">%s</a> <br>\n</li>",
-             }
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-             for(j=1; j<=nlstate+ndeath;j++) {
+  fprintf(fichtm,"\
-               ppij=0.;
+  - (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): \
-               for(i=1; i<=nlstate;i++) {
+    <a href=\"%s\">%s</a> <br>\n</li>",
-                 if (mobilav==1)
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+  fprintf(fichtm,"\
-                 else {
+  - 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",
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-                 }
+  fprintf(fichtm,"\
-                 if (h*hstepm/YEARM*stepm== yearp) {
+  - 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",
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-                 }
+  fprintf(fichtm,"\
-               } /* end i */
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-               if (h*hstepm/YEARM*stepm==yearp) {
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-                 fprintf(ficresf," %.3f", ppij);
-               }
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-             }/* end j */
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-           } /* end h */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*      <br>",fileres,fileres,fileres,fileres); */
-         } /* end agec */
+ /*  else  */
-       } /* end yearp */
+ /*    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); */
-     } /* end cptcod */
+  fflush(fichtm);
-   } /* end  cptcov */
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  m=pow(2,cptcoveff);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   fclose(ficresf);
- }
+  jj1=0;
+  for(k1=1; k1<=m;k1++){
- /************** Forecasting *****not tested NB*************/
+    for(i1=1; i1<=ncodemax[k1];i1++){
- 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){
+      jj1++;
+      if (cptcovn > 0) {
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   int *popage;
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   double calagedatem, agelim, kk1, kk2;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   double *popeffectif,*popcount;
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   double ***p3mat,***tabpop,***tabpopprev;
+      }
-   double ***mobaverage;
+      for(cpt=1; cpt<=nlstate;cpt++) {
-   char filerespop[FILENAMELENGTH];
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+      }
-   agelim=AGESUP;
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   strcpy(filerespop,"pop");
+    } /* end i1 */
-   strcat(filerespop,fileres);
+  }/* End k1 */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+  fprintf(fichtm,"</ul>");
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+  fflush(fichtm);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ }
-   }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+ /******************* Gnuplot file **************/
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   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;
-   if (mobilav!=0) {
+   int ng=0;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ /*   } */
-     }
-   }
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*#endif */
-   if (stepm<=12) stepsize=1;
+   m=pow(2,cptcoveff);
-   agelim=AGESUP;
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
-   hstepm=1;
+  /* 1eme*/
-   hstepm=hstepm/stepm;
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-   if (popforecast==1) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-       printf("Problem with population file : %s\n",popfile);exit(0);
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-     }
+ set ylabel \"Probability\" \n\
-     popage=ivector(0,AGESUP);
+ set ter png small size 320, 240\n\
-     popeffectif=vector(0,AGESUP);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-     popcount=vector(0,AGESUP);
+      for (i=1; i<= nlstate ; i ++) {
-     i=1;
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-     imx=i;
+      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);
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+      for (i=1; i<= nlstate ; i ++) {
-   }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+      }
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-       k=k+1;
+      for (i=1; i<= nlstate ; i ++) {
-       fprintf(ficrespop,"\n#******");
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       for(j=1;j<=cptcoveff;j++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
-       }
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-       fprintf(ficrespop,"******\n");
+    }
-       fprintf(ficrespop,"# Age");
+   }
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+   /*2 eme*/
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
+   for (k1=1; k1<= m ; k1 ++) {
-       for (cpt=0; cpt<=0;cpt++) {
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+     for (i=1; i<= nlstate+1 ; i ++) {
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       k=2*i;
-           nhstepm = nhstepm/hstepm;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-           oldm=oldms;savm=savms;
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       }
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-           for (h=0; h<=nhstepm; h++){
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       for (j=1; j<= nlstate+1 ; j ++) {
-             }
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-             for(j=1; j<=nlstate+ndeath;j++) {
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-               kk1=0.;kk2=0;
+       }
-               for(i=1; i<=nlstate;i++) {
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-                 if (mobilav==1)
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+       for (j=1; j<= nlstate+1 ; j ++) {
-                 else {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-                 }
+       }
-               }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-               if (h==(int)(calagedatem+12*cpt)){
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+     }
-                   /*fprintf(ficrespop," %.3f", kk1);
+   }
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
+   /*3eme*/
-             }
-             for(i=1; i<=nlstate;i++){
+   for (k1=1; k1<= m ; k1 ++) {
-               kk1=0.;
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-                 for(j=1; j<=nlstate;j++){
+       /*       k=2+nlstate*(2*cpt-2); */
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+       k=2+(nlstate+1)*(cpt-1);
-                 }
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-             }
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           }
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       }
+       */
-   /******/
+       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+       }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-           nhstepm = nhstepm/hstepm;
+     }
+   }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+   /* CV preval stable (period) */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-           for (h=0; h<=nhstepm; h++){
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       k=3;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+       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);
-             for(j=1; j<=nlstate+ndeath;j++) {
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-               kk1=0.;kk2=0;
+ set ter png small size 320, 240\n\
-               for(i=1; i<=nlstate;i++) {
+ unset log y\n\
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-               }
+       for (i=1; i<= nlstate ; i ++){
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+         if(i==1)
-             }
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-           }
+         else
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           fprintf(ficgp,", '' ");
-         }
+         l=(nlstate+ndeath)*(i-1)+1;
-       }
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-    }
+         for (j=1; j<= (nlstate-1) ; j ++)
-   }
+           fprintf(ficgp,"+$%d",k+l+j);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       } /* nlstate */
+       fprintf(ficgp,"\n");
-   if (popforecast==1) {
+     } /* end cpt state*/
-     free_ivector(popage,0,AGESUP);
+   } /* end covariate */
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
+   /* proba elementaires */
-   }
+   for(i=1,jk=1; i <=nlstate; i++){
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(k=1; k <=(nlstate+ndeath); k++){
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (k != i) {
-   fclose(ficrespop);
+         for(j=1; j <=ncovmodel; j++){
- } /* End of popforecast */
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
- int fileappend(FILE *fichier, char *optionfich)
+           fprintf(ficgp,"\n");
- {
+         }
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+       }
-     printf("Problem with file: %s\n", optionfich);
+     }
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+    }
-     return (0);
+   /*goto avoid;*/
-   }
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   fflush(fichier);
+      for(jk=1; jk <=m; jk++) {
-   return (1);
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
- }
+        if (ng==2)
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
- /**************** function prwizard **********************/
+          fprintf(ficgp,"\nset title \"Probability\"\n");
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
- {
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
-   /* Wizard to print covariance matrix template */
+          k3=i;
+          for(k=1; k<=(nlstate+ndeath); k++) {
-   char ca[32], cb[32], cc[32];
+            if (k != k2){
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+              if(ng==2)
-   int numlinepar;
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+              else
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-   for(i=1; i <=nlstate; i++){
+              for(j=3; j <=ncovmodel; j++) {
-     jj=0;
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-     for(j=1; j <=nlstate+ndeath; j++){
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-       if(j==i) continue;
+                /*        ij++; */
-       jj++;
+                /* } */
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+                /* else */
-       printf("%1d%1d",i,j);
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       fprintf(ficparo,"%1d%1d",i,j);
+              }
-       for(k=1; k<=ncovmodel;k++){
+              fprintf(ficgp,")/(1");
-         /*        printf(" %lf",param[i][j][k]); */
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+              for(k1=1; k1 <=nlstate; k1++){
-         printf(" 0.");
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-         fprintf(ficparo," 0.");
+                ij=1;
-       }
+                for(j=3; j <=ncovmodel; j++){
-       printf("\n");
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-       fprintf(ficparo,"\n");
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-     }
+                  /*   ij++; */
-   }
+                  /* } */
-   printf("# Scales (for hessian or gradient estimation)\n");
+                  /* else */
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                }
-   for(i=1; i <=nlstate; i++){
+                fprintf(ficgp,")");
-     jj=0;
+              }
-     for(j=1; j <=nlstate+ndeath; j++){
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-       if(j==i) continue;
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-       jj++;
+              i=i+ncovmodel;
-       fprintf(ficparo,"%1d%1d",i,j);
+            }
-       printf("%1d%1d",i,j);
+          } /* end k */
-       fflush(stdout);
+        } /* end k2 */
-       for(k=1; k<=ncovmodel;k++){
+      } /* end jk */
-         /*      printf(" %le",delti3[i][j][k]); */
+    } /* end ng */
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+  avoid:
-         printf(" 0.");
+    fflush(ficgp);
-         fprintf(ficparo," 0.");
+ }  /* end gnuplot */
-       }
-       numlinepar++;
-       printf("\n");
+ /*************** Moving average **************/
-       fprintf(ficparo,"\n");
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-     }
-   }
+   int i, cpt, cptcod;
-   printf("# Covariance matrix\n");
+   int modcovmax =1;
- /* # 121 Var(a12)\n\ */
+   int mobilavrange, mob;
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   double age;
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                            a covariate has 2 modalities */
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
- /* # 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" */
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-   fflush(stdout);
+     if(mobilav==1) mobilavrange=5; /* default */
-   fprintf(ficparo,"# Covariance matrix\n");
+     else mobilavrange=mobilav;
-   /* # 121 Var(a12)\n\ */
+     for (age=bage; age<=fage; age++)
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+       for (i=1; i<=nlstate;i++)
-   /* #   ...\n\ */
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
-   for(itimes=1;itimes<=2;itimes++){
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-     jj=0;
+        we use a 5 terms etc. until the borders are no more concerned.
-     for(i=1; i <=nlstate; i++){
+     */
-       for(j=1; j <=nlstate+ndeath; j++){
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-         if(j==i) continue;
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-         for(k=1; k<=ncovmodel;k++){
+         for (i=1; i<=nlstate;i++){
-           jj++;
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-           ca[0]= k+'a'-1;ca[1]='\0';
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-           if(itimes==1){
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-             printf("#%1d%1d%d",i,j,k);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-           }else{
+               }
-             printf("%1d%1d%d",i,j,k);
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+           }
-             /*  printf(" %.5le",matcov[i][j]); */
+         }
-           }
+       }/* end age */
-           ll=0;
+     }/* end mob */
-           for(li=1;li <=nlstate; li++){
+   }else return -1;
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+   return 0;
-               if(lj==li) continue;
+ }/* End movingaverage */
-               for(lk=1;lk<=ncovmodel;lk++){
-                 ll++;
-                 if(ll<=jj){
+ /************** Forecasting ******************/
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+ 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){
-                   if(ll<jj){
+   /* proj1, year, month, day of starting projection
-                     if(itimes==1){
+      agemin, agemax range of age
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+      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 */
-                   }else{
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-                     if(itimes==1){
+   double *popeffectif,*popcount;
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+   double ***p3mat;
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+   double ***mobaverage;
-                     }else{
+   char fileresf[FILENAMELENGTH];
-                       printf(" 0.");
-                       fprintf(ficparo," 0.");
+   agelim=AGESUP;
-                     }
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-                   }
-                 }
+   strcpy(fileresf,"f");
-               } /* end lk */
+   strcat(fileresf,fileres);
-             } /* end lj */
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-           } /* end li */
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-           printf("\n");
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-           fprintf(ficparo,"\n");
+   }
-           numlinepar++;
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-         } /* end k*/
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-       } /*end j */
-     } /* end i */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   } /* end itimes */
+   if (mobilav!=0) {
- } /* end of prwizard */
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /******************* Gompertz Likelihood ******************************/
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- double gompertz(double x[])
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- {
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   double A,B,L=0.0,sump=0.,num=0.;
+     }
-   int i,n=0; /* n is the size of the sample */
+   }
-   for (i=0;i<=imx-1 ; i++) {
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-     sump=sump+weight[i];
+   if (stepm<=12) stepsize=1;
-     /*    sump=sump+1;*/
+   if(estepm < stepm){
-     num=num+1;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
    }
+   else  hstepm=estepm;
-   /* for (i=0; i<=imx; i++)
+   hstepm=hstepm/stepm;
-      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]);*/
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
-   for (i=1;i<=imx ; i++)
+   anprojmean=yp;
-     {
+   yp2=modf((yp1*12),&yp);
-       if (cens[i] == 1 && wav[i]>1)
+   mprojmean=yp;
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
-       if (cens[i] == 0 && wav[i]>1)
+   if(jprojmean==0) jprojmean=1;
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   if(mprojmean==0) jprojmean=1;
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+   i1=cptcoveff;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   if (cptcovn < 1){i1=1;}
-       if (wav[i] > 1 ) { /* ??? */
-         L=L+A*weight[i];
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-         /*      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(ficresf,"#****** Routine prevforecast **\n");
-     }
+ /*            if (h==(int)(YEARM*yearp)){ */
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-   return -2*L*num/sump;
+       k=k+1;
- }
+       fprintf(ficresf,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
- /******************* Printing html file ***********/
+         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]]);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+       }
-                   int lastpass, int stepm, int weightopt, char model[],\
+       fprintf(ficresf,"******\n");
-                   int imx,  double p[],double **matcov,double agemortsup){
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   int i,k;
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
-   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," p%d%d",i,j);
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+         fprintf(ficresf," p.%d",j);
-   for (i=1;i<=2;i++)
+       }
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+         fprintf(ficresf,"\n");
-   fprintf(fichtm,"</ul>");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+         for (agec=fage; agec>=(ageminpar-1); agec--){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-  for (k=agegomp;k<(agemortsup-2);k++)
+           oldm=oldms;savm=savms;
-    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]);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
-   fflush(fichtm);
+             if (h*hstepm/YEARM*stepm ==yearp) {
- }
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
- /******************* Gnuplot file **************/
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+             }
-   char dirfileres[132],optfileres[132];
+             for(j=1; j<=nlstate+ndeath;j++) {
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+               ppij=0.;
-   int ng;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-   /*#ifdef windows */
+                 else {
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-     /*#endif */
+                 }
+                 if (h*hstepm/YEARM*stepm== yearp) {
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-   strcpy(dirfileres,optionfilefiname);
+                 }
-   strcpy(optfileres,"vpl");
+               } /* end i */
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+               if (h*hstepm/YEARM*stepm==yearp) {
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+                 fprintf(ficresf," %.3f", ppij);
-   fprintf(ficgp, "set ter png small\n set log y\n");
+               }
-   fprintf(ficgp, "set size 0.65,0.65\n");
+             }/* end j */
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+           } /* end h */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- }
+         } /* end agec */
+       } /* end yearp */
+     } /* end cptcod */
+   } /* end  cptcov */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /***********************************************/
- /**************** Main Program *****************/
+   fclose(ficresf);
- /***********************************************/
+ }
- int main(int argc, char *argv[])
+ /************** 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){
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   int linei, month, year,iout;
+   int *popage;
-   int jj, ll, li, lj, lk, imk;
+   double calagedatem, agelim, kk1, kk2;
-   int numlinepar=0; /* Current linenumber of parameter file */
+   double *popeffectif,*popcount;
-   int itimes;
+   double ***p3mat,***tabpop,***tabpopprev;
-   int NDIM=2;
+   double ***mobaverage;
+   char filerespop[FILENAMELENGTH];
-   char ca[32], cb[32], cc[32];
-   char dummy[]="                         ";
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /*  FILE *fichtm; *//* Html File */
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /* FILE *ficgp;*/ /*Gnuplot File */
+   agelim=AGESUP;
-   struct stat info;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   double agedeb, agefin,hf;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   double fret;
-   double **xi,tmp,delta;
+   strcpy(filerespop,"pop");
+   strcat(filerespop,fileres);
-   double dum; /* Dummy variable */
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-   double ***p3mat;
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   double ***mobaverage;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   int *indx;
+   }
-   char line[MAXLINE], linepar[MAXLINE];
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+   if (mobilav!=0) {
-   int c,  h , cpt,l;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int ju,jl, mi;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+     }
-   int mobilav=0,popforecast=0;
+   }
-   int hstepm, nhstepm;
-   int agemortsup;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   float  sumlpop=0.;
+   if (stepm<=12) stepsize=1;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   agelim=AGESUP;
-   double bage, fage, age, agelim, agebase;
+   hstepm=1;
-   double ftolpl=FTOL;
+   hstepm=hstepm/stepm;
-   double **prlim;
-   double *severity;
+   if (popforecast==1) {
-   double ***param; /* Matrix of parameters */
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-   double  *p;
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   double **matcov; /* Matrix of covariance */
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   double ***delti3; /* Scale */
+     }
-   double *delti; /* Scale */
+     popage=ivector(0,AGESUP);
-   double ***eij, ***vareij;
+     popeffectif=vector(0,AGESUP);
-   double **varpl; /* Variances of prevalence limits by age */
+     popcount=vector(0,AGESUP);
-   double *epj, vepp;
-   double kk1, kk2;
+     i=1;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   double **ximort;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+     imx=i;
-   int *dcwave;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
-   char z[1]="c", occ;
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-   char  *strt, strtend[80];
+       k=k+1;
-   char *stratrunc;
+       fprintf(ficrespop,"\n#******");
-   int lstra;
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   long total_usecs;
+       }
+       fprintf(ficrespop,"******\n");
- /*   setlocale (LC_ALL, ""); */
+       fprintf(ficrespop,"# Age");
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- /*   textdomain (PACKAGE); */
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
- /*   setlocale (LC_CTYPE, ""); */
- /*   setlocale (LC_MESSAGES, ""); */
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   (void) gettimeofday(&start_time,&tzp);
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   curr_time=start_time;
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   tm = *localtime(&start_time.tv_sec);
+           nhstepm = nhstepm/hstepm;
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
- /*  printf("Localtime (at start)=%s",strstart); */
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- /*  tp.tv_sec = tp.tv_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+           for (h=0; h<=nhstepm; h++){
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+             if (h==(int) (calagedatem+YEARM*cpt)) {
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+             }
- /*   tp.tv_sec = mktime(&tmg); */
+             for(j=1; j<=nlstate+ndeath;j++) {
- /*   strt=asctime(&tmg); */
+               kk1=0.;kk2=0;
- /*   printf("Time(after) =%s",strstart);  */
+               for(i=1; i<=nlstate;i++) {
- /*  (void) time (&time_value);
+                 if (mobilav==1)
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
- *  tm = *localtime(&time_value);
+                 else {
- *  strstart=asctime(&tm);
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+                 }
- */
+               }
+               if (h==(int)(calagedatem+12*cpt)){
-   nberr=0; /* Number of errors and warnings */
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   nbwarn=0;
+                   /*fprintf(ficrespop," %.3f", kk1);
-   getcwd(pathcd, size);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
-   printf("\n%s\n%s",version,fullversion);
+             }
-   if(argc <=1){
+             for(i=1; i<=nlstate;i++){
-     printf("\nEnter the parameter file name: ");
+               kk1=0.;
-     fgets(pathr,FILENAMELENGTH,stdin);
+                 for(j=1; j<=nlstate;j++){
-     i=strlen(pathr);
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-     if(pathr[i-1]=='\n')
+                 }
-       pathr[i-1]='\0';
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-    for (tok = pathr; tok != NULL; ){
+             }
-       printf("Pathr |%s|\n",pathr);
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-       printf("val= |%s| pathr=%s\n",val,pathr);
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-       strcpy (pathtot, val);
+           }
-       if(pathr[0] == '\0') break; /* Dirty */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     }
+         }
-   }
+       }
-   else{
-     strcpy(pathtot,argv[1]);
+   /******/
-   }
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   /*cygwin_split_path(pathtot,path,optionfile);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   /* cutv(path,optionfile,pathtot,'\\');*/
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   /* Split argv[0], imach program to get pathimach */
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+           oldm=oldms;savm=savms;
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-  /*   strcpy(pathimach,argv[0]); */
+           for (h=0; h<=nhstepm; h++){
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+             }
-   chdir(path); /* Can be a relative path */
+             for(j=1; j<=nlstate+ndeath;j++) {
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+               kk1=0.;kk2=0;
-     printf("Current directory %s!\n",pathcd);
+               for(i=1; i<=nlstate;i++) {
-   strcpy(command,"mkdir ");
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   strcat(command,optionfilefiname);
+               }
-   if((outcmd=system(command)) != 0){
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+             }
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+           }
-     /* fclose(ficlog); */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*     exit(1); */
+         }
-   }
+       }
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+    }
- /*     perror("mkdir"); */
+   }
- /*   } */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /*-------- arguments in the command line --------*/
+   if (popforecast==1) {
-   /* Log file */
+     free_ivector(popage,0,AGESUP);
-   strcat(filelog, optionfilefiname);
+     free_vector(popeffectif,0,AGESUP);
-   strcat(filelog,".log");    /* */
+     free_vector(popcount,0,AGESUP);
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+   }
-     printf("Problem with logfile %s\n",filelog);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     goto end;
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   }
+   fclose(ficrespop);
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+ } /* End of popforecast */
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+ int fileappend(FILE *fichier, char *optionfich)
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+ {
-  path=%s \n\
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-  optionfile=%s\n\
+     printf("Problem with file: %s\n", optionfich);
-  optionfilext=%s\n\
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+     return (0);
+   }
-   printf("Local time (at start):%s",strstart);
+   fflush(fichier);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+   return (1);
-   fflush(ficlog);
+ }
- /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+ /**************** function prwizard **********************/
-   /* */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   strcpy(fileres,"r");
+ {
-   strcat(fileres, optionfilefiname);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+   /* Wizard to print covariance matrix template */
-   /*---------arguments file --------*/
+   char ca[32], cb[32], cc[32];
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+   int numlinepar;
-     printf("Problem with optionfile %s\n",optionfile);
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fflush(ficlog);
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     goto end;
+   for(i=1; i <=nlstate; i++){
-   }
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
+       jj++;
-   strcpy(filereso,"o");
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   strcat(filereso,fileres);
+       printf("%1d%1d",i,j);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+       fprintf(ficparo,"%1d%1d",i,j);
-     printf("Problem with Output resultfile: %s\n", filereso);
+       for(k=1; k<=ncovmodel;k++){
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+         /*        printf(" %lf",param[i][j][k]); */
-     fflush(ficlog);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-     goto end;
+         printf(" 0.");
-   }
+         fprintf(ficparo," 0.");
+       }
-   /* Reads comments: lines beginning with '#' */
+       printf("\n");
-   numlinepar=0;
+       fprintf(ficparo,"\n");
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-     ungetc(c,ficpar);
+   }
-     fgets(line, MAXLINE, ficpar);
+   printf("# Scales (for hessian or gradient estimation)\n");
-     numlinepar++;
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-     puts(line);
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-     fputs(line,ficparo);
+   for(i=1; i <=nlstate; i++){
-     fputs(line,ficlog);
+     jj=0;
-   }
+     for(j=1; j <=nlstate+ndeath; j++){
-   ungetc(c,ficpar);
+       if(j==i) continue;
+       jj++;
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+       fprintf(ficparo,"%1d%1d",i,j);
-   numlinepar++;
+       printf("%1d%1d",i,j);
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+       fflush(stdout);
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       for(k=1; k<=ncovmodel;k++){
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+         /*      printf(" %le",delti3[i][j][k]); */
-   fflush(ficlog);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+         printf(" 0.");
-     ungetc(c,ficpar);
+         fprintf(ficparo," 0.");
-     fgets(line, MAXLINE, ficpar);
+       }
-     numlinepar++;
+       numlinepar++;
-     puts(line);
+       printf("\n");
-     fputs(line,ficparo);
+       fprintf(ficparo,"\n");
-     fputs(line,ficlog);
+     }
    }
-   ungetc(c,ficpar);
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   covar=matrix(0,NCOVMAX,1,n);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+ /* # 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\ */
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   /* # 121 Var(a12)\n\ */
-   delti=delti3[1][1];
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   /* #   ...\n\ */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   for(itimes=1;itimes<=2;itimes++){
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     jj=0;
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     for(i=1; i <=nlstate; i++){
-     fclose (ficparo);
+       for(j=1; j <=nlstate+ndeath; j++){
-     fclose (ficlog);
+         if(j==i) continue;
-     goto end;
+         for(k=1; k<=ncovmodel;k++){
-     exit(0);
+           jj++;
-   }
+           ca[0]= k+'a'-1;ca[1]='\0';
-   else if(mle==-3) {
+           if(itimes==1){
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+             printf("#%1d%1d%d",i,j,k);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+           }else{
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+             printf("%1d%1d%d",i,j,k);
-     matcov=matrix(1,npar,1,npar);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-   }
+             /*  printf(" %.5le",matcov[i][j]); */
-   else{
+           }
-     /* Read guess parameters */
+           ll=0;
-     /* Reads comments: lines beginning with '#' */
+           for(li=1;li <=nlstate; li++){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-       ungetc(c,ficpar);
+               if(lj==li) continue;
-       fgets(line, MAXLINE, ficpar);
+               for(lk=1;lk<=ncovmodel;lk++){
-       numlinepar++;
+                 ll++;
-       puts(line);
+                 if(ll<=jj){
-       fputs(line,ficparo);
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-       fputs(line,ficlog);
+                   if(ll<jj){
-     }
+                     if(itimes==1){
-     ungetc(c,ficpar);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+                     }else{
-     for(i=1; i <=nlstate; i++){
+                       printf(" 0.");
-       j=0;
+                       fprintf(ficparo," 0.");
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+                     }
-         if(jj==i) continue;
+                   }else{
-         j++;
+                     if(itimes==1){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-         if ((i1 != i) && (j1 != j)){
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-           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);
+                     }
-         }
+                   }
-         fprintf(ficparo,"%1d%1d",i1,j1);
+                 }
-         if(mle==1)
+               } /* end lk */
-           printf("%1d%1d",i,j);
+             } /* end lj */
-         fprintf(ficlog,"%1d%1d",i,j);
+           } /* end li */
-         for(k=1; k<=ncovmodel;k++){
+           printf("\n");
-           fscanf(ficpar," %lf",&param[i][j][k]);
+           fprintf(ficparo,"\n");
-           if(mle==1){
+           numlinepar++;
-             printf(" %lf",param[i][j][k]);
+         } /* end k*/
-             fprintf(ficlog," %lf",param[i][j][k]);
+       } /*end j */
-           }
+     } /* end i */
-           else
+   } /* end itimes */
-             fprintf(ficlog," %lf",param[i][j][k]);
-           fprintf(ficparo," %lf",param[i][j][k]);
+ } /* end of prwizard */
-         }
+ /******************* Gompertz Likelihood ******************************/
-         fscanf(ficpar,"\n");
+ double gompertz(double x[])
-         numlinepar++;
+ {
-         if(mle==1)
+   double A,B,L=0.0,sump=0.,num=0.;
-           printf("\n");
+   int i,n=0; /* n is the size of the sample */
-         fprintf(ficlog,"\n");
-         fprintf(ficparo,"\n");
+   for (i=0;i<=imx-1 ; i++) {
-       }
+     sump=sump+weight[i];
-     }
+     /*    sump=sump+1;*/
-     fflush(ficlog);
+     num=num+1;
+   }
-     p=param[1][1];
-     /* Reads comments: lines beginning with '#' */
+   /* for (i=0; i<=imx; i++)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+      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]);*/
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   for (i=1;i<=imx ; i++)
-       numlinepar++;
+     {
-       puts(line);
+       if (cens[i] == 1 && wav[i]>1)
-       fputs(line,ficparo);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-       fputs(line,ficlog);
-     }
+       if (cens[i] == 0 && wav[i]>1)
-     ungetc(c,ficpar);
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-     for(i=1; i <=nlstate; i++){
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       if (wav[i] > 1 ) { /* ??? */
-         if ((i1-i)*(j1-j)!=0){
+         L=L+A*weight[i];
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+         /*      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]);*/
-           exit(1);
+       }
-         }
+     }
-         printf("%1d%1d",i,j);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-         fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
+   return -2*L*num/sump;
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+ }
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+ #ifdef GSL
-           fprintf(ficlog," %le",delti3[i][j][k]);
+ /******************* Gompertz_f Likelihood ******************************/
-         }
+ double gompertz_f(const gsl_vector *v, void *params)
-         fscanf(ficpar,"\n");
+ {
-         numlinepar++;
+   double A,B,LL=0.0,sump=0.,num=0.;
-         printf("\n");
+   double *x= (double *) v->data;
-         fprintf(ficparo,"\n");
+   int i,n=0; /* n is the size of the sample */
-         fprintf(ficlog,"\n");
-       }
+   for (i=0;i<=imx-1 ; i++) {
-     }
+     sump=sump+weight[i];
-     fflush(ficlog);
+     /*    sump=sump+1;*/
+     num=num+1;
-     delti=delti3[1][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 (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]);*/
-     /* Reads comments: lines beginning with '#' */
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   for (i=1;i<=imx ; i++)
-       ungetc(c,ficpar);
+     {
-       fgets(line, MAXLINE, ficpar);
+       if (cens[i] == 1 && wav[i]>1)
-       numlinepar++;
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       puts(line);
-       fputs(line,ficparo);
+       if (cens[i] == 0 && wav[i]>1)
-       fputs(line,ficlog);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-     }
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-     ungetc(c,ficpar);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     matcov=matrix(1,npar,1,npar);
+       if (wav[i] > 1 ) { /* ??? */
-     for(i=1; i <=npar; i++){
+         LL=LL+A*weight[i];
-       fscanf(ficpar,"%s",&str);
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-       if(mle==1)
+       }
-         printf("%s",str);
+     }
-       fprintf(ficlog,"%s",str);
-       fprintf(ficparo,"%s",str);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-       for(j=1; j <=i; j++){
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-         fscanf(ficpar," %le",&matcov[i][j]);
-         if(mle==1){
+   return -2*LL*num/sump;
-           printf(" %.5le",matcov[i][j]);
+ }
-         }
+ #endif
-         fprintf(ficlog," %.5le",matcov[i][j]);
-         fprintf(ficparo," %.5le",matcov[i][j]);
+ /******************* Printing html file ***********/
-       }
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-       fscanf(ficpar,"\n");
+                   int lastpass, int stepm, int weightopt, char model[],\
-       numlinepar++;
+                   int imx,  double p[],double **matcov,double agemortsup){
-       if(mle==1)
+   int i,k;
-         printf("\n");
-       fprintf(ficlog,"\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(ficparo,"\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++)
-     for(i=1; i <=npar; i++)
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-       for(j=i+1;j<=npar;j++)
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-         matcov[i][j]=matcov[j][i];
+   fprintf(fichtm,"</ul>");
-     if(mle==1)
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-       printf("\n");
-     fprintf(ficlog,"\n");
+  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
-     fflush(ficlog);
+  for (k=agegomp;k<(agemortsup-2);k++)
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+   fflush(fichtm);
-     strcat(rfileres,".");    /* */
+ }
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+ /******************* Gnuplot file **************/
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     }
+   char dirfileres[132],optfileres[132];
-     fprintf(ficres,"#%s\n",version);
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   }    /* End of mle != -3 */
+   int ng;
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+   /*#ifdef windows */
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+     /*#endif */
-   }
-   n= lastobs;
+   strcpy(dirfileres,optionfilefiname);
-   severity = vector(1,maxwav);
+   strcpy(optfileres,"vpl");
-   outcome=imatrix(1,maxwav+1,1,n);
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   num=lvector(1,n);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   moisnais=vector(1,n);
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-   annais=vector(1,n);
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-   moisdc=vector(1,n);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-   andc=vector(1,n);
-   agedc=vector(1,n);
+ }
-   cod=ivector(1,n);
-   weight=vector(1,n);
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ {
-   mint=matrix(1,maxwav,1,n);
-   anint=matrix(1,maxwav,1,n);
+   /*-------- data file ----------*/
-   s=imatrix(1,maxwav+1,1,n);
+   FILE *fic;
-   tab=ivector(1,NCOVMAX);
+   char dummy[]="                         ";
-   ncodemax=ivector(1,8);
+   int i, j, n;
+   int linei, month, year,iout;
-   i=1;
+   char line[MAXLINE], linetmp[MAXLINE];
-   linei=0;
+   char stra[80], strb[80];
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+   char *stratrunc;
-     linei=linei+1;
+   int lstra;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-       if(line[j] == '\t')
-         line[j] = ' ';
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     }
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       ;
+   }
-     };
-     line[j+1]=0;  /* Trims blanks at end of line */
+   i=1;
-     if(line[0]=='#'){
+   linei=0;
-       fprintf(ficlog,"Comment line\n%s\n",line);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       printf("Comment line\n%s\n",line);
+     linei=linei+1;
-       continue;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     }
+       if(line[j] == '\t')
+         line[j] = ' ';
-     for (j=maxwav;j>=1;j--){
+     }
-       cutv(stra, strb,line,' ');
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       errno=0;
+       ;
-       lval=strtol(strb,&endptr,10);
+     };
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     line[j+1]=0;  /* Trims blanks at end of line */
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     if(line[0]=='#'){
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+       fprintf(ficlog,"Comment line\n%s\n",line);
-         exit(1);
+       printf("Comment line\n%s\n",line);
-       }
+       continue;
-       s[j][i]=lval;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       strcpy(line,stra);
+     for (j=0; line[j]!='\0';j++){
-       cutv(stra, strb,line,' ');
+       line[j]=linetmp[j];
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
-       }
-       else  if(iout=sscanf(strb,"%s.") != 0){
-         month=99;
+     for (j=maxwav;j>=1;j--){
-         year=9999;
+       cutv(stra, strb, line, ' ');
-       }else{
+       if(strb[0]=='.') { /* Missing status */
-         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);
+         lval=-1;
-         exit(1);
+       }else{
-       }
+         errno=0;
-       anint[j][i]= (double) year;
+         lval=strtol(strb,&endptr,10);
-       mint[j][i]= (double)month;
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       strcpy(line,stra);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     } /* ENd Waves */
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
-     cutv(stra, strb,line,' ');
+           return 1;
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         }
-     }
+       }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+       s[j][i]=lval;
-       month=99;
-       year=9999;
+       strcpy(line,stra);
-     }else{
+       cutv(stra, strb,line,' ');
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       exit(1);
+       }
-     }
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     andc[i]=(double) year;
+         month=99;
-     moisdc[i]=(double) month;
+         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 interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     cutv(stra, strb,line,' ');
+         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);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         return 1;
-     }
+       }
-     else  if(iout=sscanf(strb,"%s.") != 0){
+       anint[j][i]= (double) year;
-       month=99;
+       mint[j][i]= (double)month;
-       year=9999;
+       strcpy(line,stra);
-     }else{
+     } /* ENd Waves */
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
-       exit(1);
+     cutv(stra, strb,line,' ');
-     }
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     annais[i]=(double)(year);
+     }
-     moisnais[i]=(double)(month);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     strcpy(line,stra);
+       month=99;
+       year=9999;
-     cutv(stra, strb,line,' ');
+     }else{
-     errno=0;
+       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);
-     dval=strtod(strb,&endptr);
+         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);
-     if( strb[0]=='\0' || (*endptr != '\0')){
+         return 1;
-       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);
+     andc[i]=(double) year;
-     }
+     moisdc[i]=(double) month;
-     weight[i]=dval;
+     strcpy(line,stra);
-     strcpy(line,stra);
+     cutv(stra, strb,line,' ');
-     for (j=ncovcol;j>=1;j--){
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       cutv(stra, strb,line,' ');
+     }
-       errno=0;
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-       lval=strtol(strb,&endptr,10);
+       month=99;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       year=9999;
-         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);
+     }else{
-         exit(1);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-       }
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-       if(lval <-1 || lval >1){
+         return 1;
-         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 \
+     if (year==9999) {
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-  For example, for multinomial values like 1, 2 and 3,\n \
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
-  build V1=0 V2=0 for the reference value (1),\n \
+         return 1;
-         V1=1 V2=0 for (2) \n \
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+     }
-  output of IMaCh is often meaningless.\n \
+     annais[i]=(double)(year);
-  Exiting.\n",lval,linei, i,line,j);
+     moisnais[i]=(double)(month);
-         exit(1);
+     strcpy(line,stra);
-       }
-       covar[j][i]=(double)(lval);
+     cutv(stra, strb,line,' ');
-       strcpy(line,stra);
+     errno=0;
-     }
+     dval=strtod(strb,&endptr);
-     lstra=strlen(stra);
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       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);
-       stratrunc = &(stra[lstra-9]);
+       fflush(ficlog);
-       num[i]=atol(stratrunc);
+       return 1;
      }
-     else
+     weight[i]=dval;
-       num[i]=atol(stra);
+     strcpy(line,stra);
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+     for (j=ncovcol;j>=1;j--){
+       cutv(stra, strb,line,' ');
-     i=i+1;
+       if(strb[0]=='.') { /* Missing status */
-   } /* End loop reading  data */
+         lval=-1;
-   fclose(fic);
+       }else{
-   /* printf("ii=%d", ij);
+         errno=0;
-      scanf("%d",i);*/
+         lval=strtol(strb,&endptr,10);
-   imx=i-1; /* Number of individuals */
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-   /* for (i=1; i<=imx; i++){
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+           return 1;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+         }
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+       }
-     }*/
+       if(lval <-1 || lval >1){
-    /*  for (i=1; i<=imx; i++){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-      if (s[4][i]==9)  s[4][i]=-1;
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-      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]));}*/
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+  For example, for multinomial values like 1, 2 and 3,\n \
-   /* for (i=1; i<=imx; i++) */
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-      else weight[i]=1;*/
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
-   /* Calculation of the number of parameters from char model */
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   Tprod=ivector(1,15);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-   Tvaraff=ivector(1,15);
+  For example, for multinomial values like 1, 2 and 3,\n \
-   Tvard=imatrix(1,15,1,2);
+  build V1=0 V2=0 for the reference value (1),\n \
-   Tage=ivector(1,15);
+         V1=1 V2=0 for (2) \n \
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+  output of IMaCh is often meaningless.\n \
-     j=0, j1=0, k1=1, k2=1;
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-     j=nbocc(model,'+'); /* j=Number of '+' */
+         return 1;
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+       }
-     cptcovn=j+1;
+       covar[j][i]=(double)(lval);
-     cptcovprod=j1; /*Number of products */
+       strcpy(line,stra);
+     }
-     strcpy(modelsav,model);
+     lstra=strlen(stra);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-       printf("Error. Non available option model=%s ",model);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+       stratrunc = &(stra[lstra-9]);
-       goto end;
+       num[i]=atol(stratrunc);
      }
+     else
-     /* This loop fills the array Tvar from the string 'model'.*/
+       num[i]=atol(stra);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-     for(i=(j+1); i>=1;i--){
+       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(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+     i=i+1;
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+   } /* End loop reading  data */
-       /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /* Model includes a product */
+   *imax=i-1; /* Number of individuals */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+   fclose(fic);
-         if (strcmp(strc,"age")==0) { /* Vn*age */
-           cptcovprod--;
+   return (0);
-           cutv(strb,stre,strd,'V');
+   endread:
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+     printf("Exiting readdata: ");
-           cptcovage++;
+     fclose(fic);
-             Tage[cptcovage]=i;
+     return (1);
-             /*printf("stre=%s ", stre);*/
-         }
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+ }
-           cutv(strb,stre,strc,'V');
+ void removespace(char *str) {
-           Tvar[i]=atoi(stre);
+   char *p1 = str, *p2 = str;
-           cptcovage++;
+   do
-           Tage[cptcovage]=i;
+     while (*p2 == ' ')
-         }
+       p2++;
-         else {  /* Age is not in the model */
+   while (*p1++ = *p2++);
-           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 */
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-           Tprod[k1]=i;
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-           Tvard[k1][1]=atoi(strc); /* m*/
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-           Tvard[k1][2]=atoi(stre); /* n */
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+    * - cptcovage number of covariates with age*products =2
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+    * - cptcovs number of simple covariates
-           for (k=1; k<=lastobs;k++)
+    * - 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
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+    *     which is a new column after the 9 (ncovcol) variables.
-           k1++;
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-           k2=k2+2;
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-         }
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-       }
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-       else { /* no more sum */
+  */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ {
-        /*  scanf("%d",i);*/
+   int i, j, k, ks;
-       cutv(strd,strc,strb,'V');
+   int i1, j1, k1, k2;
-       Tvar[i]=atoi(strc);
+   char modelsav[80];
-       }
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-       strcpy(modelsav,stra);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+   /*removespace(model);*/
-         scanf("%d",i);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-     } /* end of loop + */
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-   } /* end model */
+     j=nbocc(model,'+'); /**< j=Number of '+' */
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
+                   /* including age products which are counted in cptcovage.
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-   printf("cptcovprod=%d ", cptcovprod);
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+     strcpy(modelsav,model);
-   scanf("%d ",i);*/
+     if (strstr(model,"AGE") !=0){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-     /*  if(mle==1){*/
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-   if (weightopt != 1) { /* Maximisation without weights*/
+       return 1;
-     for(i=1;i<=n;i++) weight[i]=1.0;
+     }
-   }
+     if (strstr(model,"v") !=0){
-     /*-calculation of age at interview from date of interview and age at death -*/
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-   agev=matrix(1,maxwav,1,imx);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
+       return 1;
-   for (i=1; i<=imx; i++) {
+     }
-     for(m=2; (m<= maxwav); m++) {
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+     /*   Design
-         anint[m][i]=9999;
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-         s[m][i]=-1;
+      *  <          ncovcol=8                >
-       }
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+      *   k=  1    2      3       4     5       6      7        8
-         nberr++;
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-         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);
+      *  covar[k,i], value of kth covariate if not including age for individual 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);
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-         s[m][i]=-1;
+      *  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
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+      *  Tage[++cptcovage]=k
-         nberr++;
+      *       if products, new covar are created after ncovcol with k1
-         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]);
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-         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]);
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
-       }
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-     }
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-   }
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+      *  <          ncovcol=8                >
-   for (i=1; i<=imx; i++)  {
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-     for(m=firstpass; (m<= lastpass); m++){
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         if (s[m][i] >= nlstate+1) {
+      * p Tprod[1]@2={                         6, 5}
-           if(agedc[i]>0)
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-               agev[m][i]=agedc[i];
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+      *How to reorganize?
-             else {
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-               if ((int)andc[i]!=9999){
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-                 nbwarn++;
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+      * Struct []
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+      */
-                 agev[m][i]=-1;
-               }
+     /* This loop fills the array Tvar from the string 'model'.*/
-             }
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-         }
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-                                  years but with the precision of a month */
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+     /*  k=1 Tvar[1]=2 (from V2) */
-             agev[m][i]=1;
+     /*  k=5 Tvar[5] */
-           else if(agev[m][i] <agemin){
+     /* for (k=1; k<=cptcovn;k++) { */
-             agemin=agev[m][i];
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+     /*  } */
-           }
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           else if(agev[m][i] >agemax){
+     /*
-             agemax=agev[m][i];
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-           }
+         Tvar[k]=0;
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+     cptcovage=0;
-           /*     agev[m][i] = age[i]+2*m;*/
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-         }
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-         else { /* =9 */
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-           agev[m][i]=1;
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-           s[m][i]=-1;
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-         }
+       /*scanf("%d",i);*/
-       }
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-       else /*= 0 Unknown */
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         agev[m][i]=1;
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-     }
+           /* covar is not filled and then is empty */
+           cptcovprod--;
-   }
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-   for (i=1; i<=imx; i++)  {
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-     for(m=firstpass; (m<=lastpass); m++){
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-       if (s[m][i] > (nlstate+ndeath)) {
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-         nberr++;
+           /*printf("stre=%s ", stre);*/
-         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);
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-         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);
+           cptcovprod--;
-         goto end;
+           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*/
-   /*for (i=1; i<=imx; i++){
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-   for (m=firstpass; (m<lastpass); m++){
+           cptcovn++;
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+           cptcovprodnoage++;k1++;
- }
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
- }*/
+                                   because this model-covariate is a construction we invent a new column
+                                   ncovcol + k1
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-   agegomp=(int)agemin;
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-   free_vector(severity,1,maxwav);
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-   free_imatrix(outcome,1,maxwav+1,1,n);
+           k2=k2+2;
-   free_vector(moisnais,1,n);
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-   free_vector(annais,1,n);
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-   /* free_matrix(mint,1,maxwav,1,n);
+           for (i=1; i<=lastobs;i++){
-      free_matrix(anint,1,maxwav,1,n);*/
+             /* Computes the new covariate which is a product of
-   free_vector(moisdc,1,n);
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-   free_vector(andc,1,n);
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+           }
+         } /* End age is not in the model */
-   wav=ivector(1,imx);
+       } /* End if model includes a product */
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+       else { /* no more sum */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+        /*  scanf("%d",i);*/
+         cutl(strd,strc,strb,'V');
-   /* Concatenates waves */
+         ks++; /**< Number of simple covariates */
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+         cptcovn++;
+         Tvar[k]=atoi(strd);
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+       }
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   Tcode=ivector(1,100);
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+         scanf("%d",i);*/
-   ncodemax[1]=1;
+     } /* end of loop + */
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   } /* end model */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-                                  the estimations*/
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   h=0;
-   m=pow(2,cptcoveff);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
-   for(k=1;k<=cptcoveff; k++){
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-     for(i=1; i <=(m/pow(2,k));i++){
-       for(j=1; j <= ncodemax[k]; j++){
+   scanf("%d ",i);*/
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
-           h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   endread:
-         }
+     printf("Exiting decodemodel: ");
-       }
+     return (1);
-     }
+ }
-   }
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-      codtab[1][2]=1;codtab[2][2]=2; */
+ {
-   /* for(i=1; i <=m ;i++){
+   int i, m;
-      for(k=1; k <=cptcovn; k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   for (i=1; i<=imx; i++) {
-      }
+     for(m=2; (m<= maxwav); m++) {
-      printf("\n");
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-      }
+         anint[m][i]=9999;
-      scanf("%d",i);*/
+         s[m][i]=-1;
+       }
-   /*------------ gnuplot -------------*/
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-   strcpy(optionfilegnuplot,optionfilefiname);
+         *nberr++;
-   if(mle==-3)
+         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);
-     strcat(optionfilegnuplot,"-mort");
+         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);
-   strcat(optionfilegnuplot,".gp");
+         s[m][i]=-1;
+       }
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-     printf("Problem with file %s",optionfilegnuplot);
+         *nberr++;
-   }
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-   else{
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-     fprintf(ficgp,"\n# %s\n", version);
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+       }
-     fprintf(ficgp,"set missing 'NaNq'\n");
+     }
    }
-   /*  fclose(ficgp);*/
-   /*--------- index.htm --------*/
+   for (i=1; i<=imx; i++)  {
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+     for(m=firstpass; (m<= lastpass); m++){
-   if(mle==-3)
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-     strcat(optionfilehtm,"-mort");
+         if (s[m][i] >= nlstate+1) {
-   strcat(optionfilehtm,".htm");
+           if(agedc[i]>0)
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+               agev[m][i]=agedc[i];
-   }
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             else {
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+               if ((int)andc[i]!=9999){
-   strcat(optionfilehtmcov,"-cov.htm");
+                 nbwarn++;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-   }
+                 agev[m][i]=-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\
+         }
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+                                  years but with the precision of a month */
-   }
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-   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\
+           else if(agev[m][i] < *agemin){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+             *agemin=agev[m][i];
- \n\
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
- <hr  size=\"2\" color=\"#EC5E5E\">\
+           }
-  <ul><li><h4>Parameter files</h4>\n\
+           else if(agev[m][i] >*agemax){
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+             *agemax=agev[m][i];
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+           }
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-  - Date and time at start: %s</ul>\n",\
+           /*     agev[m][i] = age[i]+2*m;*/
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+         }
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+         else { /* =9 */
-           fileres,fileres,\
+           agev[m][i]=1;
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+           s[m][i]=-1;
-   fflush(fichtm);
+         }
+       }
-   strcpy(pathr,path);
+       else /*= 0 Unknown */
-   strcat(pathr,optionfilefiname);
+         agev[m][i]=1;
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+     }
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+   }
-      and prints on file fileres'p'. */
+   for (i=1; i<=imx; i++)  {
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
-   fprintf(fichtm,"\n");
+         *nberr++;
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+         return 1;
-           imx,agemin,agemax,jmin,jmax,jmean);
+       }
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     }
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   }
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   /*for (i=1; i<=imx; i++){
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   for (m=firstpass; (m<lastpass); m++){
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
-   /* For 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*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-   if (mle==-3){
-     ximort=matrix(1,NDIM,1,NDIM);
+   return (0);
-     cens=ivector(1,n);
+   endread:
-     ageexmed=vector(1,n);
+     printf("Exiting calandcheckages: ");
-     agecens=vector(1,n);
+     return (1);
-     dcwave=ivector(1,n);
+ }
-     for (i=1; i<=imx; i++){
-       dcwave[i]=-1;
+ /***********************************************/
-       for (m=firstpass; m<=lastpass; m++)
+ /**************** Main Program *****************/
-         if (s[m][i]>nlstate) {
+ /***********************************************/
-           dcwave[i]=m;
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+ int main(int argc, char *argv[])
-           break;
+ {
-         }
+ #ifdef GSL
-     }
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
-     for (i=1; i<=imx; i++) {
+   int rval = GSL_CONTINUE;
-       if (wav[i]>0){
+   int status = GSL_SUCCESS;
-         ageexmed[i]=agev[mw[1][i]][i];
+   double ssval;
-         j=wav[i];
+ #endif
-         agecens[i]=1.;
+   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 (ageexmed[i]> 1 && wav[i] > 0){
+   int linei, month, year,iout;
-           agecens[i]=agev[mw[j][i]][i];
+   int jj, ll, li, lj, lk, imk;
-           cens[i]= 1;
+   int numlinepar=0; /* Current linenumber of parameter file */
-         }else if (ageexmed[i]< 1)
+   int itimes;
-           cens[i]= -1;
+   int NDIM=2;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   int vpopbased=0;
-           cens[i]=0 ;
-       }
+   char ca[32], cb[32], cc[32];
-       else cens[i]=-1;
+   /*  FILE *fichtm; *//* Html File */
-     }
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
-     for (i=1;i<=NDIM;i++) {
+   double agedeb, agefin,hf;
-       for (j=1;j<=NDIM;j++)
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
-     }
+   double fret;
+   double **xi,tmp,delta;
-     p[1]=0.0268; p[NDIM]=0.083;
-     /*printf("%lf %lf", p[1], p[2]);*/
+   double dum; /* Dummy variable */
+   double ***p3mat;
+   double ***mobaverage;
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   int *indx;
-     strcpy(filerespow,"pow-mort");
+   char line[MAXLINE], linepar[MAXLINE];
-     strcat(filerespow,fileres);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   char pathr[MAXLINE], pathimach[MAXLINE];
-       printf("Problem with resultfile: %s\n", filerespow);
+   char **bp, *tok, *val; /* pathtot */
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   int firstobs=1, lastobs=10;
-     }
+   int sdeb, sfin; /* Status at beginning and end */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   int c,  h , cpt,l;
-     /*  for (i=1;i<=nlstate;i++)
+   int ju,jl, mi;
-         for(j=1;j<=nlstate+ndeath;j++)
+   int i1,j1, jk,aa,bb, stepsize, ij;
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-     */
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-     fprintf(ficrespow,"\n");
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+   int agemortsup;
-     fclose(ficrespow);
+   float  sumlpop=0.;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-     for(i=1; i <=NDIM; i++)
+   double bage, fage, age, agelim, agebase;
-       for(j=i+1;j<=NDIM;j++)
+   double ftolpl=FTOL;
-         matcov[i][j]=matcov[j][i];
+   double **prlim;
+   double ***param; /* Matrix of parameters */
-     printf("\nCovariance matrix\n ");
+   double  *p;
-     for(i=1; i <=NDIM; i++) {
+   double **matcov; /* Matrix of covariance */
-       for(j=1;j<=NDIM;j++){
+   double ***delti3; /* Scale */
-         printf("%f ",matcov[i][j]);
+   double *delti; /* Scale */
-       }
+   double ***eij, ***vareij;
-       printf("\n ");
+   double **varpl; /* Variances of prevalence limits by age */
-     }
+   double *epj, vepp;
+   double kk1, kk2;
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-     for (i=1;i<=NDIM;i++)
+   double **ximort;
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
+   int *dcwave;
-     lsurv=vector(1,AGESUP);
-     lpop=vector(1,AGESUP);
+   char z[1]="c", occ;
-     tpop=vector(1,AGESUP);
-     lsurv[agegomp]=100000;
+   /*char  *strt;*/
+   char strtend[80];
-     for (k=agegomp;k<=AGESUP;k++) {
-       agemortsup=k;
+   long total_usecs;
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     }
+ /*   setlocale (LC_ALL, ""); */
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     for (k=agegomp;k<agemortsup;k++)
+ /*   textdomain (PACKAGE); */
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
-     for (k=agegomp;k<agemortsup;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-       sumlpop=sumlpop+lpop[k];
+   rstart_time = time(NULL);
-     }
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
-     tpop[agegomp]=sumlpop;
+   curr_time=start_time;
-     for (k=agegomp;k<(agemortsup-3);k++){
+   /*tml = *localtime(&start_time.tm_sec);*/
-       /*  tpop[k+1]=2;*/
+   /* strcpy(strstart,asctime(&tml)); */
-       tpop[k+1]=tpop[k]-lpop[k];
+   strcpy(strstart,asctime(&start_time));
-     }
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+ /*  tm = *localtime(&start_time.tm_sec); */
-     for (k=agegomp;k<(agemortsup-2);k++)
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-       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]);
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ /*   strt=asctime(&tmg); */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-                      stepm, weightopt,\
+ *  tm = *localtime(&time_value);
-                      model,imx,p,matcov,agemortsup);
+ *  strstart=asctime(&tm);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-     free_vector(lsurv,1,AGESUP);
+ */
-     free_vector(lpop,1,AGESUP);
-     free_vector(tpop,1,AGESUP);
+   nberr=0; /* Number of errors and warnings */
-   } /* Endof if mle==-3 */
+   nbwarn=0;
+   getcwd(pathcd, size);
-   else{ /* For mle >=1 */
+   printf("\n%s\n%s",version,fullversion);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   if(argc <=1){
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     printf("\nEnter the parameter file name: ");
-     for (k=1; k<=npar;k++)
+     fgets(pathr,FILENAMELENGTH,stdin);
-       printf(" %d %8.5f",k,p[k]);
+     i=strlen(pathr);
-     printf("\n");
+     if(pathr[i-1]=='\n')
-     globpr=1; /* to print the contributions */
+       pathr[i-1]='\0';
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     i=strlen(pathr);
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-     for (k=1; k<=npar;k++)
+       pathr[i-1]='\0';
-       printf(" %d %8.5f",k,p[k]);
+    for (tok = pathr; tok != NULL; ){
-     printf("\n");
+       printf("Pathr |%s|\n",pathr);
-     if(mle>=1){ /* Could be 1 or 2 */
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+       printf("val= |%s| pathr=%s\n",val,pathr);
-     }
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
-     /*--------- 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);
+   }
+   else{
+     strcpy(pathtot,argv[1]);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   }
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /*cygwin_split_path(pathtot,path,optionfile);
-     for(i=1,jk=1; i <=nlstate; i++){
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-       for(k=1; k <=(nlstate+ndeath); k++){
+   /* cutv(path,optionfile,pathtot,'\\');*/
-         if (k != i) {
-           printf("%d%d ",i,k);
+   /* Split argv[0], imach program to get pathimach */
-           fprintf(ficlog,"%d%d ",i,k);
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-           fprintf(ficres,"%1d%1d ",i,k);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           for(j=1; j <=ncovmodel; j++){
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-             printf("%lf ",p[jk]);
+  /*   strcpy(pathimach,argv[0]); */
-             fprintf(ficlog,"%lf ",p[jk]);
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-             fprintf(ficres,"%lf ",p[jk]);
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-             jk++;
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           }
+   chdir(path); /* Can be a relative path */
-           printf("\n");
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-           fprintf(ficlog,"\n");
+     printf("Current directory %s!\n",pathcd);
-           fprintf(ficres,"\n");
+   strcpy(command,"mkdir ");
-         }
+   strcat(command,optionfilefiname);
-       }
+   if((outcmd=system(command)) != 0){
-     }
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     if(mle!=0){
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-       /* Computing hessian and covariance matrix */
+     /* fclose(ficlog); */
-       ftolhess=ftol; /* Usually correct */
+ /*     exit(1); */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+   }
-     }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+ /*     perror("mkdir"); */
-     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++){
+   /*-------- arguments in the command line --------*/
-       for(j=1; j <=nlstate+ndeath; j++){
-         if (j!=i) {
+   /* Log file */
-           fprintf(ficres,"%1d%1d",i,j);
+   strcat(filelog, optionfilefiname);
-           printf("%1d%1d",i,j);
+   strcat(filelog,".log");    /* */
-           fprintf(ficlog,"%1d%1d",i,j);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-           for(k=1; k<=ncovmodel;k++){
+     printf("Problem with logfile %s\n",filelog);
-             printf(" %.5e",delti[jk]);
+     goto end;
-             fprintf(ficlog," %.5e",delti[jk]);
+   }
-             fprintf(ficres," %.5e",delti[jk]);
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-             jk++;
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-           }
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-           printf("\n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-           fprintf(ficlog,"\n");
+  path=%s \n\
-           fprintf(ficres,"\n");
+  optionfile=%s\n\
-         }
+  optionfilext=%s\n\
-       }
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     }
+   printf("Local time (at start):%s",strstart);
-     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,"Local time (at start): %s",strstart);
-     if(mle>=1)
+   fflush(ficlog);
-       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");
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     /* # 121 Var(a12)\n\ */
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   /* */
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   strcpy(fileres,"r");
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   strcat(fileres, optionfilefiname);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     /* # 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\ */
+   /*---------arguments file --------*/
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     /* Just to have a covariance matrix which will be more understandable
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-        even is we still don't want to manage dictionary of variables
+     fflush(ficlog);
-     */
+     /* goto end; */
-     for(itimes=1;itimes<=2;itimes++){
+     exit(70);
-       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++){
+   strcpy(filereso,"o");
-             jj++;
+   strcat(filereso,fileres);
-             ca[0]= k+'a'-1;ca[1]='\0';
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-             if(itimes==1){
+     printf("Problem with Output resultfile: %s\n", filereso);
-               if(mle>=1)
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-                 printf("#%1d%1d%d",i,j,k);
+     fflush(ficlog);
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+     goto end;
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+   }
-             }else{
-               if(mle>=1)
+   /* Reads comments: lines beginning with '#' */
-                 printf("%1d%1d%d",i,j,k);
+   numlinepar=0;
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+     ungetc(c,ficpar);
-             }
+     fgets(line, MAXLINE, ficpar);
-             ll=0;
+     numlinepar++;
-             for(li=1;li <=nlstate; li++){
+     fputs(line,stdout);
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+     fputs(line,ficparo);
-                 if(lj==li) continue;
+     fputs(line,ficlog);
-                 for(lk=1;lk<=ncovmodel;lk++){
+   }
-                   ll++;
+   ungetc(c,ficpar);
-                   if(ll<=jj){
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-                     if(ll<jj){
+   numlinepar++;
-                       if(itimes==1){
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-                         if(mle>=1)
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   fflush(ficlog);
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                       }else{
+     ungetc(c,ficpar);
-                         if(mle>=1)
+     fgets(line, MAXLINE, ficpar);
-                           printf(" %.5e",matcov[jj][ll]);
+     numlinepar++;
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+     fputs(line, stdout);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+     //puts(line);
-                       }
+     fputs(line,ficparo);
-                     }else{
+     fputs(line,ficlog);
-                       if(itimes==1){
+   }
-                         if(mle>=1)
+   ungetc(c,ficpar);
-                           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);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-                       }else{
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-                         if(mle>=1)
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-                           printf(" %.5e",matcov[jj][ll]);
+      v1+v2*age+v2*v3 makes cptcovn = 3
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   */
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   if (strlen(model)>1)
-                       }
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
-                     }
+   else
-                   }
+     ncovmodel=2;
-                 } /* end lk */
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-               } /* end lj */
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-             } /* end li */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-             if(mle>=1)
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-               printf("\n");
+     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);
-             fprintf(ficlog,"\n");
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-             fprintf(ficres,"\n");
+     fflush(stdout);
-             numlinepar++;
+     fclose (ficlog);
-           } /* end k*/
+     goto end;
-         } /*end j */
+   }
-       } /* end i */
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     } /* end itimes */
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     fflush(ficlog);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     fflush(ficres);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-       ungetc(c,ficpar);
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-       fgets(line, MAXLINE, ficpar);
+     fclose (ficparo);
-       puts(line);
+     fclose (ficlog);
-       fputs(line,ficparo);
+     goto end;
-     }
+     exit(0);
-     ungetc(c,ficpar);
+   }
+   else if(mle==-3) {
-     estepm=0;
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf 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);
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     if (fage <= 2) {
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       bage = ageminpar;
+     matcov=matrix(1,npar,1,npar);
-       fage = agemaxpar;
+   }
-     }
+   else{
+     /* Read guessed parameters */
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     /* Reads comments: lines beginning with '#' */
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       numlinepar++;
-       ungetc(c,ficpar);
+       fputs(line,stdout);
-       fgets(line, MAXLINE, ficpar);
+       fputs(line,ficparo);
-       puts(line);
+       fputs(line,ficlog);
-       fputs(line,ficparo);
+     }
-     }
+     ungetc(c,ficpar);
-     ungetc(c,ficpar);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     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);
+     for(i=1; i <=nlstate; i++){
-     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);
+       j=0;
-     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);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         if(jj==i) continue;
-     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);
+         j++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         if ((i1 != i) && (j1 != j)){
-       ungetc(c,ficpar);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-       fgets(line, MAXLINE, ficpar);
+ It might be a problem of design; if ncovcol and the model are correct\n \
-       puts(line);
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-       fputs(line,ficparo);
+           exit(1);
-     }
+         }
-     ungetc(c,ficpar);
+         fprintf(ficparo,"%1d%1d",i1,j1);
+         if(mle==1)
+           printf("%1d%1d",i,j);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+         fprintf(ficlog,"%1d%1d",i,j);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+         for(k=1; k<=ncovmodel;k++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+           if(mle==1){
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+             printf(" %lf",param[i][j][k]);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           else
-       ungetc(c,ficpar);
+             fprintf(ficlog," %lf",param[i][j][k]);
-       fgets(line, MAXLINE, ficpar);
+           fprintf(ficparo," %lf",param[i][j][k]);
-       puts(line);
+         }
-       fputs(line,ficparo);
+         fscanf(ficpar,"\n");
-     }
+         numlinepar++;
-     ungetc(c,ficpar);
+         if(mle==1)
+           printf("\n");
-     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(ficlog,"\n");
-     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(ficparo,"\n");
-     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);
+     fflush(ficlog);
-     /* day and month of proj2 are not used but only year anproj2.*/
+     /* Reads scales values */
+     p=param[1][1];
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /* Reads comments: lines beginning with '#' */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+       fgets(line, MAXLINE, ficpar);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+       numlinepar++;
+       fputs(line,stdout);
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+       fputs(line,ficparo);
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+       fputs(line,ficlog);
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     }
+     ungetc(c,ficpar);
-    /*------------ free_vector  -------------*/
-    /*  chdir(path); */
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     free_ivector(wav,1,imx);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+         if ((i1-i)*(j1-j)!=0){
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+           exit(1);
-     free_lvector(num,1,n);
+         }
-     free_vector(agedc,1,n);
+         printf("%1d%1d",i,j);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     fclose(ficparo);
+         for(k=1; k<=ncovmodel;k++){
-     fclose(ficres);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
-     strcpy(filerespl,"pl");
+         fscanf(ficpar,"\n");
-     strcat(filerespl,fileres);
+         numlinepar++;
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+         printf("\n");
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+         fprintf(ficparo,"\n");
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+         fprintf(ficlog,"\n");
-     }
+       }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     }
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     fflush(ficlog);
-     pstamp(ficrespl);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     /* Reads covariance matrix */
-     fprintf(ficrespl,"#Age ");
+     delti=delti3[1][1];
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-     fprintf(ficrespl,"\n");
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-     prlim=matrix(1,nlstate,1,nlstate);
+     /* Reads comments: lines beginning with '#' */
-     agebase=ageminpar;
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     agelim=agemaxpar;
+       ungetc(c,ficpar);
-     ftolpl=1.e-10;
+       fgets(line, MAXLINE, ficpar);
-     i1=cptcoveff;
+       numlinepar++;
-     if (cptcovn < 1){i1=1;}
+       fputs(line,stdout);
+       fputs(line,ficparo);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       fputs(line,ficlog);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     }
-         k=k+1;
+     ungetc(c,ficpar);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-         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(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(i=1; i <=npar; i++){
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fscanf(ficpar,"%s",str);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       if(mle==1)
-         }
+         printf("%s",str);
-         fprintf(ficrespl,"******\n");
+       fprintf(ficlog,"%s",str);
-         printf("******\n");
+       fprintf(ficparo,"%s",str);
-         fprintf(ficlog,"******\n");
+       for(j=1; j <=i; j++){
+         fscanf(ficpar," %le",&matcov[i][j]);
-         for (age=agebase; age<=agelim; age++){
+         if(mle==1){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           printf(" %.5le",matcov[i][j]);
-           fprintf(ficrespl,"%.0f ",age );
+         }
-           for(j=1;j<=cptcoveff;j++)
+         fprintf(ficlog," %.5le",matcov[i][j]);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-           for(i=1; i<=nlstate;i++)
+       }
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       fscanf(ficpar,"\n");
-           fprintf(ficrespl,"\n");
+       numlinepar++;
-         }
+       if(mle==1)
-       }
+         printf("\n");
-     }
+       fprintf(ficlog,"\n");
-     fclose(ficrespl);
+       fprintf(ficparo,"\n");
+     }
-     /*------------- h Pij x at various ages ------------*/
+     for(i=1; i <=npar; i++)
+       for(j=i+1;j<=npar;j++)
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+         matcov[i][j]=matcov[j][i];
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     if(mle==1)
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       printf("\n");
-     }
+     fprintf(ficlog,"\n");
-     printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     fflush(ficlog);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*-------- Rewriting parameter file ----------*/
-     /*if (stepm<=24) stepsize=2;*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     agelim=AGESUP;
+     strcat(rfileres,".");    /* */
-     hstepm=stepsize*YEARM; /* Every year of age */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-     /* hstepm=1;   aff par mois*/
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     pstamp(ficrespij);
+     }
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     fprintf(ficres,"#%s\n",version);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   }    /* End of mle != -3 */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficrespij,"\n#****** ");
+   n= lastobs;
-         for(j=1;j<=cptcoveff;j++)
+   num=lvector(1,n);
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   moisnais=vector(1,n);
-         fprintf(ficrespij,"******\n");
+   annais=vector(1,n);
+   moisdc=vector(1,n);
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+   andc=vector(1,n);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   agedc=vector(1,n);
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   cod=ivector(1,n);
+   weight=vector(1,n);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   mint=matrix(1,maxwav,1,n);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   anint=matrix(1,maxwav,1,n);
-           oldm=oldms;savm=savms;
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   tab=ivector(1,NCOVMAX);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
+   /* Reads data from file datafile */
-               fprintf(ficrespij," %1d-%1d",i,j);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-           fprintf(ficrespij,"\n");
+     goto end;
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+   /* Calculation of the number of parameters from char model */
-             for(i=1; i<=nlstate;i++)
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-               for(j=1; j<=nlstate+ndeath;j++)
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
-             fprintf(ficrespij,"\n");
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-           }
+         k=1 Tvar[1]=2 (from V2)
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     */
-           fprintf(ficrespij,"\n");
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-         }
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-       }
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
-     }
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   /* For model-covariate k tells which data-covariate to use but
+     because this model-covariate is a construction we invent a new column
-     fclose(ficrespij);
+     ncovcol + k1
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     Tvar[3=V1*V4]=4+1 etc */
-     for(i=1;i<=AGESUP;i++)
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-       for(j=1;j<=NCOVMAX;j++)
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-         for(k=1;k<=NCOVMAX;k++)
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-           probs[i][j][k]=0.;
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-     /*---------- Forecasting ------------------*/
+   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
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-     if(prevfcast==1){
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-       /*    if(stepm ==1){*/
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+covariates (3 plus signs)
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-       /*      }  */
+                       */
-       /*      else{ */
-       /*        erreur=108; */
+   if(decodemodel(model, lastobs) == 1)
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     goto end;
-       /*        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); */
-       /*      } */
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-     }
+     nbwarn++;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-     /*---------- Health expectancies and variances ------------*/
+   }
+     /*  if(mle==1){*/
-     strcpy(filerest,"t");
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     strcat(filerest,fileres);
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-     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;
+     /*-calculation of age at interview from date of interview and age at death -*/
-     }
+   agev=matrix(1,maxwav,1,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(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
-     strcpy(filerese,"e");
-     strcat(filerese,fileres);
+   agegomp=(int)agemin;
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   free_vector(moisnais,1,n);
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   free_vector(annais,1,n);
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   /* free_matrix(mint,1,maxwav,1,n);
-     }
+      free_matrix(anint,1,maxwav,1,n);*/
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   free_vector(moisdc,1,n);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   free_vector(andc,1,n);
+   /* */
-     strcpy(fileresstde,"stde");
-     strcat(fileresstde,fileres);
+   wav=ivector(1,imx);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   /* Concatenates waves */
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   /* */
-     strcpy(filerescve,"cve");
-     strcat(filerescve,fileres);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   ncodemax[1]=1;
-     }
+   Ndum =ivector(-1,NCOVMAX);
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   if (ncovmodel > 2)
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-     strcpy(fileresv,"v");
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-     strcat(fileresv,fileres);
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   h=0;
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-     }
+   /*if (cptcovn > 0) */
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   m=pow(2,cptcoveff);
-     /* 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);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     /*  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",\
+     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 */
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-     */
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
+           h++;
-     if (mobilav!=0) {
+           if (h>m)
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             h=1;
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+            *     h     1     2     3     4
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+            *______________________________
-       }
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-     }
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+            *     4     2     2     1     1
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+            *     5 i=3 1 i=2 1     2     1
-         k=k+1;
+            *     6     2     1     2     1
-         fprintf(ficrest,"\n#****** ");
+            *     7 i=4 1     2     2     1
-         for(j=1;j<=cptcoveff;j++)
+            *     8     2     2     2     1
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *     9 i=5 1 i=3 1 i=2 1     1
-         fprintf(ficrest,"******\n");
+            *    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
-         for(j=1;j<=cptcoveff;j++) {
+            *    15 i=8 1     2     2     1
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    16     2     2     2     1
-           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]]);
+           codtab[h][k]=j;
-         }
+           /*codtab[h][Tvar[k]]=j;*/
-         fprintf(ficreseij,"******\n");
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
-         fprintf(ficresstdeij,"******\n");
+         }
-         fprintf(ficrescveij,"******\n");
+       }
+     }
-         fprintf(ficresvij,"\n#****** ");
+   }
-         for(j=1;j<=cptcoveff;j++)
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      codtab[1][2]=1;codtab[2][2]=2; */
-         fprintf(ficresvij,"******\n");
+   /* for(i=1; i <=m ;i++){
+      for(k=1; k <=cptcovn; k++){
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-         oldm=oldms;savm=savms;
+      }
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+      printf("\n");
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+      }
+      scanf("%d",i);*/
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+  free_ivector(Ndum,-1,NCOVMAX);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
-         if(popbased==1){
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
-         }
+   /*------------ gnuplot -------------*/
+   strcpy(optionfilegnuplot,optionfilefiname);
-         pstamp(ficrest);
+   if(mle==-3)
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     strcat(optionfilegnuplot,"-mort");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+   strcat(optionfilegnuplot,".gp");
-         fprintf(ficrest,"\n");
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-         epj=vector(1,nlstate+1);
+     printf("Problem with file %s",optionfilegnuplot);
-         for(age=bage; age <=fage ;age++){
+   }
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   else{
-           if (popbased==1) {
+     fprintf(ficgp,"\n# %s\n", version);
-             if(mobilav ==0){
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-               for(i=1; i<=nlstate;i++)
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-                 prlim[i][i]=probs[(int)age][i][k];
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-             }else{ /* mobilav */
+   }
-               for(i=1; i<=nlstate;i++)
+   /*  fclose(ficgp);*/
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+   /*--------- index.htm --------*/
-             }
-           }
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   if(mle==-3)
-           fprintf(ficrest," %4.0f",age);
+     strcat(optionfilehtm,"-mort");
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+   strcat(optionfilehtm,".htm");
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     printf("Problem with %s \n",optionfilehtm);
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     exit(0);
-             }
+   }
-             epj[nlstate+1] +=epj[j];
-           }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
-           for(i=1, vepp=0.;i <=nlstate;i++)
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-             for(j=1;j <=nlstate;j++)
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-               vepp += vareij[i][j][(int)age];
+   }
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+   else{
-           for(j=1;j <=nlstate;j++){
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-           }
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-           fprintf(ficrest,"\n");
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-         }
+   }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-         free_vector(epj,1,nlstate+1);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       }
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     }
+ \n\
-     free_vector(weight,1,n);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-     free_imatrix(Tvard,1,15,1,2);
+  <ul><li><h4>Parameter files</h4>\n\
-     free_imatrix(s,1,maxwav+1,1,n);
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-     free_matrix(anint,1,maxwav,1,n);
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-     free_matrix(mint,1,maxwav,1,n);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     free_ivector(cod,1,n);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-     free_ivector(tab,1,NCOVMAX);
+  - Date and time at start: %s</ul>\n",\
-     fclose(ficreseij);
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     fclose(ficresstdeij);
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-     fclose(ficrescveij);
+           fileres,fileres,\
-     fclose(ficresvij);
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-     fclose(ficrest);
+   fflush(fichtm);
-     fclose(ficpar);
+   strcpy(pathr,path);
-     /*------- Variance of period (stable) prevalence------*/
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+      and prints on file fileres'p'. */
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-       exit(0);
-     }
+   fprintf(fichtm,"\n");
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+           imx,agemin,agemax,jmin,jmax,jmean);
-         k=k+1;
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         fprintf(ficresvpl,"\n#****** ");
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         for(j=1;j<=cptcoveff;j++)
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         fprintf(ficresvpl,"******\n");
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-       }
-     }
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     fclose(ficresvpl);
+   if (mle==-3){
+     ximort=matrix(1,NDIM,1,NDIM);
-     /*---------- End : free ----------------*/
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     cens=ivector(1,n);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     ageexmed=vector(1,n);
+     agecens=vector(1,n);
-   }  /* mle==-3 arrives here for freeing */
+     dcwave=ivector(1,n);
-   free_matrix(prlim,1,nlstate,1,nlstate);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     for (i=1; i<=imx; i++){
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       dcwave[i]=-1;
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       for (m=firstpass; m<=lastpass; m++)
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+         if (s[m][i]>nlstate) {
-     free_matrix(covar,0,NCOVMAX,1,n);
+           dcwave[i]=m;
-     free_matrix(matcov,1,npar,1,npar);
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     /*free_vector(delti,1,npar);*/
+           break;
-     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);
+     for (i=1; i<=imx; i++) {
-     free_ivector(ncodemax,1,8);
+       if (wav[i]>0){
-     free_ivector(Tvar,1,15);
+         ageexmed[i]=agev[mw[1][i]][i];
-     free_ivector(Tprod,1,15);
+         j=wav[i];
-     free_ivector(Tvaraff,1,15);
+         agecens[i]=1.;
-     free_ivector(Tage,1,15);
-     free_ivector(Tcode,1,100);
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+           cens[i]= 1;
-     free_imatrix(codtab,1,100,1,10);
+         }else if (ageexmed[i]< 1)
-   fflush(fichtm);
+           cens[i]= -1;
-   fflush(ficgp);
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+           cens[i]=0 ;
+       }
-   if((nberr >0) || (nbwarn>0)){
+       else cens[i]=-1;
-     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{
+     for (i=1;i<=NDIM;i++) {
-     printf("End of Imach\n");
+       for (j=1;j<=NDIM;j++)
-     fprintf(ficlog,"End of Imach\n");
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-   }
+     }
-   printf("See log file on %s\n",filelog);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-   (void) gettimeofday(&end_time,&tzp);
+     /*printf("%lf %lf", p[1], p[2]);*/
-   tm = *localtime(&end_time.tv_sec);
-   tmg = *gmtime(&end_time.tv_sec);
-   strcpy(strtend,asctime(&tm));
+ #ifdef GSL
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+ #else
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     strcpy(filerespow,"pow-mort");
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     strcat(filerespow,fileres);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+       printf("Problem with resultfile: %s\n", filerespow);
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     }
-   fclose(fichtm);
+ #ifdef GSL
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-   fclose(fichtmcov);
+ #else
-   fclose(ficgp);
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   fclose(ficlog);
+ #endif
-   /*------ End -----------*/
+     /*  for (i=1;i<=nlstate;i++)
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-    printf("Before Current directory %s!\n",pathcd);
+     */
-    if(chdir(pathcd) != 0)
+     fprintf(ficrespow,"\n");
-     printf("Can't move to directory %s!\n",path);
+ #ifdef GSL
-   if(getcwd(pathcd,MAXLINE) > 0)
+     /* gsl starts here */
-     printf("Current directory %s!\n",pathcd);
+     T = gsl_multimin_fminimizer_nmsimplex;
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     gsl_multimin_fminimizer *sfm = NULL;
-   sprintf(plotcmd,"gnuplot");
+     gsl_vector *ss, *x;
- #ifndef UNIX
+     gsl_multimin_function minex_func;
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
- #endif
+     /* Initial vertex size vector */
-   if(!stat(plotcmd,&info)){
+     ss = gsl_vector_alloc (NDIM);
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     if (ss == NULL){
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-     }else
+     }
-       strcpy(pplotcmd,plotcmd);
+     /* Set all step sizes to 1 */
- #ifdef UNIX
+     gsl_vector_set_all (ss, 0.001);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
-     if(!stat(plotcmd,&info)){
+     /* Starting point */
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
-     }else
+     x = gsl_vector_alloc (NDIM);
-       strcpy(pplotcmd,plotcmd);
- #endif
+     if (x == NULL){
-   }else
+       gsl_vector_free(ss);
-     strcpy(pplotcmd,plotcmd);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-   if((outcmd=system(plotcmd)) != 0){
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     printf("\n Problem with gnuplot\n");
+ /*     gsl_vector_set(x, 1, 0.083); */
-   }
+     gsl_vector_set(x, 0, p[1]);
-   printf(" Wait...");
+     gsl_vector_set(x, 1, p[2]);
-   while (z[0] != 'q') {
-     /* chdir(path); */
+     minex_func.f = &gompertz_f;
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     minex_func.n = NDIM;
-     scanf("%s",z);
+     minex_func.params = (void *)&p; /* ??? */
- /*     if (z[0] == 'c') system("./imach"); */
-     if (z[0] == 'e') {
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-       system(optionfilehtm);
-     }
+     printf("Iterations beginning .....\n\n");
-     else if (z[0] == 'g') system(plotcmd);
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-     else if (z[0] == 'q') exit(0);
-   }
+     iteri=0;
-   end:
+     while (rval == GSL_CONTINUE){
-   while (z[0] != 'q') {
+       iteri++;
-     printf("\nType  q for exiting: ");
+       status = gsl_multimin_fminimizer_iterate(sfm);
-     scanf("%s",z);
-   }
+       if (status) printf("error: %s\n", gsl_strerror (status));
- }
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+     gsl_vector_free(x); /* initial values */
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ #endif
+     fclose(ficrespow);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     for(i=1; i <=NDIM; i++)
+       for(j=i+1;j<=NDIM;j++)
+         matcov[i][j]=matcov[j][i];
+     printf("\nCovariance matrix\n ");
+     for(i=1; i <=NDIM; i++) {
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
+     }
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     for (i=1;i<=NDIM;i++)
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     lsurv=vector(1,AGESUP);
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
+     for (k=agegomp;k<=AGESUP;k++) {
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
+     }
+     tpop[agegomp]=sumlpop;
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+                      stepm, weightopt,\
+                      model,imx,p,matcov,agemortsup);
+     free_vector(lsurv,1,AGESUP);
+     free_vector(lpop,1,AGESUP);
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
+   } /* Endof if mle==-3 */
+   else{ /* For mle >=1 */
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     if(mle>=1){ /* Could be 1 or 2 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     /*--------- results files --------------*/
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
+       ftolhess=ftol; /* Usually correct */
+       hesscov(matcov, p, npar, delti, ftolhess, func);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+           fprintf(ficres,"\n");
+         }
+       }
+     }
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     if(mle>=1)
+       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+     /* # 121 Var(a12)\n\ */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     /* Just to have a covariance matrix which will be more understandable
+        even is we still don't want to manage dictionary of variables
+     */
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
+           for(k=1; k<=ncovmodel;k++){
+             jj++;
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
+               if(mle>=1)
+                 printf("#%1d%1d%d",i,j,k);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
+               if(mle>=1)
+                 printf("%1d%1d%d",i,j,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
+             }
+             ll=0;
+             for(li=1;li <=nlstate; li++){
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
+                   ll++;
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
+                     if(ll<jj){
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }else{
+                       if(itimes==1){
+                         if(mle>=1)
+                           printf(" Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                       }else{
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
+                     }
+                   }
+                 } /* end lk */
+               } /* end lj */
+             } /* end li */
+             if(mle>=1)
+               printf("\n");
+             fprintf(ficlog,"\n");
+             fprintf(ficres,"\n");
+             numlinepar++;
+           } /* end k*/
+         } /*end j */
+       } /* end i */
+     } /* end itimes */
+     fflush(ficlog);
+     fflush(ficres);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     estepm=0;
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
+     if (fage <= 2) {
+       bage = ageminpar;
+       fage = agemaxpar;
+     }
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
+     fprintf(ficres,"pop_based=%d\n",popbased);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
+      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+    /*------------ free_vector  -------------*/
+    /*  chdir(path); */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     free_lvector(num,1,n);
+     free_vector(agedc,1,n);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     fclose(ficparo);
+     fclose(ficres);
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
+     fclose(ficrespl);
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
+ #endif
+     /*------------- h Pij x at various ages ------------*/
+ #include "hpijx.h"
+     fclose(ficrespij);
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1;i<=AGESUP;i++)
+       for(j=1;j<=NCOVMAX;j++)
+         for(k=1;k<=NCOVMAX;k++)
+           probs[i][j][k]=0.;
+     /*---------- Forecasting ------------------*/
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
+       /*    if(stepm ==1){*/
+       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+       /*      }  */
+       /*      else{ */
+       /*        erreur=108; */
+       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       /*      } */
+     }
+     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     */
+     if (mobilav!=0) {
+       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       }
+     }
+     /*---------- Health expectancies, no variances ------------*/
+     strcpy(filerese,"e");
+     strcat(filerese,fileres);
+     if((ficreseij=fopen(filerese,"w"))==NULL) {
+       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     }
+     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficreseij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficreseij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficreseij);
+     /*---------- Health expectancies and variances ------------*/
+     strcpy(filerest,"t");
+     strcat(filerest,fileres);
+     if((ficrest=fopen(filerest,"w"))==NULL) {
+       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     }
+     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileres);
+     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     }
+     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     strcpy(filerescve,"cve");
+     strcat(filerescve,fileres);
+     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     }
+     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     strcpy(fileresv,"v");
+     strcat(fileresv,fileres);
+     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     }
+     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficrest,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"******\n");
+         fprintf(ficresstdeij,"\n#****** ");
+         fprintf(ficrescveij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
+         fprintf(ficresstdeij,"******\n");
+         fprintf(ficrescveij,"******\n");
+         fprintf(ficresvij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"******\n");
+         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
+         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+         pstamp(ficrest);
+         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+           oldm=oldms;savm=savms; /* Segmentation fault */
+           cptcod= 0; /* To be deleted */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+           if(vpopbased==1)
+             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
+           else
+             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"# Age e.. (std) ");
+           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+           fprintf(ficrest,"\n");
+           epj=vector(1,nlstate+1);
+           for(age=bage; age <=fage ;age++){
+             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+             if (vpopbased==1) {
+               if(mobilav ==0){
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=probs[(int)age][i][k];
+               }else{ /* mobilav */
+                 for(i=1; i<=nlstate;i++)
+                   prlim[i][i]=mobaverage[(int)age][i][k];
+               }
+             }
+             fprintf(ficrest," %4.0f",age);
+             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               }
+               epj[nlstate+1] +=epj[j];
+             }
+             for(i=1, vepp=0.;i <=nlstate;i++)
+               for(j=1;j <=nlstate;j++)
+                 vepp += vareij[i][j][(int)age];
+             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+             for(j=1;j <=nlstate;j++){
+               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             }
+             fprintf(ficrest,"\n");
+           }
+         }
+         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+         free_vector(epj,1,nlstate+1);
+       /*}*/
+     }
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
+     /*------- Variance of period (stable) prevalence------*/
+     strcpy(fileresvpl,"vpl");
+     strcat(fileresvpl,fileres);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+         fprintf(ficresvpl,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvpl,"******\n");
+         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         oldm=oldms;savm=savms;
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     /*---------- End : free ----------------*/
+     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }  /* mle==-3 arrives here for freeing */
+  endfree:
+     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
+     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     free_matrix(covar,0,NCOVMAX,1,n);
+     free_matrix(matcov,1,npar,1,npar);
+     /*free_vector(delti,1,npar);*/
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_matrix(agev,1,maxwav,1,imx);
+     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     free_ivector(ncodemax,1,NCOVMAX);
+     free_ivector(Tvar,1,NCOVMAX);
+     free_ivector(Tprod,1,NCOVMAX);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
+     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     free_imatrix(codtab,1,100,1,10);
+   fflush(fichtm);
+   fflush(ficgp);
+   if((nberr >0) || (nbwarn>0)){
+     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+   }else{
+     printf("End of Imach\n");
+     fprintf(ficlog,"End of Imach\n");
+   }
+   printf("See log file on %s\n",filelog);
+   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+   /*(void) gettimeofday(&end_time,&tzp);*/
+   rend_time = time(NULL);
+   end_time = *localtime(&rend_time);
+   /* tml = *localtime(&end_time.tm_sec); */
+   strcpy(strtend,asctime(&end_time));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
+   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
+   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+ /*   if(fileappend(fichtm,optionfilehtm)){ */
+   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtm);
+   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+   fclose(fichtmcov);
+   fclose(ficgp);
+   fclose(ficlog);
+   /*------ End -----------*/
+    printf("Before Current directory %s!\n",pathcd);
+    if(chdir(pathcd) != 0)
+     printf("Can't move to directory %s!\n",path);
+   if(getcwd(pathcd,MAXLINE) > 0)
+     printf("Current directory %s!\n",pathcd);
+   /*strcat(plotcmd,CHARSEPARATOR);*/
+   sprintf(plotcmd,"gnuplot");
+ #ifdef _WIN32
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #ifdef __unix
+     strcpy(plotcmd,GNUPLOTPROGRAM);
+     if(!stat(plotcmd,&info)){
+       printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
+     }else
+       strcpy(pplotcmd,plotcmd);
+ #endif
+   }else
+     strcpy(pplotcmd,plotcmd);
+   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   if((outcmd=system(plotcmd)) != 0){
+     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+   }
+   printf(" Successful, please wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef __APPLE__
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elif __linux
+       sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
+ #else
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #endif
+       printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+       system(pplotcmd);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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

Removed from v.1.125
changed lines
	Added in v.1.162