imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.125 and 1.161

-version 1.125, 2006/04/04 15:20:31
+version 1.161, 2014/09/15 20:41:41
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 '\\'
+ /* #include <libintl.h> */
- #else
+ /* #define _(String) gettext (String) */
- #define DIRSEPARATOR '\\'
- #define CHARSEPARATOR "\\"
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- #define ODIRSEPARATOR '/'
- #endif
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- /* $Id$ */
+ #define FILENAMELENGTH 132
- /* $State$ */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- char fullversion[]="$Revision$ $Date$";
- char strstart[80];
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ #define NINTERVMAX 8
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- int npar=NPARMAX;
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- int nlstate=2; /* Number of live states */
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- int ndeath=1; /* Number of dead states */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ #define MAXN 20000
- int popbased=0;
+ #define YEARM 12. /**< Number of months per year */
+ #define AGESUP 130
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define AGEBASE 40
- int maxwav; /* Maxim number of waves */
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #ifdef _WIN32
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define DIRSEPARATOR '\\'
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define CHARSEPARATOR "\\"
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #define ODIRSEPARATOR '/'
- int mle, weightopt;
+ #else
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ #define DIRSEPARATOR '/'
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ #define CHARSEPARATOR "/"
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ #define ODIRSEPARATOR '\\'
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ #endif
- double jmean; /* Mean space between 2 waves */
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ /* $Id$ */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ /* $State$ */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficlog, *ficrespow;
+ char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
- int globpr; /* Global variable for printing or not */
+ char fullversion[]="$Revision$ $Date$";
- double fretone; /* Only one call to likelihood */
+ char strstart[80];
- long ipmx; /* Number of contributions */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- double sw; /* Sum of weights */
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- char filerespow[FILENAMELENGTH];
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- FILE *ficresilk;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- FILE *ficresprobmorprev;
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- FILE *fichtm, *fichtmcov; /* Html File */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- FILE *ficreseij;
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char filerese[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- FILE *ficresstdeij;
+ int cptcov=0; /* Working variable */
- char fileresstde[FILENAMELENGTH];
+ int npar=NPARMAX;
- FILE *ficrescveij;
+ int nlstate=2; /* Number of live states */
- char filerescve[FILENAMELENGTH];
+ int ndeath=1; /* Number of dead states */
- FILE  *ficresvij;
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- char fileresv[FILENAMELENGTH];
+ int popbased=0;
- FILE  *ficresvpl;
- char fileresvpl[FILENAMELENGTH];
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char title[MAXLINE];
+ int maxwav=0; /* Maxim number of waves */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- char command[FILENAMELENGTH];
+                    to the likelihood and the sum of weights (done by funcone)*/
- int  outcmd=0;
+ int mle=1, weightopt=0;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[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
- char filelog[FILENAMELENGTH]; /* Log file */
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- char filerest[FILENAMELENGTH];
+ double jmean=1; /* Mean space between 2 waves */
- char fileregp[FILENAMELENGTH];
+ double **matprod2(); /* test */
- char popfile[FILENAMELENGTH];
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ FILE *ficlog, *ficrespow;
- struct timezone tzp;
+ int globpr=0; /* Global variable for printing or not */
- extern int gettimeofday();
+ double fretone; /* Only one call to likelihood */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ long ipmx=0; /* Number of contributions */
- long time_value;
+ double sw; /* Sum of weights */
- extern long time();
+ char filerespow[FILENAMELENGTH];
- char strcurr[80], strfor[80];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficresilk;
- char *endptr;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- long lval;
+ FILE *ficresprobmorprev;
- double dval;
+ FILE *fichtm, *fichtmcov; /* Html File */
+ FILE *ficreseij;
- #define NR_END 1
+ char filerese[FILENAMELENGTH];
- #define FREE_ARG char*
+ FILE *ficresstdeij;
- #define FTOL 1.0e-10
+ char fileresstde[FILENAMELENGTH];
+ FILE *ficrescveij;
- #define NRANSI
+ char filerescve[FILENAMELENGTH];
- #define ITMAX 200
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- #define TOL 2.0e-4
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- #define CGOLD 0.3819660
+ char title[MAXLINE];
- #define ZEPS 1.0e-10
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- #define GOLD 1.618034
+ char command[FILENAMELENGTH];
- #define GLIMIT 100.0
+ int  outcmd=0;
- #define TINY 1.0e-20
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- static double maxarg1,maxarg2;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ char filelog[FILENAMELENGTH]; /* Log file */
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ char filerest[FILENAMELENGTH];
+ char fileregp[FILENAMELENGTH];
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ char popfile[FILENAMELENGTH];
- #define rint(a) floor(a+0.5)
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- static double sqrarg;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ /* struct timezone tzp; */
- int agegomp= AGEGOMP;
+ /* extern int gettimeofday(); */
+ struct tm tml, *gmtime(), *localtime();
- int imx;
- int stepm=1;
+ extern time_t time();
- /* Stepm, step in month: minimum step interpolation*/
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
- int estepm;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ struct tm tm;
- int m,nb;
+ char strcurr[80], strfor[80];
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ char *endptr;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ long lval;
- double **pmmij, ***probs;
+ double dval;
- double *ageexmed,*agecens;
- double dateintmean=0;
+ #define NR_END 1
+ #define FREE_ARG char*
- double *weight;
+ #define FTOL 1.0e-10
- int **s; /* Status */
- double *agedc, **covar, idx;
+ #define NRANSI
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ #define ITMAX 200
- double *lsurv, *lpop, *tpop;
+ #define TOL 2.0e-4
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ #define CGOLD 0.3819660
+ #define ZEPS 1.0e-10
- /**************** split *************************/
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- {
+ #define GOLD 1.618034
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ #define GLIMIT 100.0
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ #define TINY 1.0e-20
-   */
-   char  *ss;                            /* pointer */
+ static double maxarg1,maxarg2;
-   int   l1, l2;                         /* length counters */
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-   l1 = strlen(path );                   /* length of path */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ #define rint(a) floor(a+0.5)
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ static double sqrarg;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-     /* get current working directory */
+ int agegomp= AGEGOMP;
-     /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ int imx;
-       return( GLOCK_ERROR_GETCWD );
+ int stepm=1;
-     }
+ /* Stepm, step in month: minimum step interpolation*/
-     /* got dirc from getcwd*/
-     printf(" DIRC = %s \n",dirc);
+ int estepm;
-   } else {                              /* strip direcotry from path */
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-     ss++;                               /* after this, the filename */
-     l2 = strlen( ss );                  /* length of filename */
+ int m,nb;
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ long *num;
-     strcpy( name, ss );         /* save file name */
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-     dirc[l1-l2] = 0;                    /* add zero */
+ double **pmmij, ***probs;
-     printf(" DIRC2 = %s \n",dirc);
+ double *ageexmed,*agecens;
-   }
+ double dateintmean=0;
-   /* We add a separator at the end of dirc if not exists */
-   l1 = strlen( dirc );                  /* length of directory */
+ double *weight;
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ int **s; /* Status */
-     dirc[l1] =  DIRSEPARATOR;
+ double *agedc;
-     dirc[l1+1] = 0;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-     printf(" DIRC3 = %s \n",dirc);
+                   * covar=matrix(0,NCOVMAX,1,n);
-   }
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   ss = strrchr( name, '.' );            /* find last / */
+ double  idx;
-   if (ss >0){
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-     ss++;
+ int *Ndum; /** Freq of modality (tricode */
-     strcpy(ext,ss);                     /* save extension */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-     l1= strlen( name);
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-     l2= strlen(ss)+1;
+ double *lsurv, *lpop, *tpop;
-     strncpy( finame, name, l1-l2);
-     finame[l1-l2]= 0;
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-   }
+ double ftolhess; /**< Tolerance for computing hessian */
-   return( 0 );                          /* we're done */
+ /**************** split *************************/
- }
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ {
+   /* 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)
+   */
- void replace_back_to_slash(char *s, char*t)
+   char  *ss;                            /* pointer */
- {
+   int   l1, l2;                         /* length counters */
-   int i;
-   int lg=0;
+   l1 = strlen(path );                   /* length of path */
-   i=0;
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-   lg=strlen(t);
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   for(i=0; i<= lg; i++) {
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     (s[i] = t[i]);
+     strcpy( name, path );               /* we got the fullname name because no directory */
-     if (t[i]== '\\') s[i]='/';
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   }
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- }
+     /* get current working directory */
+     /*    extern  char* getcwd ( char *buf , int len);*/
- int nbocc(char *s, char occ)
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
- {
+       return( GLOCK_ERROR_GETCWD );
-   int i,j=0;
+     }
-   int lg=20;
+     /* got dirc from getcwd*/
-   i=0;
+     printf(" DIRC = %s \n",dirc);
-   lg=strlen(s);
+   } else {                              /* strip direcotry from path */
-   for(i=0; i<= lg; i++) {
+     ss++;                               /* after this, the filename */
-   if  (s[i] == occ ) j++;
+     l2 = strlen( ss );                  /* length of filename */
-   }
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   return j;
+     strcpy( name, ss );         /* save file name */
- }
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     dirc[l1-l2] = 0;                    /* add zero */
- void cutv(char *u,char *v, char*t, char occ)
+     printf(" DIRC2 = %s \n",dirc);
- {
+   }
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+   /* We add a separator at the end of dirc if not exists */
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+   l1 = strlen( dirc );                  /* length of directory */
-      gives u="abcedf" and v="ghi2j" */
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   int i,lg,j,p=0;
+     dirc[l1] =  DIRSEPARATOR;
-   i=0;
+     dirc[l1+1] = 0;
-   for(j=0; j<=strlen(t)-1; j++) {
+     printf(" DIRC3 = %s \n",dirc);
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+   }
-   }
+   ss = strrchr( name, '.' );            /* find last / */
+   if (ss >0){
-   lg=strlen(t);
+     ss++;
-   for(j=0; j<p; j++) {
+     strcpy(ext,ss);                     /* save extension */
-     (u[j] = t[j]);
+     l1= strlen( name);
-   }
+     l2= strlen(ss)+1;
-      u[p]='\0';
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
-    for(j=0; j<= lg; j++) {
+   }
-     if (j>=(p+1))(v[j-p-1] = t[j]);
-   }
+   return( 0 );                          /* we're done */
  }
- /********************** nrerror ********************/
+ /******************************************/
- void nrerror(char error_text[])
- {
+ void replace_back_to_slash(char *s, char*t)
-   fprintf(stderr,"ERREUR ...\n");
+ {
-   fprintf(stderr,"%s\n",error_text);
+   int i;
-   exit(EXIT_FAILURE);
+   int lg=0;
- }
+   i=0;
- /*********************** vector *******************/
+   lg=strlen(t);
- double *vector(int nl, int nh)
+   for(i=0; i<= lg; i++) {
- {
+     (s[i] = t[i]);
-   double *v;
+     if (t[i]== '\\') s[i]='/';
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   }
-   if (!v) nrerror("allocation failure in vector");
+ }
-   return v-nl+NR_END;
- }
+ char *trimbb(char *out, char *in)
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
- /************************ free vector ******************/
+   char *s;
- void free_vector(double*v, int nl, int nh)
+   s=out;
- {
+   while (*in != '\0'){
-   free((FREE_ARG)(v+nl-NR_END));
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- }
+       in++;
+     }
- /************************ivector *******************************/
+     *out++ = *in++;
- int *ivector(long nl,long nh)
+   }
- {
+   *out='\0';
-   int *v;
+   return s;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ }
-   if (!v) nrerror("allocation failure in ivector");
-   return v-nl+NR_END;
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- }
+ {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
- /******************free ivector **************************/
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- void free_ivector(int *v, long nl, long nh)
+      gives blocc="abcdef2ghi" and alocc="j".
- {
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
-   free((FREE_ARG)(v+nl-NR_END));
+   */
- }
+   char *s, *t;
+   t=in;s=in;
- /************************lvector *******************************/
+   while ((*in != occ) && (*in != '\0')){
- long *lvector(long nl,long nh)
+     *alocc++ = *in++;
- {
+   }
-   long *v;
+   if( *in == occ){
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+     *(alocc)='\0';
-   if (!v) nrerror("allocation failure in ivector");
+     s=++in;
-   return v-nl+NR_END;
+   }
- }
+   if (s == t) {/* occ not found */
- /******************free lvector **************************/
+     *(alocc-(in-s))='\0';
- void free_lvector(long *v, long nl, long nh)
+     in=s;
- {
+   }
-   free((FREE_ARG)(v+nl-NR_END));
+   while ( *in != '\0'){
- }
+     *blocc++ = *in++;
+   }
- /******************* imatrix *******************************/
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   *blocc='\0';
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   return t;
- {
+ }
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   int **m;
+ {
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-   /* allocate pointers to rows */
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+      gives blocc="abcdef2ghi" and alocc="j".
-   if (!m) nrerror("allocation failure 1 in matrix()");
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   m += NR_END;
+   */
-   m -= nrl;
+   char *s, *t;
+   t=in;s=in;
+   while (*in != '\0'){
-   /* allocate rows and set pointers to them */
+     while( *in == occ){
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+       *blocc++ = *in++;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+       s=in;
-   m[nrl] += NR_END;
+     }
-   m[nrl] -= ncl;
+     *blocc++ = *in++;
+   }
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   if (s == t) /* occ not found */
+     *(blocc-(in-s))='\0';
-   /* return pointer to array of pointers to rows */
+   else
-   return m;
+     *(blocc-(in-s)-1)='\0';
- }
+   in=s;
+   while ( *in != '\0'){
- /****************** free_imatrix *************************/
+     *alocc++ = *in++;
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   }
-       int **m;
-       long nch,ncl,nrh,nrl;
+   *alocc='\0';
-      /* free an int matrix allocated by imatrix() */
+   return s;
- {
+ }
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-   free((FREE_ARG) (m+nrl-NR_END));
+ int nbocc(char *s, char occ)
- }
+ {
+   int i,j=0;
- /******************* matrix *******************************/
+   int lg=20;
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   i=0;
- {
+   lg=strlen(s);
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   for(i=0; i<= lg; i++) {
-   double **m;
+   if  (s[i] == occ ) j++;
+   }
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   return j;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ }
-   m += NR_END;
-   m -= nrl;
+ /* void cutv(char *u,char *v, char*t, char occ) */
+ /* { */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   m[nrl] += NR_END;
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   m[nrl] -= ncl;
+ /*   int i,lg,j,p=0; */
+ /*   i=0; */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*   lg=strlen(t); */
-   return m;
+ /*   for(j=0; j<=lg-1; j++) { */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-    */
+ /*   } */
- }
+ /*   for(j=0; j<p; j++) { */
- /*************************free matrix ************************/
+ /*     (u[j] = t[j]); */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ /*   } */
- {
+ /*      u[p]='\0'; */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+ /*    for(j=0; j<= lg; j++) { */
- }
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
+ /*   } */
- /******************* ma3x *******************************/
+ /* } */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
- {
+ #ifdef _WIN32
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ char * strsep(char **pp, const char *delim)
-   double ***m;
+ {
+   char *p, *q;
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   if ((p = *pp) == NULL)
-   m += NR_END;
+     return 0;
-   m -= nrl;
+   if ((q = strpbrk (p, delim)) != NULL)
+   {
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+     *pp = q + 1;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     *q = '\0';
-   m[nrl] += NR_END;
+   }
-   m[nrl] -= ncl;
+   else
+     *pp = 0;
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   return p;
+ }
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ #endif
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   m[nrl][ncl] += NR_END;
+ /********************** nrerror ********************/
-   m[nrl][ncl] -= nll;
-   for (j=ncl+1; j<=nch; j++)
+ void nrerror(char error_text[])
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ {
+   fprintf(stderr,"ERREUR ...\n");
-   for (i=nrl+1; i<=nrh; i++) {
+   fprintf(stderr,"%s\n",error_text);
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   exit(EXIT_FAILURE);
-     for (j=ncl+1; j<=nch; j++)
+ }
-       m[i][j]=m[i][j-1]+nlay;
+ /*********************** vector *******************/
-   }
+ double *vector(int nl, int nh)
-   return m;
+ {
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   double *v;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   */
+   if (!v) nrerror("allocation failure in vector");
- }
+   return v-nl+NR_END;
+ }
- /*************************free ma3x ************************/
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ /************************ free vector ******************/
- {
+ void free_vector(double*v, int nl, int nh)
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ {
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   free((FREE_ARG)(v+nl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+ }
- }
+ /************************ivector *******************************/
- /*************** function subdirf ***********/
+ int *ivector(long nl,long nh)
- char *subdirf(char fileres[])
+ {
- {
+   int *v;
-   /* Caution optionfilefiname is hidden */
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   strcpy(tmpout,optionfilefiname);
+   if (!v) nrerror("allocation failure in ivector");
-   strcat(tmpout,"/"); /* Add to the right */
+   return v-nl+NR_END;
-   strcat(tmpout,fileres);
+ }
-   return tmpout;
- }
+ /******************free ivector **************************/
+ void free_ivector(int *v, long nl, long nh)
- /*************** function subdirf2 ***********/
+ {
- char *subdirf2(char fileres[], char *preop)
+   free((FREE_ARG)(v+nl-NR_END));
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /************************lvector *******************************/
-   strcpy(tmpout,optionfilefiname);
+ long *lvector(long nl,long nh)
-   strcat(tmpout,"/");
+ {
-   strcat(tmpout,preop);
+   long *v;
-   strcat(tmpout,fileres);
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   return tmpout;
+   if (!v) nrerror("allocation failure in ivector");
- }
+   return v-nl+NR_END;
+ }
- /*************** function subdirf3 ***********/
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ /******************free lvector **************************/
- {
+ void free_lvector(long *v, long nl, long nh)
+ {
-   /* Caution optionfilefiname is hidden */
+   free((FREE_ARG)(v+nl-NR_END));
-   strcpy(tmpout,optionfilefiname);
+ }
-   strcat(tmpout,"/");
-   strcat(tmpout,preop);
+ /******************* imatrix *******************************/
-   strcat(tmpout,preop2);
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   strcat(tmpout,fileres);
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   return tmpout;
+ {
- }
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   int **m;
- /***************** f1dim *************************/
- extern int ncom;
+   /* allocate pointers to rows */
- extern double *pcom,*xicom;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- extern double (*nrfunc)(double []);
+   if (!m) nrerror("allocation failure 1 in matrix()");
+   m += NR_END;
- double f1dim(double x)
+   m -= nrl;
- {
-   int j;
-   double f;
+   /* allocate rows and set pointers to them */
-   double *xt;
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   xt=vector(1,ncom);
+   m[nrl] += NR_END;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   m[nrl] -= ncl;
-   f=(*nrfunc)(xt);
-   free_vector(xt,1,ncom);
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   return f;
- }
+   /* return pointer to array of pointers to rows */
+   return m;
- /*****************brent *************************/
+ }
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- {
+ /****************** free_imatrix *************************/
-   int iter;
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   double a,b,d,etemp;
+       int **m;
-   double fu,fv,fw,fx;
+       long nch,ncl,nrh,nrl;
-   double ftemp;
+      /* free an int matrix allocated by imatrix() */
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ {
-   double e=0.0;
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   free((FREE_ARG) (m+nrl-NR_END));
-   a=(ax < cx ? ax : cx);
+ }
-   b=(ax > cx ? ax : cx);
-   x=w=v=bx;
+ /******************* matrix *******************************/
-   fw=fv=fx=(*f)(x);
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-   for (iter=1;iter<=ITMAX;iter++) {
+ {
-     xm=0.5*(a+b);
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   double **m;
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     printf(".");fflush(stdout);
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-     fprintf(ficlog,".");fflush(ficlog);
+   if (!m) nrerror("allocation failure 1 in matrix()");
- #ifdef DEBUG
+   m += NR_END;
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   m -= nrl;
-     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)))) { */
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
- #endif
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   m[nrl] += NR_END;
-       *xmin=x;
+   m[nrl] -= ncl;
-       return fx;
-     }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     ftemp=fu;
+   return m;
-     if (fabs(e) > tol1) {
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-       r=(x-w)*(fx-fv);
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
-       q=(x-v)*(fx-fw);
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-       p=(x-v)*q-(x-w)*r;
+    */
-       q=2.0*(q-r);
+ }
-       if (q > 0.0) p = -p;
-       q=fabs(q);
+ /*************************free matrix ************************/
-       etemp=e;
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-       e=d;
+ {
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   free((FREE_ARG)(m+nrl-NR_END));
-       else {
+ }
-         d=p/q;
-         u=x+d;
+ /******************* ma3x *******************************/
-         if (u-a < tol2 || b-u < tol2)
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-           d=SIGN(tol1,xm-x);
+ {
-       }
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-     } else {
+   double ***m;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     fu=(*f)(u);
+   m += NR_END;
-     if (fu <= fx) {
+   m -= nrl;
-       if (u >= x) a=x; else b=x;
-       SHFT(v,w,x,u)
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-         SHFT(fv,fw,fx,fu)
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-         } else {
+   m[nrl] += NR_END;
-           if (u < x) a=u; else b=u;
+   m[nrl] -= ncl;
-           if (fu <= fw || w == x) {
-             v=w;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-             w=u;
-             fv=fw;
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-             fw=fu;
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-           } else if (fu <= fv || v == x || v == w) {
+   m[nrl][ncl] += NR_END;
-             v=u;
+   m[nrl][ncl] -= nll;
-             fv=fu;
+   for (j=ncl+1; j<=nch; j++)
-           }
+     m[nrl][j]=m[nrl][j-1]+nlay;
-         }
-   }
+   for (i=nrl+1; i<=nrh; i++) {
-   nrerror("Too many iterations in brent");
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   *xmin=x;
+     for (j=ncl+1; j<=nch; j++)
-   return fx;
+       m[i][j]=m[i][j-1]+nlay;
- }
+   }
+   return m;
- /****************** mnbrak ***********************/
+   /*  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)
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   */
-             double (*func)(double))
+ }
- {
-   double ulim,u,r,q, dum;
+ /*************************free ma3x ************************/
-   double fu;
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ {
-   *fa=(*func)(*ax);
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   *fb=(*func)(*bx);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   if (*fb > *fa) {
+   free((FREE_ARG)(m+nrl-NR_END));
-     SHFT(dum,*ax,*bx,dum)
+ }
-       SHFT(dum,*fb,*fa,dum)
-       }
+ /*************** function subdirf ***********/
-   *cx=(*bx)+GOLD*(*bx-*ax);
+ char *subdirf(char fileres[])
-   *fc=(*func)(*cx);
+ {
-   while (*fb > *fc) {
+   /* Caution optionfilefiname is hidden */
-     r=(*bx-*ax)*(*fb-*fc);
+   strcpy(tmpout,optionfilefiname);
-     q=(*bx-*cx)*(*fb-*fa);
+   strcat(tmpout,"/"); /* Add to the right */
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   strcat(tmpout,fileres);
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   return tmpout;
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+ }
-     if ((*bx-u)*(u-*cx) > 0.0) {
-       fu=(*func)(u);
+ /*************** function subdirf2 ***********/
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ char *subdirf2(char fileres[], char *preop)
-       fu=(*func)(u);
+ {
-       if (fu < *fc) {
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   /* Caution optionfilefiname is hidden */
-           SHFT(*fb,*fc,fu,(*func)(u))
+   strcpy(tmpout,optionfilefiname);
-           }
+   strcat(tmpout,"/");
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   strcat(tmpout,preop);
-       u=ulim;
+   strcat(tmpout,fileres);
-       fu=(*func)(u);
+   return tmpout;
-     } else {
+ }
-       u=(*cx)+GOLD*(*cx-*bx);
-       fu=(*func)(u);
+ /*************** function subdirf3 ***********/
-     }
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-     SHFT(*ax,*bx,*cx,u)
+ {
-       SHFT(*fa,*fb,*fc,fu)
-       }
+   /* Caution optionfilefiname is hidden */
- }
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
- /*************** linmin ************************/
+   strcat(tmpout,preop);
+   strcat(tmpout,preop2);
- int ncom;
+   strcat(tmpout,fileres);
- double *pcom,*xicom;
+   return tmpout;
- double (*nrfunc)(double []);
+ }
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ /***************** f1dim *************************/
- {
+ extern int ncom;
-   double brent(double ax, double bx, double cx,
+ extern double *pcom,*xicom;
-                double (*f)(double), double tol, double *xmin);
+ extern double (*nrfunc)(double []);
-   double f1dim(double x);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ double f1dim(double x)
-               double *fc, double (*func)(double));
+ {
    int j;
-   double xx,xmin,bx,ax;
+   double f;
-   double fx,fb,fa;
+   double *xt;
-   ncom=n;
+   xt=vector(1,ncom);
-   pcom=vector(1,n);
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   xicom=vector(1,n);
+   f=(*nrfunc)(xt);
-   nrfunc=func;
+   free_vector(xt,1,ncom);
-   for (j=1;j<=n;j++) {
+   return f;
-     pcom[j]=p[j];
+ }
-     xicom[j]=xi[j];
-   }
+ /*****************brent *************************/
-   ax=0.0;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-   xx=1.0;
+ {
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   int iter;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   double a,b,d,etemp;
- #ifdef DEBUG
+   double fu=0,fv,fw,fx;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   double ftemp;
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
- #endif
+   double e=0.0;
-   for (j=1;j<=n;j++) {
-     xi[j] *= xmin;
+   a=(ax < cx ? ax : cx);
-     p[j] += xi[j];
+   b=(ax > cx ? ax : cx);
-   }
+   x=w=v=bx;
-   free_vector(xicom,1,n);
+   fw=fv=fx=(*f)(x);
-   free_vector(pcom,1,n);
+   for (iter=1;iter<=ITMAX;iter++) {
- }
+     xm=0.5*(a+b);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
- char *asc_diff_time(long time_sec, char ascdiff[])
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
- {
+     printf(".");fflush(stdout);
-   long sec_left, days, hours, minutes;
+     fprintf(ficlog,".");fflush(ficlog);
-   days = (time_sec) / (60*60*24);
+ #ifdef DEBUG
-   sec_left = (time_sec) % (60*60*24);
+     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);
-   hours = (sec_left) / (60*60) ;
+     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);
-   sec_left = (sec_left) %(60*60);
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-   minutes = (sec_left) /60;
+ #endif
-   sec_left = (sec_left) % (60);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+       *xmin=x;
-   return ascdiff;
+       return fx;
- }
+     }
+     ftemp=fu;
- /*************** powell ************************/
+     if (fabs(e) > tol1) {
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+       r=(x-w)*(fx-fv);
-             double (*func)(double []))
+       q=(x-v)*(fx-fw);
- {
+       p=(x-v)*q-(x-w)*r;
-   void linmin(double p[], double xi[], int n, double *fret,
+       q=2.0*(q-r);
-               double (*func)(double []));
+       if (q > 0.0) p = -p;
-   int i,ibig,j;
+       q=fabs(q);
-   double del,t,*pt,*ptt,*xit;
+       etemp=e;
-   double fp,fptt;
+       e=d;
-   double *xits;
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-   int niterf, itmp;
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+       else {
-   pt=vector(1,n);
+         d=p/q;
-   ptt=vector(1,n);
+         u=x+d;
-   xit=vector(1,n);
+         if (u-a < tol2 || b-u < tol2)
-   xits=vector(1,n);
+           d=SIGN(tol1,xm-x);
-   *fret=(*func)(p);
+       }
-   for (j=1;j<=n;j++) pt[j]=p[j];
+     } else {
-   for (*iter=1;;++(*iter)) {
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     fp=(*fret);
+     }
-     ibig=0;
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-     del=0.0;
+     fu=(*f)(u);
-     last_time=curr_time;
+     if (fu <= fx) {
-     (void) gettimeofday(&curr_time,&tzp);
+       if (u >= x) a=x; else b=x;
-     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);
+       SHFT(v,w,x,u)
-     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);
+         SHFT(fv,fw,fx,fu)
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+         } else {
-    for (i=1;i<=n;i++) {
+           if (u < x) a=u; else b=u;
-       printf(" %d %.12f",i, p[i]);
+           if (fu <= fw || w == x) {
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+             v=w;
-       fprintf(ficrespow," %.12lf", p[i]);
+             w=u;
-     }
+             fv=fw;
-     printf("\n");
+             fw=fu;
-     fprintf(ficlog,"\n");
+           } else if (fu <= fv || v == x || v == w) {
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+             v=u;
-     if(*iter <=3){
+             fv=fu;
-       tm = *localtime(&curr_time.tv_sec);
+           }
-       strcpy(strcurr,asctime(&tm));
+         }
- /*       asctime_r(&tm,strcurr); */
+   }
-       forecast_time=curr_time;
+   nrerror("Too many iterations in brent");
-       itmp = strlen(strcurr);
+   *xmin=x;
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   return fx;
-         strcurr[itmp-1]='\0';
+ }
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+ /****************** mnbrak ***********************/
-       for(niterf=10;niterf<=30;niterf+=10){
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-         tmf = *localtime(&forecast_time.tv_sec);
+             double (*func)(double))
- /*      asctime_r(&tmf,strfor); */
+ {
-         strcpy(strfor,asctime(&tmf));
+   double ulim,u,r,q, dum;
-         itmp = strlen(strfor);
+   double fu;
-         if(strfor[itmp-1]=='\n')
-         strfor[itmp-1]='\0';
+   *fa=(*func)(*ax);
-         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);
+   *fb=(*func)(*bx);
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+   if (*fb > *fa) {
-       }
+     SHFT(dum,*ax,*bx,dum)
-     }
+       SHFT(dum,*fb,*fa,dum)
-     for (i=1;i<=n;i++) {
+       }
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       fptt=(*fret);
+   *fc=(*func)(*cx);
- #ifdef DEBUG
+   while (*fb > *fc) {
-       printf("fret=%lf \n",*fret);
+     r=(*bx-*ax)*(*fb-*fc);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+     q=(*bx-*cx)*(*fb-*fa);
- #endif
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       printf("%d",i);fflush(stdout);
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
-       linmin(p,xit,n,fret,func);
+     if ((*bx-u)*(u-*cx) > 0.0) {
-       if (fabs(fptt-(*fret)) > del) {
+       fu=(*func)(u);
-         del=fabs(fptt-(*fret));
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
-         ibig=i;
+       fu=(*func)(u);
-       }
+       if (fu < *fc) {
- #ifdef DEBUG
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-       printf("%d %.12e",i,(*fret));
+           SHFT(*fb,*fc,fu,(*func)(u))
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+           }
-       for (j=1;j<=n;j++) {
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+       u=ulim;
-         printf(" x(%d)=%.12e",j,xit[j]);
+       fu=(*func)(u);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+     } else {
-       }
+       u=(*cx)+GOLD*(*cx-*bx);
-       for(j=1;j<=n;j++) {
+       fu=(*func)(u);
-         printf(" p=%.12e",p[j]);
+     }
-         fprintf(ficlog," p=%.12e",p[j]);
+     SHFT(*ax,*bx,*cx,u)
-       }
+       SHFT(*fa,*fb,*fc,fu)
-       printf("\n");
+       }
-       fprintf(ficlog,"\n");
+ }
- #endif
-     }
+ /*************** linmin ************************/
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- #ifdef DEBUG
+ int ncom;
-       int k[2],l;
+ double *pcom,*xicom;
-       k[0]=1;
+ double (*nrfunc)(double []);
-       k[1]=-1;
-       printf("Max: %.12e",(*func)(p));
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+ {
-       for (j=1;j<=n;j++) {
+   double brent(double ax, double bx, double cx,
-         printf(" %.12e",p[j]);
+                double (*f)(double), double tol, double *xmin);
-         fprintf(ficlog," %.12e",p[j]);
+   double f1dim(double x);
-       }
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-       printf("\n");
+               double *fc, double (*func)(double));
-       fprintf(ficlog,"\n");
+   int j;
-       for(l=0;l<=1;l++) {
+   double xx,xmin,bx,ax;
-         for (j=1;j<=n;j++) {
+   double fx,fb,fa;
-           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]);
+   ncom=n;
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   pcom=vector(1,n);
-         }
+   xicom=vector(1,n);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   nrfunc=func;
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   for (j=1;j<=n;j++) {
-       }
+     pcom[j]=p[j];
- #endif
+     xicom[j]=xi[j];
+   }
+   ax=0.0;
-       free_vector(xit,1,n);
+   xx=1.0;
-       free_vector(xits,1,n);
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-       free_vector(ptt,1,n);
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-       free_vector(pt,1,n);
+ #ifdef DEBUG
-       return;
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     }
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ #endif
-     for (j=1;j<=n;j++) {
+   for (j=1;j<=n;j++) {
-       ptt[j]=2.0*p[j]-pt[j];
+     xi[j] *= xmin;
-       xit[j]=p[j]-pt[j];
+     p[j] += xi[j];
-       pt[j]=p[j];
+   }
-     }
+   free_vector(xicom,1,n);
-     fptt=(*func)(ptt);
+   free_vector(pcom,1,n);
-     if (fptt < fp) {
+ }
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-       if (t < 0.0) {
+ char *asc_diff_time(long time_sec, char ascdiff[])
-         linmin(p,xit,n,fret,func);
+ {
-         for (j=1;j<=n;j++) {
+   long sec_left, days, hours, minutes;
-           xi[j][ibig]=xi[j][n];
+   days = (time_sec) / (60*60*24);
-           xi[j][n]=xit[j];
+   sec_left = (time_sec) % (60*60*24);
-         }
+   hours = (sec_left) / (60*60) ;
- #ifdef DEBUG
+   sec_left = (sec_left) %(60*60);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   minutes = (sec_left) /60;
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   sec_left = (sec_left) % (60);
-         for(j=1;j<=n;j++){
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-           printf(" %.12e",xit[j]);
+   return ascdiff;
-           fprintf(ficlog," %.12e",xit[j]);
+ }
-         }
-         printf("\n");
+ /*************** powell ************************/
-         fprintf(ficlog,"\n");
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
- #endif
+             double (*func)(double []))
-       }
+ {
-     }
+   void linmin(double p[], double xi[], int n, double *fret,
-   }
+               double (*func)(double []));
- }
+   int i,ibig,j;
+   double del,t,*pt,*ptt,*xit;
- /**** Prevalence limit (stable or period prevalence)  ****************/
+   double fp,fptt;
+   double *xits;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+   int niterf, itmp;
- {
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+   pt=vector(1,n);
-      matrix by transitions matrix until convergence is reached */
+   ptt=vector(1,n);
+   xit=vector(1,n);
-   int i, ii,j,k;
+   xits=vector(1,n);
-   double min, max, maxmin, maxmax,sumnew=0.;
+   *fret=(*func)(p);
-   double **matprod2();
+   for (j=1;j<=n;j++) pt[j]=p[j];
-   double **out, cov[NCOVMAX], **pmij();
+     rcurr_time = time(NULL);
-   double **newm;
+   for (*iter=1;;++(*iter)) {
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+     fp=(*fret);
+     ibig=0;
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+     del=0.0;
-     for (j=1;j<=nlstate+ndeath;j++){
+     rlast_time=rcurr_time;
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     /* (void) gettimeofday(&curr_time,&tzp); */
-     }
+     rcurr_time = time(NULL);
+     curr_time = *localtime(&rcurr_time);
-    cov[1]=1.;
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+    for (i=1;i<=n;i++) {
-     newm=savm;
+       printf(" %d %.12f",i, p[i]);
-     /* Covariates have to be included here again */
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-      cov[2]=agefin;
+       fprintf(ficrespow," %.12lf", p[i]);
+     }
-       for (k=1; k<=cptcovn;k++) {
+     printf("\n");
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     fprintf(ficlog,"\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]]);*/
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-       }
+     if(*iter <=3){
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       tml = *localtime(&rcurr_time);
-       for (k=1; k<=cptcovprod;k++)
+       strcpy(strcurr,asctime(&tml));
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ /*       asctime_r(&tm,strcurr); */
+       rforecast_time=rcurr_time;
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+       itmp = strlen(strcurr);
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+         strcurr[itmp-1]='\0';
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+       printf("\nConsidering the time needed for this 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);
-     savm=oldm;
+       for(niterf=10;niterf<=30;niterf+=10){
-     oldm=newm;
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-     maxmax=0.;
+         forecast_time = *localtime(&rforecast_time);
-     for(j=1;j<=nlstate;j++){
+ /*      asctime_r(&tmf,strfor); */
-       min=1.;
+         strcpy(strfor,asctime(&forecast_time));
-       max=0.;
+         itmp = strlen(strfor);
-       for(i=1; i<=nlstate; i++) {
+         if(strfor[itmp-1]=='\n')
-         sumnew=0;
+         strfor[itmp-1]='\0';
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+         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);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+         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);
-         max=FMAX(max,prlim[i][j]);
+       }
-         min=FMIN(min,prlim[i][j]);
+     }
-       }
+     for (i=1;i<=n;i++) {
-       maxmin=max-min;
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       maxmax=FMAX(maxmax,maxmin);
+       fptt=(*fret);
-     }
+ #ifdef DEBUG
-     if(maxmax < ftolpl){
+       printf("fret=%lf \n",*fret);
-       return prlim;
+       fprintf(ficlog,"fret=%lf \n",*fret);
-     }
+ #endif
-   }
+       printf("%d",i);fflush(stdout);
- }
+       fprintf(ficlog,"%d",i);fflush(ficlog);
+       linmin(p,xit,n,fret,func);
- /*************** transition probabilities ***************/
+       if (fabs(fptt-(*fret)) > del) {
+         del=fabs(fptt-(*fret));
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+         ibig=i;
- {
+       }
-   double s1, s2;
+ #ifdef DEBUG
-   /*double t34;*/
+       printf("%d %.12e",i,(*fret));
-   int i,j,j1, nc, ii, jj;
+       fprintf(ficlog,"%d %.12e",i,(*fret));
+       for (j=1;j<=n;j++) {
-     for(i=1; i<= nlstate; i++){
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-       for(j=1; j<i;j++){
+         printf(" x(%d)=%.12e",j,xit[j]);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       }
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       for(j=1;j<=n;j++) {
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+         printf(" p=%.12e",p[j]);
-         }
+         fprintf(ficlog," p=%.12e",p[j]);
-         ps[i][j]=s2;
+       }
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       printf("\n");
-       }
+       fprintf(ficlog,"\n");
-       for(j=i+1; j<=nlstate+ndeath;j++){
+ #endif
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     }
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+ #ifdef DEBUG
-         }
+       int k[2],l;
-         ps[i][j]=s2;
+       k[0]=1;
-       }
+       k[1]=-1;
-     }
+       printf("Max: %.12e",(*func)(p));
-     /*ps[3][2]=1;*/
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       for (j=1;j<=n;j++) {
-     for(i=1; i<= nlstate; i++){
+         printf(" %.12e",p[j]);
-       s1=0;
+         fprintf(ficlog," %.12e",p[j]);
-       for(j=1; j<i; j++)
+       }
-         s1+=exp(ps[i][j]);
+       printf("\n");
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       fprintf(ficlog,"\n");
-         s1+=exp(ps[i][j]);
+       for(l=0;l<=1;l++) {
-       ps[i][i]=1./(s1+1.);
+         for (j=1;j<=n;j++) {
-       for(j=1; j<i; j++)
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         }
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-     } /* end i */
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       }
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ #endif
-       for(jj=1; jj<= nlstate+ndeath; jj++){
-         ps[ii][jj]=0;
-         ps[ii][ii]=1;
+       free_vector(xit,1,n);
-       }
+       free_vector(xits,1,n);
-     }
+       free_vector(ptt,1,n);
+       free_vector(pt,1,n);
+       return;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     }
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
- /*         printf("ddd %lf ",ps[ii][jj]); */
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
- /*       } */
+       ptt[j]=2.0*p[j]-pt[j];
- /*       printf("\n "); */
+       xit[j]=p[j]-pt[j];
- /*        } */
+       pt[j]=p[j];
- /*        printf("\n ");printf("%lf ",cov[2]); */
+     }
-        /*
+     fptt=(*func)(ptt);
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-       goto end;*/
+       /* x1 f1=fp x2 f2=*fret x3 f3=fptt, xm fm */
-     return ps;
+       /* 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)
+          will reach at f3 = fm + h^2/2 f''m  ; f" = (f1 -2f2 +f3 ) / h**2 */
- /**************** Product of 2 matrices ******************/
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+       /* Thus we compare delta(2h) with observed f1-f3 */
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+       /* or best gain on one ancient line 'del' with total gain f1-f2 = f1 - f2 - 'del' with del */
- {
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+       t= t- del*SQR(fp-fptt);
-   /* in, b, out are matrice of pointers which should have been initialized
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
-      before: only the contents of out is modified. The function returns
+       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);
-      a pointer to pointers identical to out */
+ #ifdef DEBUG
-   long i, j, k;
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-   for(i=nrl; i<= nrh; i++)
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-     for(k=ncolol; k<=ncoloh; k++)
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
-         out[i][k] +=in[i][j]*b[j][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);
+       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);
-   return out;
+ #endif
- }
+       if (t < 0.0) { /* Then we use it for last direction */
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
+         for (j=1;j<=n;j++) {
- /************* Higher Matrix Product ***************/
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+         }
- {
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-   /* Computes the transition matrix starting at age 'age' over
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
-      'nhstepm*hstepm*stepm' months (i.e. until
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+ #ifdef DEBUG
-      nhstepm*hstepm matrices.
+         for(j=1;j<=n;j++){
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+           printf(" %.12e",xit[j]);
-      (typically every 2 years instead of every month which is too big
+           fprintf(ficlog," %.12e",xit[j]);
-      for the memory).
+         }
-      Model is determined by parameters x and covariates have to be
+         printf("\n");
-      included manually here.
+         fprintf(ficlog,"\n");
+ #endif
-      */
+       }
+     }
-   int i, j, d, h, k;
+   }
-   double **out, cov[NCOVMAX];
+ }
-   double **newm;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   /* Hstepm could be zero and should return the unit matrix */
-   for (i=1;i<=nlstate+ndeath;i++)
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-     for (j=1;j<=nlstate+ndeath;j++){
+ {
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+      matrix by transitions matrix until convergence is reached */
-     }
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   int i, ii,j,k;
-   for(h=1; h <=nhstepm; h++){
+   double min, max, maxmin, maxmax,sumnew=0.;
-     for(d=1; d <=hstepm; d++){
+   /* double **matprod2(); */ /* test */
-       newm=savm;
+   double **out, cov[NCOVMAX+1], **pmij();
-       /* Covariates have to be included here again */
+   double **newm;
-       cov[1]=1.;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-       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]]];
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-       for (k=1; k<=cptcovage;k++)
+     for (j=1;j<=nlstate+ndeath;j++){
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       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]]];
+    cov[1]=1.;
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+     newm=savm;
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+     /* Covariates have to be included here again */
-       savm=oldm;
+     cov[2]=agefin;
-       oldm=newm;
-     }
+     for (k=1; k<=cptcovn;k++) {
-     for(i=1; i<=nlstate+ndeath; i++)
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-       for(j=1;j<=nlstate+ndeath;j++) {
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-         po[i][j][h]=newm[i][j];
+     }
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-          */
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-       }
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-   } /* end h */
-   return po;
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- }
+     /*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]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
- /*************** log-likelihood *************/
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
- double func( double *x)
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
- {
-   int i, ii, j, k, mi, d, kk;
+     savm=oldm;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+     oldm=newm;
-   double **out;
+     maxmax=0.;
-   double sw; /* Sum of weights */
+     for(j=1;j<=nlstate;j++){
-   double lli; /* Individual log likelihood */
+       min=1.;
-   int s1, s2;
+       max=0.;
-   double bbh, survp;
+       for(i=1; i<=nlstate; i++) {
-   long ipmx;
+         sumnew=0;
-   /*extern weight */
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-   /* We are differentiating ll according to initial status */
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-   /*for(i=1;i<imx;i++)
+         max=FMAX(max,prlim[i][j]);
-     printf(" %d\n",s[4][i]);
+         min=FMIN(min,prlim[i][j]);
-   */
+       }
-   cov[1]=1.;
+       maxmin=max-min;
+       maxmax=FMAX(maxmax,maxmin);
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+     }
+     if(maxmax < ftolpl){
-   if(mle==1){
+       return prlim;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   }
-       for(mi=1; mi<= wav[i]-1; mi++){
+ }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+ /*************** transition probabilities ***************/
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-           }
+ {
-         for(d=0; d<dh[mi][i]; d++){
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-           newm=savm;
+      computes the probability to be observed in state j being in state i by appying the
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+      model to the ncovmodel covariates (including constant and age).
-           for (kk=1; kk<=cptcovage;kk++) {
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-           }
+      ncth covariate in the global vector x is given by the formula:
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-           savm=oldm;
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-           oldm=newm;
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-         } /* end mult */
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+   */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+   double s1, lnpijopii;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+   /*double t34;*/
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+   int i,j,j1, nc, ii, jj;
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     for(i=1; i<= nlstate; i++){
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       for(j=1; j<i;j++){
-          * probability in order to take into account the bias as a fraction of the way
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-          * -stepm/2 to stepm/2 .
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-          * For stepm=1 the results are the same as for previous versions of Imach.
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-          * For stepm > 1 the results are less biased than in previous versions.
+         }
-          */
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-         s1=s[mw[mi][i]][i];
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         s2=s[mw[mi+1][i]][i];
+       }
-         bbh=(double)bh[mi][i]/(double)stepm;
+       for(j=i+1; j<=nlstate+ndeath;j++){
-         /* bias bh is positive if real duration
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-          * is higher than the multiple of stepm and negative otherwise.
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-          */
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-         if( s2 > nlstate){
+         }
-           /* i.e. if s2 is a death state and if the date of death is known
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-              then the contribution to the likelihood is the probability to
+       }
-              die between last step unit time and current  step unit time,
+     }
-              which is also equal to probability to die before dh
-              minus probability to die before dh-stepm .
+     for(i=1; i<= nlstate; i++){
-              In version up to 0.92 likelihood was computed
+       s1=0;
-         as if date of death was unknown. Death was treated as any other
+       for(j=1; j<i; j++){
-         health state: the date of the interview describes the actual state
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         and not the date of a change in health state. The former idea was
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         to consider that at each interview the state was recorded
+       }
-         (healthy, disable or death) and IMaCh was corrected; but when we
+       for(j=i+1; j<=nlstate+ndeath; j++){
-         introduced the exact date of death then we should have modified
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-         the contribution of an exact death to the likelihood. This new
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-         contribution is smaller and very dependent of the step unit
+       }
-         stepm. It is no more the probability to die between last interview
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         and month of death but the probability to survive from last
+       ps[i][i]=1./(s1+1.);
-         interview up to one month before death multiplied by the
+       /* Computing other pijs */
-         probability to die within a month. Thanks to Chris
+       for(j=1; j<i; j++)
-         Jackson for correcting this bug.  Former versions increased
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         mortality artificially. The bad side is that we add another loop
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         which slows down the processing. The difference can be up to 10%
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-         lower mortality.
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-           */
+     } /* end i */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-         } else if  (s2==-2) {
+         ps[ii][jj]=0;
-           for (j=1,survp=0. ; j<=nlstate; j++)
+         ps[ii][ii]=1;
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       }
-           /*survp += out[s1][j]; */
+     }
-           lli= log(survp);
-         }
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         else if  (s2==-4) {
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-           for (j=3,survp=0. ; j<=nlstate; j++)
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     /*   } */
-           lli= log(survp);
+     /*   printf("\n "); */
-         }
+     /* } */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-         else if  (s2==-5) {
+     /*
-           for (j=1,survp=0. ; j<=2; j++)
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       goto end;*/
-           lli= log(survp);
+     return ps;
-         }
+ }
-         else{
+ /**************** Product of 2 matrices ******************/
-           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 */
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         }
+ {
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-         /*if(lli ==000.0)*/
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         /*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); */
+   /* in, b, out are matrice of pointers which should have been initialized
-         ipmx +=1;
+      before: only the contents of out is modified. The function returns
-         sw += weight[i];
+      a pointer to pointers identical to out */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   int i, j, k;
-       } /* end of wave */
+   for(i=nrl; i<= nrh; i++)
-     } /* end of individual */
+     for(k=ncolol; k<=ncoloh; k++){
-   }  else if(mle==2){
+       out[i][k]=0.;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for(j=ncl; j<=nch; j++)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         out[i][k] +=in[i][j]*b[j][k];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   return out;
-           for (j=1;j<=nlstate+ndeath;j++){
+ }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           }
+ /************* Higher Matrix Product ***************/
-         for(d=0; d<=dh[mi][i]; d++){
-           newm=savm;
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ {
-           for (kk=1; kk<=cptcovage;kk++) {
+   /* Computes the transition matrix starting at age 'age' over
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+      'nhstepm*hstepm*stepm' months (i.e. until
-           }
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+      nhstepm*hstepm matrices.
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-           savm=oldm;
+      (typically every 2 years instead of every month which is too big
-           oldm=newm;
+      for the memory).
-         } /* end mult */
+      Model is determined by parameters x and covariates have to be
+      included manually here.
-         s1=s[mw[mi][i]][i];
-         s2=s[mw[mi+1][i]][i];
+      */
-         bbh=(double)bh[mi][i]/(double)stepm;
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+   int i, j, d, h, k;
-         ipmx +=1;
+   double **out, cov[NCOVMAX+1];
-         sw += weight[i];
+   double **newm;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       } /* end of wave */
+   /* Hstepm could be zero and should return the unit matrix */
-     } /* end of individual */
+   for (i=1;i<=nlstate+ndeath;i++)
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+     for (j=1;j<=nlstate+ndeath;j++){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-       for(mi=1; mi<= wav[i]-1; mi++){
+     }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-           for (j=1;j<=nlstate+ndeath;j++){
+   for(h=1; h <=nhstepm; h++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for(d=1; d <=hstepm; d++){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       newm=savm;
-           }
+       /* Covariates have to be included here again */
-         for(d=0; d<dh[mi][i]; d++){
+       cov[1]=1.;
-           newm=savm;
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       for (k=1; k<=cptcovn;k++)
-           for (kk=1; kk<=cptcovage;kk++) {
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for (k=1; k<=cptcovage;k++)
-           }
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-           savm=oldm;
-           oldm=newm;
-         } /* end mult */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-         s1=s[mw[mi][i]][i];
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-         s2=s[mw[mi+1][i]][i];
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-         bbh=(double)bh[mi][i]/(double)stepm;
+       savm=oldm;
-         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 */
+       oldm=newm;
-         ipmx +=1;
+     }
-         sw += weight[i];
+     for(i=1; i<=nlstate+ndeath; i++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       for(j=1;j<=nlstate+ndeath;j++) {
-       } /* end of wave */
+         po[i][j][h]=newm[i][j];
-     } /* end of individual */
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+       }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     /*printf("h=%d ",h);*/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   } /* end h */
-       for(mi=1; mi<= wav[i]-1; mi++){
+ /*     printf("\n H=%d \n",h); */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   return po;
-           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);
-           }
+ /*************** log-likelihood *************/
-         for(d=0; d<dh[mi][i]; d++){
+ double func( double *x)
-           newm=savm;
+ {
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   int i, ii, j, k, mi, d, kk;
-           for (kk=1; kk<=cptcovage;kk++) {
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   double **out;
-           }
+   double sw; /* Sum of weights */
+   double lli; /* Individual log likelihood */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   int s1, s2;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   double bbh, survp;
-           savm=oldm;
+   long ipmx;
-           oldm=newm;
+   /*extern weight */
-         } /* end mult */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         s1=s[mw[mi][i]][i];
+   /*for(i=1;i<imx;i++)
-         s2=s[mw[mi+1][i]][i];
+     printf(" %d\n",s[4][i]);
-         if( s2 > nlstate){
+   */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   cov[1]=1.;
-         }else{
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-         }
-         ipmx +=1;
+   if(mle==1){
-         sw += weight[i];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /* Computes the values of the ncovmodel covariates of the model
- /*      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]); */
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-       } /* end of wave */
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-     } /* end of individual */
+          to be observed in j being in i according to the model.
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+        */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+       }
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-           for (j=1;j<=nlstate+ndeath;j++){
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+          has been calculated etc */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(mi=1; mi<= wav[i]-1; mi++){
-           }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         for(d=0; d<dh[mi][i]; d++){
+           for (j=1;j<=nlstate+ndeath;j++){
-           newm=savm;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-           for (kk=1; kk<=cptcovage;kk++) {
+           }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         for(d=0; d<dh[mi][i]; d++){
-           }
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           for (kk=1; kk<=cptcovage;kk++) {
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-           savm=oldm;
+           }
-           oldm=newm;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         } /* end mult */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
-         s1=s[mw[mi][i]][i];
+           oldm=newm;
-         s2=s[mw[mi+1][i]][i];
+         } /* end mult */
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-         ipmx +=1;
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         sw += weight[i];
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         /*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]);*/
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-       } /* end of wave */
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-     } /* end of individual */
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-   } /* End of if */
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+          * probability in order to take into account the bias as a fraction of the way
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+          * -stepm/2 to stepm/2 .
-   return -l;
+          * For stepm=1 the results are the same as for previous versions of Imach.
- }
+          * For stepm > 1 the results are less biased than in previous versions.
+          */
- /*************** log-likelihood *************/
+         s1=s[mw[mi][i]][i];
- double funcone( double *x)
+         s2=s[mw[mi+1][i]][i];
- {
+         bbh=(double)bh[mi][i]/(double)stepm;
-   /* Same as likeli but slower because of a lot of printf and if */
+         /* bias bh is positive if real duration
-   int i, ii, j, k, mi, d, kk;
+          * is higher than the multiple of stepm and negative otherwise.
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+          */
-   double **out;
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-   double lli; /* Individual log likelihood */
+         if( s2 > nlstate){
-   double llt;
+           /* i.e. if s2 is a death state and if the date of death is known
-   int s1, s2;
+              then the contribution to the likelihood is the probability to
-   double bbh, survp;
+              die between last step unit time and current  step unit time,
-   /*extern weight */
+              which is also equal to probability to die before dh
-   /* We are differentiating ll according to initial status */
+              minus probability to die before dh-stepm .
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+              In version up to 0.92 likelihood was computed
-   /*for(i=1;i<imx;i++)
+         as if date of death was unknown. Death was treated as any other
-     printf(" %d\n",s[4][i]);
+         health state: the date of the interview describes the actual state
-   */
+         and not the date of a change in health state. The former idea was
-   cov[1]=1.;
+         to consider that at each interview the state was recorded
+         (healthy, disable or death) and IMaCh was corrected; but when we
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         contribution is smaller and very dependent of the step unit
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         stepm. It is no more the probability to die between last interview
-     for(mi=1; mi<= wav[i]-1; mi++){
+         and month of death but the probability to survive from last
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+         interview up to one month before death multiplied by the
-         for (j=1;j<=nlstate+ndeath;j++){
+         probability to die within a month. Thanks to Chris
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         Jackson for correcting this bug.  Former versions increased
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         mortality artificially. The bad side is that we add another loop
-         }
+         which slows down the processing. The difference can be up to 10%
-       for(d=0; d<dh[mi][i]; d++){
+         lower mortality.
-         newm=savm;
+           */
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         }
+         } else if  (s2==-2) {
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           for (j=1,survp=0. ; j<=nlstate; j++)
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         savm=oldm;
+           /*survp += out[s1][j]; */
-         oldm=newm;
+           lli= log(survp);
-       } /* end mult */
+         }
-       s1=s[mw[mi][i]][i];
+         else if  (s2==-4) {
-       s2=s[mw[mi+1][i]][i];
+           for (j=3,survp=0. ; j<=nlstate; j++)
-       bbh=(double)bh[mi][i]/(double)stepm;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       /* bias is positive if real duration
+           lli= log(survp);
-        * is higher than the multiple of stepm and negative otherwise.
+         }
-        */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         else if  (s2==-5) {
-         lli=log(out[s1][s2] - savm[s1][s2]);
+           for (j=1,survp=0. ; j<=2; j++)
-       } else if  (s2==-2) {
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         for (j=1,survp=0. ; j<=nlstate; j++)
+           lli= log(survp);
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         }
-         lli= log(survp);
-       }else if (mle==1){
+         else{
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       } else if(mle==2){
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         }
-       } else if(mle==3){  /* exponential inter-extrapolation */
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         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 */
+         /*if(lli ==000.0)*/
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+         /*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); */
-         lli=log(out[s1][s2]); /* Original formula */
+         ipmx +=1;
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         sw += weight[i];
-         lli=log(out[s1][s2]); /* Original formula */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       } /* End of if */
+       } /* end of wave */
-       ipmx +=1;
+     } /* end of individual */
-       sw += weight[i];
+   }  else if(mle==2){
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (i=1,ipmx=0, sw=0.; i<=imx; 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 (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       if(globpr){
+       for(mi=1; mi<= wav[i]-1; mi++){
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-  %11.6f %11.6f %11.6f ", \
+           for (j=1;j<=nlstate+ndeath;j++){
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           }
-           llt +=ll[k]*gipmx/gsw;
+         for(d=0; d<=dh[mi][i]; d++){
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           newm=savm;
-         }
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         fprintf(ficresilk," %10.6f\n", -llt);
+           for (kk=1; kk<=cptcovage;kk++) {
-       }
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     } /* end of wave */
+           }
-   } /* end of individual */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           savm=oldm;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           oldm=newm;
-   if(globpr==0){ /* First time we count the contributions and weights */
+         } /* end mult */
-     gipmx=ipmx;
-     gsw=sw;
+         s1=s[mw[mi][i]][i];
-   }
+         s2=s[mw[mi+1][i]][i];
-   return -l;
+         bbh=(double)bh[mi][i]/(double)stepm;
- }
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         ipmx +=1;
+         sw += weight[i];
- /*************** function likelione ***********/
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+       } /* end of wave */
- {
+     } /* end of individual */
-   /* This routine should help understanding what is done with
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-      the selection of individuals/waves and
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-      to check the exact contribution to the likelihood.
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-      Plotting could be done.
+       for(mi=1; mi<= wav[i]-1; mi++){
-    */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   int k;
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     strcpy(fileresilk,"ilk");
+           }
-     strcat(fileresilk,fileres);
+         for(d=0; d<dh[mi][i]; d++){
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+           newm=savm;
-       printf("Problem with resultfile: %s\n", fileresilk);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+           for (kk=1; kk<=cptcovage;kk++) {
-     }
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+           }
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for(k=1; k<=nlstate; k++)
+           savm=oldm;
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+           oldm=newm;
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+         } /* end mult */
-   }
+         s1=s[mw[mi][i]][i];
-   *fretone=(*funcone)(p);
+         s2=s[mw[mi+1][i]][i];
-   if(*globpri !=0){
+         bbh=(double)bh[mi][i]/(double)stepm;
-     fclose(ficresilk);
+         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 */
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+         ipmx +=1;
-     fflush(fichtm);
+         sw += weight[i];
-   }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   return;
+       } /* end of wave */
- }
+     } /* end of individual */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- /*********** Maximum Likelihood Estimation ***************/
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- {
+           for (j=1;j<=nlstate+ndeath;j++){
-   int i,j, iter;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double **xi;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double fret;
+           }
-   double fretone; /* Only one call to likelihood */
+         for(d=0; d<dh[mi][i]; d++){
-   /*  char filerespow[FILENAMELENGTH];*/
+           newm=savm;
-   xi=matrix(1,npar,1,npar);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   for (i=1;i<=npar;i++)
+           for (kk=1; kk<=cptcovage;kk++) {
-     for (j=1;j<=npar;j++)
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+           }
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   strcpy(filerespow,"pow");
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   strcat(filerespow,fileres);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+           savm=oldm;
-     printf("Problem with resultfile: %s\n", filerespow);
+           oldm=newm;
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         } /* end mult */
-   }
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+         s1=s[mw[mi][i]][i];
-   for (i=1;i<=nlstate;i++)
+         s2=s[mw[mi+1][i]][i];
-     for(j=1;j<=nlstate+ndeath;j++)
+         if( s2 > nlstate){
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-   fprintf(ficrespow,"\n");
+         }else{
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+         }
+         ipmx +=1;
-   free_matrix(xi,1,npar,1,npar);
+         sw += weight[i];
-   fclose(ficrespow);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+ /*      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#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+       } /* end of wave */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
- }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- /**** Computes Hessian and covariance matrix ***/
+       for(mi=1; mi<= wav[i]-1; mi++){
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- {
+           for (j=1;j<=nlstate+ndeath;j++){
-   double  **a,**y,*x,pd;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double **hess;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   int i, j,jk;
+           }
-   int *indx;
+         for(d=0; d<dh[mi][i]; d++){
+           newm=savm;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+           for (kk=1; kk<=cptcovage;kk++) {
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+           }
-   double gompertz(double p[]);
-   hess=matrix(1,npar,1,npar);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+           savm=oldm;
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+           oldm=newm;
-   for (i=1;i<=npar;i++){
+         } /* end mult */
-     printf("%d",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         ipmx +=1;
-     /*  printf(" %f ",p[i]);
+         sw += weight[i];
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   }
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+       } /* end of wave */
-   for (i=1;i<=npar;i++) {
+     } /* end of individual */
-     for (j=1;j<=npar;j++)  {
+   } /* End of if */
-       if (j>i) {
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-         printf(".%d%d",i,j);fflush(stdout);
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+   return -l;
+ }
-         hess[j][i]=hess[i][j];
-         /*printf(" %lf ",hess[i][j]);*/
+ /*************** log-likelihood *************/
-       }
+ double funcone( double *x)
-     }
+ {
-   }
+   /* Same as likeli but slower because of a lot of printf and if */
-   printf("\n");
+   int i, ii, j, k, mi, d, kk;
-   fprintf(ficlog,"\n");
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   double lli; /* Individual log likelihood */
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+   double llt;
+   int s1, s2;
-   a=matrix(1,npar,1,npar);
+   double bbh, survp;
-   y=matrix(1,npar,1,npar);
+   /*extern weight */
-   x=vector(1,npar);
+   /* We are differentiating ll according to initial status */
-   indx=ivector(1,npar);
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   for (i=1;i<=npar;i++)
+   /*for(i=1;i<imx;i++)
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+     printf(" %d\n",s[4][i]);
-   ludcmp(a,npar,indx,&pd);
+   */
+   cov[1]=1.;
-   for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-     x[j]=1;
-     lubksb(a,npar,indx,x);
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for (i=1;i<=npar;i++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       matcov[i][j]=x[i];
+     for(mi=1; mi<= wav[i]-1; mi++){
-     }
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+         for (j=1;j<=nlstate+ndeath;j++){
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   printf("\n#Hessian matrix#\n");
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+         }
-   for (i=1;i<=npar;i++) {
+       for(d=0; d<dh[mi][i]; d++){
-     for (j=1;j<=npar;j++) {
+         newm=savm;
-       printf("%.3e ",hess[i][j]);
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+         for (kk=1; kk<=cptcovage;kk++) {
-     }
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     printf("\n");
+         }
-     fprintf(ficlog,"\n");
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   }
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /* Recompute Inverse */
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-   for (i=1;i<=npar;i++)
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+         savm=oldm;
-   ludcmp(a,npar,indx,&pd);
+         oldm=newm;
+       } /* end mult */
-   /*  printf("\n#Hessian matrix recomputed#\n");
+       s1=s[mw[mi][i]][i];
-   for (j=1;j<=npar;j++) {
+       s2=s[mw[mi+1][i]][i];
-     for (i=1;i<=npar;i++) x[i]=0;
+       bbh=(double)bh[mi][i]/(double)stepm;
-     x[j]=1;
+       /* bias is positive if real duration
-     lubksb(a,npar,indx,x);
+        * is higher than the multiple of stepm and negative otherwise.
-     for (i=1;i<=npar;i++){
+        */
-       y[i][j]=x[i];
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-       printf("%.3e ",y[i][j]);
+         lli=log(out[s1][s2] - savm[s1][s2]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
+       } else if  (s2==-2) {
-     }
+         for (j=1,survp=0. ; j<=nlstate; j++)
-     printf("\n");
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     fprintf(ficlog,"\n");
+         lli= log(survp);
-   }
+       }else if (mle==1){
-   */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       } else if(mle==2){
-   free_matrix(a,1,npar,1,npar);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   free_matrix(y,1,npar,1,npar);
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   free_vector(x,1,npar);
+         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 */
-   free_ivector(indx,1,npar);
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   free_matrix(hess,1,npar,1,npar);
+         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 */
+       } /* End of if */
- /*************** hessian matrix ****************/
+       ipmx +=1;
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+       sw += weight[i];
- {
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   int 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]); */
-   int l=1, lmax=20;
+       if(globpr){
-   double k1,k2;
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-   double p2[NPARMAX+1];
+  %11.6f %11.6f %11.6f ", \
-   double res;
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-   double fx;
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   int k=0,kmax=10;
+           llt +=ll[k]*gipmx/gsw;
-   double l1;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
-   fx=func(x);
+         fprintf(ficresilk," %10.6f\n", -llt);
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+       }
-   for(l=0 ; l <=lmax; l++){
+     } /* end of wave */
-     l1=pow(10,l);
+   } /* end of individual */
-     delts=delt;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     for(k=1 ; k <kmax; k=k+1){
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-       delt = delta*(l1*k);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-       p2[theta]=x[theta] +delt;
+   if(globpr==0){ /* First time we count the contributions and weights */
-       k1=func(p2)-fx;
+     gipmx=ipmx;
-       p2[theta]=x[theta]-delt;
+     gsw=sw;
-       k2=func(p2)-fx;
+   }
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   return -l;
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+ }
- #ifdef DEBUG
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+ /*************** function likelione ***********/
-       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);
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
- #endif
+ {
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   /* This routine should help understanding what is done with
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+      the selection of individuals/waves and
-         k=kmax;
+      to check the exact contribution to the likelihood.
-       }
+      Plotting could be done.
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+    */
-         k=kmax; l=lmax*10.;
+   int k;
-       }
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-         delts=delt;
+     strcpy(fileresilk,"ilk");
-       }
+     strcat(fileresilk,fileres);
-     }
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-   }
+       printf("Problem with resultfile: %s\n", fileresilk);
-   delti[theta]=delts;
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   return res;
+     }
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
- }
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+     for(k=1; k<=nlstate; k++)
- {
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   int i;
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   int l=1, l1, lmax=20;
+   }
-   double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   *fretone=(*funcone)(p);
-   int k;
+   if(*globpri !=0){
+     fclose(ficresilk);
-   fx=func(x);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   for (k=1; k<=2; k++) {
+     fflush(fichtm);
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+   }
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   return;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+ }
-     k1=func(p2)-fx;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+ /*********** Maximum Likelihood Estimation ***************/
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     k2=func(p2)-fx;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+ {
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   int i,j, iter;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   double **xi;
-     k3=func(p2)-fx;
+   double fret;
+   double fretone; /* Only one call to likelihood */
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   /*  char filerespow[FILENAMELENGTH];*/
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   xi=matrix(1,npar,1,npar);
-     k4=func(p2)-fx;
+   for (i=1;i<=npar;i++)
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     for (j=1;j<=npar;j++)
- #ifdef DEBUG
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     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);
+   strcpy(filerespow,"pow");
- #endif
+   strcat(filerespow,fileres);
-   }
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   return res;
+     printf("Problem with resultfile: %s\n", filerespow);
- }
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   }
- /************** Inverse of matrix **************/
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
- void ludcmp(double **a, int n, int *indx, double *d)
+   for (i=1;i<=nlstate;i++)
- {
+     for(j=1;j<=nlstate+ndeath;j++)
-   int i,imax,j,k;
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   double big,dum,sum,temp;
+   fprintf(ficrespow,"\n");
-   double *vv;
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-   vv=vector(1,n);
-   *d=1.0;
+   free_matrix(xi,1,npar,1,npar);
-   for (i=1;i<=n;i++) {
+   fclose(ficrespow);
-     big=0.0;
+   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-     for (j=1;j<=n;j++)
+   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     vv[i]=1.0/big;
+ }
-   }
-   for (j=1;j<=n;j++) {
+ /**** Computes Hessian and covariance matrix ***/
-     for (i=1;i<j;i++) {
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-       sum=a[i][j];
+ {
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   double  **a,**y,*x,pd;
-       a[i][j]=sum;
+   double **hess;
-     }
+   int i, j,jk;
-     big=0.0;
+   int *indx;
-     for (i=j;i<=n;i++) {
-       sum=a[i][j];
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-       for (k=1;k<j;k++)
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-         sum -= a[i][k]*a[k][j];
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-       a[i][j]=sum;
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+   double gompertz(double p[]);
-         big=dum;
+   hess=matrix(1,npar,1,npar);
-         imax=i;
-       }
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-     }
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-     if (j != imax) {
+   for (i=1;i<=npar;i++){
-       for (k=1;k<=n;k++) {
+     printf("%d",i);fflush(stdout);
-         dum=a[imax][k];
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-         a[imax][k]=a[j][k];
-         a[j][k]=dum;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-       }
-       *d = -(*d);
+     /*  printf(" %f ",p[i]);
-       vv[imax]=vv[j];
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-     }
+   }
-     indx[j]=imax;
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   for (i=1;i<=npar;i++) {
-     if (j != n) {
+     for (j=1;j<=npar;j++)  {
-       dum=1.0/(a[j][j]);
+       if (j>i) {
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+         printf(".%d%d",i,j);fflush(stdout);
-     }
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-   }
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   free_vector(vv,1,n);  /* Doesn't work */
- ;
+         hess[j][i]=hess[i][j];
- }
+         /*printf(" %lf ",hess[i][j]);*/
+       }
- void lubksb(double **a, int n, int *indx, double b[])
+     }
- {
+   }
-   int i,ii=0,ip,j;
+   printf("\n");
-   double sum;
+   fprintf(ficlog,"\n");
-   for (i=1;i<=n;i++) {
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-     ip=indx[i];
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-     sum=b[ip];
-     b[ip]=b[i];
+   a=matrix(1,npar,1,npar);
-     if (ii)
+   y=matrix(1,npar,1,npar);
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+   x=vector(1,npar);
-     else if (sum) ii=i;
+   indx=ivector(1,npar);
-     b[i]=sum;
+   for (i=1;i<=npar;i++)
-   }
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   for (i=n;i>=1;i--) {
+   ludcmp(a,npar,indx,&pd);
-     sum=b[i];
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   for (j=1;j<=npar;j++) {
-     b[i]=sum/a[i][i];
+     for (i=1;i<=npar;i++) x[i]=0;
-   }
+     x[j]=1;
- }
+     lubksb(a,npar,indx,x);
+     for (i=1;i<=npar;i++){
- void pstamp(FILE *fichier)
+       matcov[i][j]=x[i];
- {
+     }
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   }
- }
+   printf("\n#Hessian matrix#\n");
- /************ Frequencies ********************/
+   fprintf(ficlog,"\n#Hessian matrix#\n");
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
+   for (i=1;i<=npar;i++) {
- {  /* Some frequencies */
+     for (j=1;j<=npar;j++) {
+       printf("%.3e ",hess[i][j]);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-   int first;
+     }
-   double ***freq; /* Frequencies */
+     printf("\n");
-   double *pp, **prop;
+     fprintf(ficlog,"\n");
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   }
-   char fileresp[FILENAMELENGTH];
+   /* Recompute Inverse */
-   pp=vector(1,nlstate);
+   for (i=1;i<=npar;i++)
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-   strcpy(fileresp,"p");
+   ludcmp(a,npar,indx,&pd);
-   strcat(fileresp,fileres);
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   /*  printf("\n#Hessian matrix recomputed#\n");
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   for (j=1;j<=npar;j++) {
-     exit(0);
+     for (i=1;i<=npar;i++) x[i]=0;
-   }
+     x[j]=1;
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+     lubksb(a,npar,indx,x);
-   j1=0;
+     for (i=1;i<=npar;i++){
+       y[i][j]=x[i];
-   j=cptcoveff;
+       printf("%.3e ",y[i][j]);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+       fprintf(ficlog,"%.3e ",y[i][j]);
+     }
-   first=1;
+     printf("\n");
+     fprintf(ficlog,"\n");
-   for(k1=1; k1<=j;k1++){
+   }
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   */
-       j1++;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   free_matrix(a,1,npar,1,npar);
-         scanf("%d", i);*/
+   free_matrix(y,1,npar,1,npar);
-       for (i=-5; i<=nlstate+ndeath; i++)
+   free_vector(x,1,npar);
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   free_ivector(indx,1,npar);
-           for(m=iagemin; m <= iagemax+3; m++)
+   free_matrix(hess,1,npar,1,npar);
-             freq[i][jk][m]=0;
-     for (i=1; i<=nlstate; i++)
+ }
-       for(m=iagemin; m <= iagemax+3; m++)
-         prop[i][m]=0;
+ /*************** hessian matrix ****************/
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-       dateintsum=0;
+ {
-       k2cpt=0;
+   int i;
-       for (i=1; i<=imx; i++) {
+   int l=1, lmax=20;
-         bool=1;
+   double k1,k2;
-         if  (cptcovn>0) {
+   double p2[MAXPARM+1]; /* identical to x */
-           for (z1=1; z1<=cptcoveff; z1++)
+   double res;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-               bool=0;
+   double fx;
-         }
+   int k=0,kmax=10;
-         if (bool==1){
+   double l1;
-           for(m=firstpass; m<=lastpass; m++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+   fx=func(x);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     l1=pow(10,l);
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     delts=delt;
-               if (m<lastpass) {
+     for(k=1 ; k <kmax; k=k+1){
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+       delt = delta*(l1*k);
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+       p2[theta]=x[theta] +delt;
-               }
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
+       p2[theta]=x[theta]-delt;
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+       k2=func(p2)-fx;
-                 dateintsum=dateintsum+k2;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-                 k2cpt++;
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-               }
-               /*}*/
+ #ifdef DEBUGHESS
-           }
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-         }
+       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){ */
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-       pstamp(ficresp);
+         k=kmax;
-       if  (cptcovn>0) {
+       }
-         fprintf(ficresp, "\n#********** Variable ");
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         k=kmax; l=lmax*10.;
-         fprintf(ficresp, "**********\n#");
+       }
-       }
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-       for(i=1; i<=nlstate;i++)
+         delts=delt;
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       }
-       fprintf(ficresp, "\n");
+     }
+   }
-       for(i=iagemin; i <= iagemax+3; i++){
+   delti[theta]=delts;
-         if(i==iagemax+3){
+   return res;
-           fprintf(ficlog,"Total");
-         }else{
+ }
-           if(first==1){
-             first=0;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-             printf("See log file for details...\n");
+ {
-           }
+   int i;
-           fprintf(ficlog,"Age %d", i);
+   int l=1, l1, lmax=20;
-         }
+   double k1,k2,k3,k4,res,fx;
-         for(jk=1; jk <=nlstate ; jk++){
+   double p2[MAXPARM+1];
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   int k;
-             pp[jk] += freq[jk][m][i];
-         }
+   fx=func(x);
-         for(jk=1; jk <=nlstate ; jk++){
+   for (k=1; k<=2; k++) {
-           for(m=-1, pos=0; m <=0 ; m++)
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-             pos += freq[jk][m][i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-           if(pp[jk]>=1.e-10){
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-             if(first==1){
+     k1=func(p2)-fx;
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             }
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-           }else{
+     k2=func(p2)-fx;
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-           }
+     k3=func(p2)-fx;
-         }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-         for(jk=1; jk <=nlstate ; jk++){
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+     k4=func(p2)-fx;
-             pp[jk] += freq[jk][m][i];
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-         }
+ #ifdef DEBUG
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+     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);
-           pos += pp[jk];
+     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);
-           posprop += prop[jk][i];
+ #endif
-         }
+   }
-         for(jk=1; jk <=nlstate ; jk++){
+   return res;
-           if(pos>=1.e-5){
+ }
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ /************** Inverse of matrix **************/
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ void ludcmp(double **a, int n, int *indx, double *d)
-           }else{
+ {
-             if(first==1)
+   int i,imax,j,k;
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double big,dum,sum,temp;
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   double *vv;
-           }
-           if( i <= iagemax){
+   vv=vector(1,n);
-             if(pos>=1.e-5){
+   *d=1.0;
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+   for (i=1;i<=n;i++) {
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+     big=0.0;
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+     for (j=1;j<=n;j++)
-             }
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-             else
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+     vv[i]=1.0/big;
-           }
+   }
-         }
+   for (j=1;j<=n;j++) {
+     for (i=1;i<j;i++) {
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+       sum=a[i][j];
-           for(m=-1; m <=nlstate+ndeath; m++)
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-             if(freq[jk][m][i] !=0 ) {
+       a[i][j]=sum;
-             if(first==1)
+     }
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+     big=0.0;
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+     for (i=j;i<=n;i++) {
-             }
+       sum=a[i][j];
-         if(i <= iagemax)
+       for (k=1;k<j;k++)
-           fprintf(ficresp,"\n");
+         sum -= a[i][k]*a[k][j];
-         if(first==1)
+       a[i][j]=sum;
-           printf("Others in log...\n");
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-         fprintf(ficlog,"\n");
+         big=dum;
-       }
+         imax=i;
-     }
+       }
-   }
+     }
-   dateintmean=dateintsum/k2cpt;
+     if (j != imax) {
+       for (k=1;k<=n;k++) {
-   fclose(ficresp);
+         dum=a[imax][k];
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+         a[imax][k]=a[j][k];
-   free_vector(pp,1,nlstate);
+         a[j][k]=dum;
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+       }
-   /* End of Freq */
+       *d = -(*d);
- }
+       vv[imax]=vv[j];
+     }
- /************ Prevalence ********************/
+     indx[j]=imax;
- 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)
+     if (a[j][j] == 0.0) a[j][j]=TINY;
- {
+     if (j != n) {
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+       dum=1.0/(a[j][j]);
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-      We still use firstpass and lastpass as another selection.
+     }
-   */
+   }
+   free_vector(vv,1,n);  /* Doesn't work */
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+ ;
-   double ***freq; /* Frequencies */
+ }
-   double *pp, **prop;
-   double pos,posprop;
+ void lubksb(double **a, int n, int *indx, double b[])
-   double  y2; /* in fractional years */
+ {
-   int iagemin, iagemax;
+   int i,ii=0,ip,j;
+   double sum;
-   iagemin= (int) agemin;
-   iagemax= (int) agemax;
+   for (i=1;i<=n;i++) {
-   /*pp=vector(1,nlstate);*/
+     ip=indx[i];
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     sum=b[ip];
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+     b[ip]=b[i];
-   j1=0;
+     if (ii)
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   j=cptcoveff;
+     else if (sum) ii=i;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+     b[i]=sum;
+   }
-   for(k1=1; k1<=j;k1++){
+   for (i=n;i>=1;i--) {
-     for(i1=1; i1<=ncodemax[k1];i1++){
+     sum=b[i];
-       j1++;
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     b[i]=sum/a[i][i];
-       for (i=1; i<=nlstate; i++)
+   }
-         for(m=iagemin; m <= iagemax+3; m++)
+ }
-           prop[i][m]=0.0;
+ void pstamp(FILE *fichier)
-       for (i=1; i<=imx; i++) { /* Each individual */
+ {
-         bool=1;
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-         if  (cptcovn>0) {
+ }
-           for (z1=1; z1<=cptcoveff; z1++)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+ /************ Frequencies ********************/
-               bool=0;
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-         }
+ {  /* Some frequencies */
-         if (bool==1) {
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+   int first;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+   double ***freq; /* Frequencies */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   double *pp, **prop;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-               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);
+   char fileresp[FILENAMELENGTH];
-               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]]);*/
+   pp=vector(1,nlstate);
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   strcpy(fileresp,"p");
-               }
+   strcat(fileresp,fileres);
-             }
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-           } /* end selection of waves */
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-         }
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-       }
+     exit(0);
-       for(i=iagemin; i <= iagemax+3; i++){
+   }
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+   j1=0;
-           posprop += prop[jk][i];
-         }
+   j=cptcoveff;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-         for(jk=1; jk <=nlstate ; jk++){
-           if( i <=  iagemax){
+   first=1;
-             if(posprop>=1.e-5){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-             }
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-           }
+   /*    j1++;
-         }/* end jk */
+ */
-       }/* end i */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-     } /* end i1 */
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-   } /* end k1 */
+         scanf("%d", i);*/
+       for (i=-5; i<=nlstate+ndeath; i++)
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-   /*free_vector(pp,1,nlstate);*/
+           for(m=iagemin; m <= iagemax+3; m++)
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+             freq[i][jk][m]=0;
- }  /* End of prevalence */
+       for (i=1; i<=nlstate; i++)
- /************* Waves Concatenation ***************/
+         for(m=iagemin; m <= iagemax+3; m++)
+           prop[i][m]=0;
- 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)
- {
+       dateintsum=0;
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       k2cpt=0;
-      Death is a valid wave (if date is known).
+       for (i=1; i<=imx; i++) {
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+         bool=1;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-      and mw[mi+1][i]. dh depends on stepm.
+           for (z1=1; z1<=cptcoveff; z1++)
-      */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-   int i, mi, m;
+               bool=0;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+               /* 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",
-      double sum=0., jmean=0.;*/
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-   int first;
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-   int j, k=0,jk, ju, jl;
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-   double sum=0.;
+             }
-   first=0;
+         }
-   jmin=1e+5;
-   jmax=-1;
+         if (bool==1){
-   jmean=0.;
+           for(m=firstpass; m<=lastpass; m++){
-   for(i=1; i<=imx; i++){
+             k2=anint[m][i]+(mint[m][i]/12.);
-     mi=0;
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-     m=firstpass;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-     while(s[m][i] <= nlstate){
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-         mw[++mi][i]=m;
+               if (m<lastpass) {
-       if(m >=lastpass)
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-         break;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-       else
+               }
-         m++;
-     }/* end while */
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-     if (s[m][i] > nlstate){
+                 dateintsum=dateintsum+k2;
-       mi++;     /* Death is another wave */
+                 k2cpt++;
-       /* if(mi==0)  never been interviewed correctly before death */
+               }
-          /* Only death is a correct wave */
+               /*}*/
-       mw[mi][i]=m;
+           }
-     }
+         }
+       } /* end i */
-     wav[i]=mi;
-     if(mi==0){
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-       nbwarn++;
+       pstamp(ficresp);
-       if(first==0){
+       if  (cptcovn>0) {
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         fprintf(ficresp, "\n#********** Variable ");
-         first=1;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       }
+         fprintf(ficresp, "**********\n#");
-       if(first==1){
+         fprintf(ficlog, "\n#********** Variable ");
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       }
+         fprintf(ficlog, "**********\n#");
-     } /* end mi==0 */
+       }
-   } /* End individuals */
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-   for(i=1; i<=imx; i++){
+       fprintf(ficresp, "\n");
-     for(mi=1; mi<wav[i];mi++){
-       if (stepm <=0)
+       for(i=iagemin; i <= iagemax+3; i++){
-         dh[mi][i]=1;
+         if(i==iagemax+3){
-       else{
+           fprintf(ficlog,"Total");
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         }else{
-           if (agedc[i] < 2*AGESUP) {
+           if(first==1){
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             first=0;
-             if(j==0) j=1;  /* Survives at least one month after exam */
+             printf("See log file for details...\n");
-             else if(j<0){
+           }
-               nberr++;
+           fprintf(ficlog,"Age %d", i);
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         }
-               j=1; /* Temporary Dangerous patch */
+         for(jk=1; jk <=nlstate ; jk++){
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-               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]);
+             pp[jk] += freq[jk][m][i];
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+         }
-             }
+         for(jk=1; jk <=nlstate ; jk++){
-             k=k+1;
+           for(m=-1, pos=0; m <=0 ; m++)
-             if (j >= jmax){
+             pos += freq[jk][m][i];
-               jmax=j;
+           if(pp[jk]>=1.e-10){
-               ijmax=i;
+             if(first==1){
-             }
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             if (j <= jmin){
+             }
-               jmin=j;
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-               ijmin=i;
+           }else{
-             }
+             if(first==1)
-             sum=sum+j;
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+           }
-           }
+         }
-         }
-         else{
+         for(jk=1; jk <=nlstate ; jk++){
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
- /*        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]); */
+             pp[jk] += freq[jk][m][i];
+         }
-           k=k+1;
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-           if (j >= jmax) {
+           pos += pp[jk];
-             jmax=j;
+           posprop += prop[jk][i];
-             ijmax=i;
+         }
-           }
+         for(jk=1; jk <=nlstate ; jk++){
-           else if (j <= jmin){
+           if(pos>=1.e-5){
-             jmin=j;
+             if(first==1)
-             ijmin=i;
+               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);
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           }else{
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+             if(first==1)
-           if(j<0){
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             nberr++;
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             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( i <= iagemax){
-           }
+             if(pos>=1.e-5){
-           sum=sum+j;
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-         }
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-         jk= j/stepm;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-         jl= j -jk*stepm;
+             }
-         ju= j -(jk+1)*stepm;
+             else
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-           if(jl==0){
+           }
-             dh[mi][i]=jk;
+         }
-             bh[mi][i]=0;
-           }else{ /* We want a negative bias in order to only have interpolation ie
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-                   * at the price of an extra matrix product in likelihood */
+           for(m=-1; m <=nlstate+ndeath; m++)
-             dh[mi][i]=jk+1;
+             if(freq[jk][m][i] !=0 ) {
-             bh[mi][i]=ju;
+             if(first==1)
-           }
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-         }else{
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-           if(jl <= -ju){
+             }
-             dh[mi][i]=jk;
+         if(i <= iagemax)
-             bh[mi][i]=jl;       /* bias is positive if real duration
+           fprintf(ficresp,"\n");
-                                  * is higher than the multiple of stepm and negative otherwise.
+         if(first==1)
-                                  */
+           printf("Others in log...\n");
-           }
+         fprintf(ficlog,"\n");
-           else{
+       }
-             dh[mi][i]=jk+1;
+       /*}*/
-             bh[mi][i]=ju;
+   }
-           }
+   dateintmean=dateintsum/k2cpt;
-           if(dh[mi][i]==0){
-             dh[mi][i]=1; /* At least one step */
+   fclose(ficresp);
-             bh[mi][i]=ju; /* At least one step */
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-             /*  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);*/
+   free_vector(pp,1,nlstate);
-           }
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-         } /* end if mle */
+   /* End of Freq */
-       }
+ }
-     } /* end wave */
-   }
+ /************ Prevalence ********************/
-   jmean=sum/k;
+ 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)
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+ {
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+   /* 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.
- /*********** Tricode ****************************/
+   */
- void tricode(int *Tvar, int **nbcode, int imx)
- {
+   int i, m, jk, k1, i1, j1, bool, z1,j;
+   double ***freq; /* Frequencies */
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+   double *pp, **prop;
-   int cptcode=0;
+   double pos,posprop;
-   cptcoveff=0;
+   double  y2; /* in fractional years */
+   int iagemin, iagemax;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   int first; /** to stop verbosity which is redirected to log file */
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   iagemin= (int) agemin;
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   iagemax= (int) agemax;
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   /*pp=vector(1,nlstate);*/
-                                modality*/
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-       Ndum[ij]++; /*store the modality */
+   j1=0;
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+   /*j=cptcoveff;*/
-                                        Tvar[j]. If V=sex and male is 0 and
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-                                        female is 1, then  cptcode=1.*/
-     }
+   first=1;
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-     for (i=0; i<=cptcode; i++) {
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-       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 */
+       j1++;*/
-     }
+       for (i=1; i<=nlstate; i++)
-     ij=1;
+         for(m=iagemin; m <= iagemax+3; m++)
-     for (i=1; i<=ncodemax[j]; i++) {
+           prop[i][m]=0.0;
-       for (k=0; k<= maxncov; k++) {
-         if (Ndum[k] != 0) {
+       for (i=1; i<=imx; i++) { /* Each individual */
-           nbcode[Tvar[j]][ij]=k;
+         bool=1;
-           /* 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; */
+         if  (cptcovn>0) {
+           for (z1=1; z1<=cptcoveff; z1++)
-           ij++;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-         }
+               bool=0;
-         if (ij > ncodemax[j]) break;
+         }
-       }
+         if (bool==1) {
-     }
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   }
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-  for (i=1; i<=ncovmodel-2; i++) {
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-    ij=Tvar[i];
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-    Ndum[ij]++;
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-  }
+                 prop[s[m][i]][iagemax+3] += weight[i];
+               }
-  ij=1;
+             }
-  for (i=1; i<= maxncov; i++) {
+           } /* end selection of waves */
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+         }
-      Tvaraff[ij]=i; /*For printing */
+       }
-      ij++;
+       for(i=iagemin; i <= iagemax+3; i++){
-    }
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-  }
+           posprop += prop[jk][i];
+         }
-  cptcoveff=ij-1; /*Number of simple covariates*/
- }
+         for(jk=1; jk <=nlstate ; jk++){
+           if( i <=  iagemax){
- /*********** Health Expectancies ****************/
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+             } else{
+               if(first==1){
- {
+                 first=0;
-   /* Health expectancies, no variances */
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+               }
-   double age, agelim, hf;
+             }
-   double ***p3mat;
+           }
-   double eip;
+         }/* end jk */
+       }/* end i */
-   pstamp(ficreseij);
+     /*} *//* end i1 */
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   } /* end j1 */
-   fprintf(ficreseij,"# Age");
-   for(i=1; i<=nlstate;i++){
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-     for(j=1; j<=nlstate;j++){
+   /*free_vector(pp,1,nlstate);*/
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-     }
+ }  /* End of prevalence */
-     fprintf(ficreseij," e%1d. ",i);
-   }
+ /************* Waves Concatenation ***************/
-   fprintf(ficreseij,"\n");
+ 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)
+ {
-   if(estepm < stepm){
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+      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
-   else  hstepm=estepm;
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+      and mw[mi+1][i]. dh depends on stepm.
-    * This is mainly to measure the difference between two models: for example
+      */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   int i, mi, m;
-    * progression in between and thus overestimating or underestimating according
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-    * to the curvature of the survival function. If, for the same date, we
+      double sum=0., jmean=0.;*/
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   int first;
-    * to compare the new estimate of Life expectancy with the same linear
+   int j, k=0,jk, ju, jl;
-    * hypothesis. A more precise result, taking into account a more precise
+   double sum=0.;
-    * curvature will be obtained if estepm is as small as stepm. */
+   first=0;
+   jmin=1e+5;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   jmax=-1;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   jmean=0.;
-      nhstepm is the number of hstepm from age to agelim
+   for(i=1; i<=imx; i++){
-      nstepm is the number of stepm from age to agelin.
+     mi=0;
-      Look at hpijx to understand the reason of that which relies in memory size
+     m=firstpass;
-      and note for a fixed period like estepm months */
+     while(s[m][i] <= nlstate){
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-      survival function given by stepm (the optimization length). Unfortunately it
+         mw[++mi][i]=m;
-      means that if the survival funtion is printed only each two years of age and if
+       if(m >=lastpass)
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+         break;
-      results. So we changed our mind and took the option of the best precision.
+       else
-   */
+         m++;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     }/* end while */
+     if (s[m][i] > nlstate){
-   agelim=AGESUP;
+       mi++;     /* Death is another wave */
-   /* If stepm=6 months */
+       /* if(mi==0)  never been interviewed correctly before death */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+          /* Only death is a correct wave */
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+       mw[mi][i]=m;
+     }
- /* nhstepm age range expressed in number of stepm */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+     wav[i]=mi;
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     if(mi==0){
-   /* if (stepm >= YEARM) hstepm=1;*/
+       nbwarn++;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       if(first==0){
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         first=1;
-   for (age=bage; age<=fage; age ++){
+       }
+       if(first==1){
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+       }
+     } /* end mi==0 */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   } /* End individuals */
-     printf("%d|",(int)age);fflush(stdout);
+   for(i=1; i<=imx; i++){
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     for(mi=1; mi<wav[i];mi++){
+       if (stepm <=0)
+         dh[mi][i]=1;
-     /* Computing expectancies */
+       else{
-     for(i=1; i<=nlstate;i++)
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-       for(j=1; j<=nlstate;j++)
+           if (agedc[i] < 2*AGESUP) {
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+             if(j==0) j=1;  /* Survives at least one month after exam */
+             else if(j<0){
-           /*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]);*/
+               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]);
-         }
+               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);
-     fprintf(ficreseij,"%3.0f",age );
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-     for(i=1; i<=nlstate;i++){
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-       eip=0;
+             }
-       for(j=1; j<=nlstate;j++){
+             k=k+1;
-         eip +=eij[i][j][(int)age];
+             if (j >= jmax){
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+               jmax=j;
-       }
+               ijmax=i;
-       fprintf(ficreseij,"%9.4f", eip );
+             }
-     }
+             if (j <= jmin){
-     fprintf(ficreseij,"\n");
+               jmin=j;
+               ijmin=i;
-   }
+             }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             sum=sum+j;
-   printf("\n");
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-   fprintf(ficlog,"\n");
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+           }
- }
+         }
+         else{
- 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[] )
+           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]); */
- {
-   /* Covariances of health expectancies eij and of total life expectancies according
+           k=k+1;
-    to initial status i, ei. .
+           if (j >= jmax) {
-   */
+             jmax=j;
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+             ijmax=i;
-   double age, agelim, hf;
+           }
-   double ***p3matp, ***p3matm, ***varhe;
+           else if (j <= jmin){
-   double **dnewm,**doldm;
+             jmin=j;
-   double *xp, *xm;
+             ijmin=i;
-   double **gp, **gm;
+           }
-   double ***gradg, ***trgradg;
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-   int theta;
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+           if(j<0){
-   double eip, vip;
+             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]);
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+             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]);
-   xp=vector(1,npar);
+           }
-   xm=vector(1,npar);
+           sum=sum+j;
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+         }
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+         jk= j/stepm;
+         jl= j -jk*stepm;
-   pstamp(ficresstdeij);
+         ju= j -(jk+1)*stepm;
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-   fprintf(ficresstdeij,"# Age");
+           if(jl==0){
-   for(i=1; i<=nlstate;i++){
+             dh[mi][i]=jk;
-     for(j=1; j<=nlstate;j++)
+             bh[mi][i]=0;
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+           }else{ /* We want a negative bias in order to only have interpolation ie
-     fprintf(ficresstdeij," e%1d. ",i);
+                   * to avoid the price of an extra matrix product in likelihood */
-   }
+             dh[mi][i]=jk+1;
-   fprintf(ficresstdeij,"\n");
+             bh[mi][i]=ju;
+           }
-   pstamp(ficrescveij);
+         }else{
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+           if(jl <= -ju){
-   fprintf(ficrescveij,"# Age");
+             dh[mi][i]=jk;
-   for(i=1; i<=nlstate;i++)
+             bh[mi][i]=jl;       /* bias is positive if real duration
-     for(j=1; j<=nlstate;j++){
+                                  * is higher than the multiple of stepm and negative otherwise.
-       cptj= (j-1)*nlstate+i;
+                                  */
-       for(i2=1; i2<=nlstate;i2++)
+           }
-         for(j2=1; j2<=nlstate;j2++){
+           else{
-           cptj2= (j2-1)*nlstate+i2;
+             dh[mi][i]=jk+1;
-           if(cptj2 <= cptj)
+             bh[mi][i]=ju;
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+           }
-         }
+           if(dh[mi][i]==0){
-     }
+             dh[mi][i]=1; /* At least one step */
-   fprintf(ficrescveij,"\n");
+             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);*/
-   if(estepm < stepm){
+           }
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         } /* end if mle */
-   }
+       }
-   else  hstepm=estepm;
+     } /* end wave */
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   }
-    * This is mainly to measure the difference between two models: for example
+   jmean=sum/k;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   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);
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   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);
-    * progression in between and thus overestimating or underestimating according
+  }
-    * to the curvature of the survival function. If, for the same date, we
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ /*********** Tricode ****************************/
-    * to compare the new estimate of Life expectancy with the same linear
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-    * hypothesis. A more precise result, taking into account a more precise
+ {
-    * curvature will be obtained if estepm is as small as stepm. */
+   /**< 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
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-      nhstepm is the number of hstepm from age to agelim
+   /* nbcode[Tvar[j]][1]=
-      nstepm is the number of stepm from age to agelin.
+   */
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like estepm months */
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   int modmaxcovj=0; /* Modality max of covariates j */
-      survival function given by stepm (the optimization length). Unfortunately it
+   int cptcode=0; /* Modality max of covariates j */
-      means that if the survival funtion is printed only each two years of age and if
+   int modmincovj=0; /* Modality min of covariates j */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
-   */
+   cptcoveff=0;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   /* If stepm=6 months */
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   /* nhstepm age range expressed in number of stepm */
-   agelim=AGESUP;
+   /* Loop on covariates without age and products */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-   /* if (stepm >= YEARM) hstepm=1;*/
+                                modality of this covariate Vj*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+                                     * If product of Vn*Vm, still boolean *:
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+                                       modality of the nth covariate of individual i. */
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+       if (ij > modmaxcovj)
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+         modmaxcovj=ij;
+       else if (ij < modmincovj)
-   for (age=bage; age<=fage; age ++){
+         modmincovj=ij;
+       if ((ij < -1) && (ij > NCOVMAX)){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         exit(1);
+       }else
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-     /* Computing  Variances of health expectancies */
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+       /* getting the maximum value of the modality of the covariate
-        decrease memory allocation */
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     for(theta=1; theta <=npar; theta++){
+          female is 1, then modmaxcovj=1.*/
-       for(i=1; i<=npar; i++){
+     }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+     cptcode=modmaxcovj;
-       }
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+    /*for (i=0; i<=cptcode; i++) {*/
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-       for(j=1; j<= nlstate; j++){
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-         for(i=1; i<=nlstate; i++){
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-           for(h=0; h<=nhstepm-1; h++){
+       }
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-           }
+     } /* Ndum[-1] number of undefined modalities */
-         }
-       }
+     /* 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 */
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-         for(h=0; h<=nhstepm-1; h++){
+        modmincovj=3; modmaxcovj = 7;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+        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
-     }/* End theta */
+        variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
+        nbcode[Tvar[j]][1]=0;
-     for(h=0; h<=nhstepm-1; h++)
+        nbcode[Tvar[j]][2]=1;
-       for(j=1; j<=nlstate*nlstate;j++)
+        nbcode[Tvar[j]][3]=2;
-         for(theta=1; theta <=npar; theta++)
+     */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+         /*recode from 0 */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-         varhe[ij][ji][(int)age] =0.;
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      k is a modality. If we have model=V1+V1*sex
-      printf("%d|",(int)age);fflush(stdout);
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           ij++;
-      for(h=0;h<=nhstepm-1;h++){
+         }
-       for(k=0;k<=nhstepm-1;k++){
+         if (ij > ncodemax[j]) break;
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+       }  /* end of loop on */
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+     } /* end of loop on modality */
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-           for(ji=1;ji<=nlstate*nlstate;ji++)
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-       }
-     }
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     /* Computing expectancies */
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+    Ndum[ij]++;
-     for(i=1; i<=nlstate;i++)
+  }
-       for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+  ij=1;
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+    if((Ndum[i]!=0) && (i<=ncovcol)){
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-         }
+      Tvaraff[ij]=i; /*For printing (unclear) */
+      ij++;
-     fprintf(ficresstdeij,"%3.0f",age );
+    }else
-     for(i=1; i<=nlstate;i++){
+        Tvaraff[ij]=0;
-       eip=0.;
+  }
-       vip=0.;
+  ij--;
-       for(j=1; j<=nlstate;j++){
+  cptcoveff=ij; /*Number of total covariates*/
-         eip += eij[i][j][(int)age];
-         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];
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-       }
+ /*********** Health Expectancies ****************/
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-     }
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-     fprintf(ficresstdeij,"\n");
+ {
-     fprintf(ficrescveij,"%3.0f",age );
+   /* Health expectancies, no variances */
-     for(i=1; i<=nlstate;i++)
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-       for(j=1; j<=nlstate;j++){
+   int nhstepma, nstepma; /* Decreasing with age */
-         cptj= (j-1)*nlstate+i;
+   double age, agelim, hf;
-         for(i2=1; i2<=nlstate;i2++)
+   double ***p3mat;
-           for(j2=1; j2<=nlstate;j2++){
+   double eip;
-             cptj2= (j2-1)*nlstate+i2;
-             if(cptj2 <= cptj)
+   pstamp(ficreseij);
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-           }
+   fprintf(ficreseij,"# Age");
-       }
+   for(i=1; i<=nlstate;i++){
-     fprintf(ficrescveij,"\n");
+     for(j=1; j<=nlstate;j++){
+       fprintf(ficreseij," e%1d%1d ",i,j);
-   }
+     }
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+     fprintf(ficreseij," e%1d. ",i);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   }
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   fprintf(ficreseij,"\n");
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   if(estepm < stepm){
-   printf("\n");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   fprintf(ficlog,"\n");
+   }
+   else  hstepm=estepm;
-   free_vector(xm,1,npar);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   free_vector(xp,1,npar);
+    * This is mainly to measure the difference between two models: for example
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+    * progression in between and thus overestimating or underestimating according
- }
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
- /************ Variance ******************/
+    * to compare the new estimate of Life expectancy with the same linear
- 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[])
+    * hypothesis. A more precise result, taking into account a more precise
- {
+    * curvature will be obtained if estepm is as small as stepm. */
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* double **newm;*/
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   double **dnewm,**doldm;
+      nhstepm is the number of hstepm from age to agelim
-   double **dnewmp,**doldmp;
+      nstepm is the number of stepm from age to agelin.
-   int i, j, nhstepm, hstepm, h, nstepm ;
+      Look at hpijx to understand the reason of that which relies in memory size
-   int k, cptcode;
+      and note for a fixed period like estepm months */
-   double *xp;
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   double **gp, **gm;  /* for var eij */
+      survival function given by stepm (the optimization length). Unfortunately it
-   double ***gradg, ***trgradg; /*for var eij */
+      means that if the survival funtion is printed only each two years of age and if
-   double **gradgp, **trgradgp; /* for var p point j */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   double *gpp, *gmp; /* for var p point j */
+      results. So we changed our mind and took the option of the best precision.
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   */
-   double ***p3mat;
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   double age,agelim, hf;
-   double ***mobaverage;
+   agelim=AGESUP;
-   int theta;
+   /* If stepm=6 months */
-   char digit[4];
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-   char digitp[25];
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-   char fileresprobmorprev[FILENAMELENGTH];
+ /* nhstepm age range expressed in number of stepm */
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   if(popbased==1){
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     if(mobilav!=0)
+   /* if (stepm >= YEARM) hstepm=1;*/
-       strcpy(digitp,"-populbased-mobilav-");
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     else strcpy(digitp,"-populbased-nomobil-");
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
-   else
+   for (age=bage; age<=fage; age ++){
-     strcpy(digitp,"-stablbased-");
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   if (mobilav!=0) {
+     /* if (stepm >= YEARM) hstepm=1;*/
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     /* If stepm=6 months */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-     }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   }
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   strcpy(fileresprobmorprev,"prmorprev");
-   sprintf(digit,"%-d",ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+     printf("%d|",(int)age);fflush(stdout);
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     /* Computing expectancies */
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     for(i=1; i<=nlstate;i++)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+       for(j=1; j<=nlstate;j++)
-   }
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+           /* 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(ficresprobmorprev);
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+         }
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     fprintf(ficreseij,"%3.0f",age );
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+     for(i=1; i<=nlstate;i++){
-     for(i=1; i<=nlstate;i++)
+       eip=0;
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+       for(j=1; j<=nlstate;j++){
-   }
+         eip +=eij[i][j][(int)age];
-   fprintf(ficresprobmorprev,"\n");
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-   fprintf(ficgp,"\n# Routine varevsij");
+       }
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+       fprintf(ficreseij,"%9.4f", eip );
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+     }
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+     fprintf(ficreseij,"\n");
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   }
-   pstamp(ficresvij);
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   printf("\n");
-   if(popbased==1)
+   fprintf(ficlog,"\n");
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
-   else
+ }
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresvij,"# Age");
+ 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++)
-     for(j=1; j<=nlstate;j++)
+ {
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   /* Covariances of health expectancies eij and of total life expectancies according
-   fprintf(ficresvij,"\n");
+    to initial status i, ei. .
+   */
-   xp=vector(1,npar);
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   dnewm=matrix(1,nlstate,1,npar);
+   int nhstepma, nstepma; /* Decreasing with age */
-   doldm=matrix(1,nlstate,1,nlstate);
+   double age, agelim, hf;
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   double ***p3matp, ***p3matm, ***varhe;
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double **dnewm,**doldm;
+   double *xp, *xm;
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   double **gp, **gm;
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   double ***gradg, ***trgradg;
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   int theta;
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   double eip, vip;
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   }
+   xp=vector(1,npar);
-   else  hstepm=estepm;
+   xm=vector(1,npar);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+   pstamp(ficresstdeij);
-      Look at hpijx to understand the reason of that which relies in memory size
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-      and note for a fixed period like k years */
+   fprintf(ficresstdeij,"# Age");
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   for(i=1; i<=nlstate;i++){
-      survival function given by stepm (the optimization length). Unfortunately it
+     for(j=1; j<=nlstate;j++)
-      means that if the survival funtion is printed every two years of age and if
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     fprintf(ficresstdeij," e%1d. ",i);
-      results. So we changed our mind and took the option of the best precision.
+   }
-   */
+   fprintf(ficresstdeij,"\n");
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
+   pstamp(ficrescveij);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   fprintf(ficrescveij,"# Age");
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   for(i=1; i<=nlstate;i++)
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     for(j=1; j<=nlstate;j++){
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+       cptj= (j-1)*nlstate+i;
-     gp=matrix(0,nhstepm,1,nlstate);
+       for(i2=1; i2<=nlstate;i2++)
-     gm=matrix(0,nhstepm,1,nlstate);
+         for(j2=1; j2<=nlstate;j2++){
+           cptj2= (j2-1)*nlstate+i2;
+           if(cptj2 <= cptj)
-     for(theta=1; theta <=npar; theta++){
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+         }
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     }
-       }
+   fprintf(ficrescveij,"\n");
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       if (popbased==1) {
+   }
-         if(mobilav ==0){
+   else  hstepm=estepm;
-           for(i=1; i<=nlstate;i++)
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-             prlim[i][i]=probs[(int)age][i][ij];
+    * This is mainly to measure the difference between two models: for example
-         }else{ /* mobilav */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-           for(i=1; i<=nlstate;i++)
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+    * progression in between and thus overestimating or underestimating according
-         }
+    * to the curvature of the survival function. If, for the same date, we
-       }
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
-       for(j=1; j<= nlstate; j++){
+    * hypothesis. A more precise result, taking into account a more precise
-         for(h=0; h<=nhstepm; h++){
+    * curvature will be obtained if estepm is as small as stepm. */
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         }
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       }
+      nhstepm is the number of hstepm from age to agelim
-       /* This for computing probability of death (h=1 means
+      nstepm is the number of stepm from age to agelin.
-          computed over hstepm matrices product = hstepm*stepm months)
+      Look at hpijx to understand the reason of that which relies in memory size
-          as a weighted average of prlim.
+      and note for a fixed period like estepm months */
-       */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+      survival function given by stepm (the optimization length). Unfortunately it
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+      means that if the survival funtion is printed only each two years of age and if
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+      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.
-       /* end probability of death */
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   /* If stepm=6 months */
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   /* nhstepm age range expressed in number of stepm */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   agelim=AGESUP;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-       if (popbased==1) {
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         if(mobilav ==0){
+   /* if (stepm >= YEARM) hstepm=1;*/
-           for(i=1; i<=nlstate;i++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           for(i=1; i<=nlstate;i++)
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-         }
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-       }
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+   for (age=bage; age<=fage; age ++){
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         }
+     /* if (stepm >= YEARM) hstepm=1;*/
-       }
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+     /* If stepm=6 months */
-          as a weighted average of prlim.
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-       */
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
+     /* Computing  Variances of health expectancies */
-       /* end probability of death */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+        decrease memory allocation */
-       for(j=1; j<= nlstate; j++) /* vareij */
+     for(theta=1; theta <=npar; theta++){
-         for(h=0; h<=nhstepm; h++){
+       for(i=1; i<=npar; i++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         }
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+       }
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-       }
+       for(j=1; j<= nlstate; j++){
-     } /* End theta */
+         for(i=1; i<=nlstate; i++){
+           for(h=0; h<=nhstepm-1; h++){
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-     for(h=0; h<=nhstepm; h++) /* veij */
+           }
-       for(j=1; j<=nlstate;j++)
+         }
-         for(theta=1; theta <=npar; theta++)
+       }
-           trgradg[h][j][theta]=gradg[h][theta][j];
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+         for(h=0; h<=nhstepm-1; h++){
-       for(theta=1; theta <=npar; theta++)
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         trgradgp[j][theta]=gradgp[theta][j];
+         }
+     }/* End theta */
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     for(i=1;i<=nlstate;i++)
+     for(h=0; h<=nhstepm-1; h++)
-       for(j=1;j<=nlstate;j++)
+       for(j=1; j<=nlstate*nlstate;j++)
-         vareij[i][j][(int)age] =0.;
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
-     for(h=0;h<=nhstepm;h++){
-       for(k=0;k<=nhstepm;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-         for(i=1;i<=nlstate;i++)
+         varhe[ij][ji][(int)age] =0.;
-           for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+      printf("%d|",(int)age);fflush(stdout);
-       }
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-     }
+      for(h=0;h<=nhstepm-1;h++){
+       for(k=0;k<=nhstepm-1;k++){
-     /* pptj */
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-         varppt[j][i]=doldmp[j][i];
+       }
-     /* end ppptj */
+     }
-     /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+     /* Computing expectancies */
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     for(i=1; i<=nlstate;i++)
-     if (popbased==1) {
+       for(j=1; j<=nlstate;j++)
-       if(mobilav ==0){
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-         for(i=1; i<=nlstate;i++)
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-           prlim[i][i]=probs[(int)age][i][ij];
-       }else{ /* mobilav */
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-         for(i=1; i<=nlstate;i++)
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-       }
-     }
+     fprintf(ficresstdeij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-     /* This for computing probability of death (h=1 means
+       eip=0.;
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+       vip=0.;
-        as a weighted average of prlim.
+       for(j=1; j<=nlstate;j++){
-     */
+         eip += eij[i][j][(int)age];
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-     }
+       }
-     /* end probability of death */
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+     }
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     fprintf(ficresstdeij,"\n");
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+     fprintf(ficrescveij,"%3.0f",age );
-       for(i=1; i<=nlstate;i++){
+     for(i=1; i<=nlstate;i++)
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       for(j=1; j<=nlstate;j++){
-       }
+         cptj= (j-1)*nlstate+i;
-     }
+         for(i2=1; i2<=nlstate;i2++)
-     fprintf(ficresprobmorprev,"\n");
+           for(j2=1; j2<=nlstate;j2++){
+             cptj2= (j2-1)*nlstate+i2;
-     fprintf(ficresvij,"%.0f ",age );
+             if(cptj2 <= cptj)
-     for(i=1; i<=nlstate;i++)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-       for(j=1; j<=nlstate;j++){
+           }
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+       }
-       }
+     fprintf(ficrescveij,"\n");
-     fprintf(ficresvij,"\n");
-     free_matrix(gp,0,nhstepm,1,nlstate);
+   }
-     free_matrix(gm,0,nhstepm,1,nlstate);
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   } /* End age */
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   printf("\n");
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   fprintf(ficlog,"\n");
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   free_vector(xm,1,npar);
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   free_vector(xp,1,npar);
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
- /*   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));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+ /************ Variance ******************/
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+ 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[])
-   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);
+   /* Variance of health expectancies */
-   /*  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);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- */
+   /* double **newm;*/
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+   double **dnewm,**doldm;
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   double **dnewmp,**doldmp;
+   int i, j, nhstepm, hstepm, h, nstepm ;
-   free_vector(xp,1,npar);
+   int k, cptcode;
-   free_matrix(doldm,1,nlstate,1,nlstate);
+   double *xp;
-   free_matrix(dnewm,1,nlstate,1,npar);
+   double **gp, **gm;  /* for var eij */
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double ***gradg, ***trgradg; /*for var eij */
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   double **gradgp, **trgradgp; /* for var p point j */
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double *gpp, *gmp; /* for var p point j */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   fclose(ficresprobmorprev);
+   double ***p3mat;
-   fflush(ficgp);
+   double age,agelim, hf;
-   fflush(fichtm);
+   double ***mobaverage;
- }  /* end varevsij */
+   int theta;
+   char digit[4];
- /************ Variance of prevlim ******************/
+   char digitp[25];
- 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[])
- {
+   char fileresprobmorprev[FILENAMELENGTH];
-   /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   if(popbased==1){
-   double **newm;
+     if(mobilav!=0)
-   double **dnewm,**doldm;
+       strcpy(digitp,"-populbased-mobilav-");
-   int i, j, nhstepm, hstepm;
+     else strcpy(digitp,"-populbased-nomobil-");
-   int k, cptcode;
+   }
-   double *xp;
+   else
-   double *gp, *gm;
+     strcpy(digitp,"-stablbased-");
-   double **gradg, **trgradg;
-   double age,agelim;
+   if (mobilav!=0) {
-   int theta;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   pstamp(ficresvpl);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(ficresvpl,"# Age");
+     }
-   for(i=1; i<=nlstate;i++)
+   }
-       fprintf(ficresvpl," %1d-%1d",i,i);
-   fprintf(ficresvpl,"\n");
+   strcpy(fileresprobmorprev,"prmorprev");
+   sprintf(digit,"%-d",ij);
-   xp=vector(1,npar);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   dnewm=matrix(1,nlstate,1,npar);
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   doldm=matrix(1,nlstate,1,nlstate);
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   strcat(fileresprobmorprev,fileres);
-   hstepm=1*YEARM; /* Every year of age */
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   agelim = AGESUP;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   }
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-     if (stepm >= YEARM) hstepm=1;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-     gradg=matrix(1,npar,1,nlstate);
+   pstamp(ficresprobmorprev);
-     gp=vector(1,nlstate);
+   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);
-     gm=vector(1,nlstate);
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     for(theta=1; theta <=npar; theta++){
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     for(i=1; i<=nlstate;i++)
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-       }
+   }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   fprintf(ficresprobmorprev,"\n");
-       for(i=1;i<=nlstate;i++)
+   fprintf(ficgp,"\n# Routine varevsij");
-         gp[i] = prlim[i][i];
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ /*   } */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       for(i=1;i<=nlstate;i++)
+   pstamp(ficresvij);
-         gm[i] = prlim[i][i];
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   if(popbased==1)
-       for(i=1;i<=nlstate;i++)
+     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);
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   else
-     } /* End theta */
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   fprintf(ficresvij,"# Age");
-     trgradg =matrix(1,nlstate,1,npar);
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++)
-     for(j=1; j<=nlstate;j++)
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-       for(theta=1; theta <=npar; theta++)
+   fprintf(ficresvij,"\n");
-         trgradg[j][theta]=gradg[theta][j];
+   xp=vector(1,npar);
-     for(i=1;i<=nlstate;i++)
+   dnewm=matrix(1,nlstate,1,npar);
-       varpl[i][(int)age] =0.;
+   doldm=matrix(1,nlstate,1,nlstate);
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     for(i=1;i<=nlstate;i++)
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
-     fprintf(ficresvpl,"%.0f ",age );
+   gmp=vector(nlstate+1,nlstate+ndeath);
-     for(i=1; i<=nlstate;i++)
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-     fprintf(ficresvpl,"\n");
+   if(estepm < stepm){
-     free_vector(gp,1,nlstate);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     free_vector(gm,1,nlstate);
+   }
-     free_matrix(gradg,1,npar,1,nlstate);
+   else  hstepm=estepm;
-     free_matrix(trgradg,1,nlstate,1,npar);
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   } /* End age */
+   /* 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
-   free_vector(xp,1,npar);
+      nstepm is the number of stepm from age to agelin.
-   free_matrix(doldm,1,nlstate,1,npar);
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
- }
+      means that if the survival funtion is printed every two years of age and if
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
- /************ Variance of one-step probabilities  ******************/
+      results. So we changed our mind and took the option of the best precision.
- 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[])
+   */
- {
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   int i, j=0,  i1, k1, l1, t, tj;
+   agelim = AGESUP;
-   int k2, l2, j1,  z1;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   int k=0,l, cptcode;
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   int first=1, first1;
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   double **dnewm,**doldm;
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-   double *xp;
+     gp=matrix(0,nhstepm,1,nlstate);
-   double *gp, *gm;
+     gm=matrix(0,nhstepm,1,nlstate);
-   double **gradg, **trgradg;
-   double **mu;
-   double age,agelim, cov[NCOVMAX];
+     for(theta=1; theta <=npar; theta++){
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-   int theta;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   char fileresprob[FILENAMELENGTH];
+       }
-   char fileresprobcov[FILENAMELENGTH];
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-   char fileresprobcor[FILENAMELENGTH];
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   double ***varpij;
+       if (popbased==1) {
+         if(mobilav ==0){
-   strcpy(fileresprob,"prob");
+           for(i=1; i<=nlstate;i++)
-   strcat(fileresprob,fileres);
+             prlim[i][i]=probs[(int)age][i][ij];
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+         }else{ /* mobilav */
-     printf("Problem with resultfile: %s\n", fileresprob);
+           for(i=1; i<=nlstate;i++)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-   }
+         }
-   strcpy(fileresprobcov,"probcov");
+       }
-   strcat(fileresprobcov,fileres);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+       for(j=1; j<= nlstate; j++){
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+         for(h=0; h<=nhstepm; h++){
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-   }
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-   strcpy(fileresprobcor,"probcor");
+         }
-   strcat(fileresprobcor,fileres);
+       }
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+       /* This for computing probability of death (h=1 means
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+          computed over hstepm matrices product = hstepm*stepm months)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+          as a weighted average of prlim.
-   }
+       */
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+       }
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+       /* end probability of death */
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   fprintf(ficresprob,"# Age");
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-   pstamp(ficresprobcov);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+       if (popbased==1) {
-   pstamp(ficresprobcor);
+         if(mobilav ==0){
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+           for(i=1; i<=nlstate;i++)
-   fprintf(ficresprobcor,"# Age");
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
+           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+ndeath);j++){
+         }
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       }
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-     }
+         for(h=0; h<=nhstepm; h++){
-  /* fprintf(ficresprob,"\n");
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-   fprintf(ficresprobcov,"\n");
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   fprintf(ficresprobcor,"\n");
+         }
-  */
+       }
-  xp=vector(1,npar);
+       /* This for computing probability of death (h=1 means
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+          computed over hstepm matrices product = hstepm*stepm months)
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+          as a weighted average of prlim.
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+       */
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   first=1;
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-   fprintf(ficgp,"\n# Routine varprob");
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+       }
-   fprintf(fichtm,"\n");
+       /* end probability of death */
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+       for(j=1; j<= nlstate; j++) /* vareij */
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+         for(h=0; h<=nhstepm; h++){
-   file %s<br>\n",optionfilehtmcov);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   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");
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-   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. \
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
- 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 \
- standard deviations wide on each axis. <br>\
+     } /* End theta */
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     for(h=0; h<=nhstepm; h++) /* veij */
-   cov[1]=1;
+       for(j=1; j<=nlstate;j++)
-   tj=cptcoveff;
+         for(theta=1; theta <=npar; theta++)
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   j1=0;
-   for(t=1; t<=tj;t++){
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-     for(i1=1; i1<=ncodemax[t];i1++){
+       for(theta=1; theta <=npar; theta++)
-       j1++;
+         trgradgp[j][theta]=gradgp[theta][j];
-       if  (cptcovn>0) {
-         fprintf(ficresprob, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         fprintf(ficresprob, "**********\n#\n");
+     for(i=1;i<=nlstate;i++)
-         fprintf(ficresprobcov, "\n#********** Variable ");
+       for(j=1;j<=nlstate;j++)
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         vareij[i][j][(int)age] =0.;
-         fprintf(ficresprobcov, "**********\n#\n");
+     for(h=0;h<=nhstepm;h++){
-         fprintf(ficgp, "\n#********** Variable ");
+       for(k=0;k<=nhstepm;k++){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-         fprintf(ficgp, "**********\n#\n");
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+         for(i=1;i<=nlstate;i++)
+           for(j=1;j<=nlstate;j++)
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-         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\">");
+     }
-         fprintf(ficresprobcor, "\n#********** Variable ");
+     /* pptj */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-         fprintf(ficresprobcor, "**********\n#");
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-       }
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-       for (age=bage; age<=fage; age ++){
+         varppt[j][i]=doldmp[j][i];
-         cov[2]=age;
+     /* end ppptj */
-         for (k=1; k<=cptcovn;k++) {
+     /*  x centered again */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-         }
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (k=1; k<=cptcovprod;k++)
+     if (popbased==1) {
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       if(mobilav ==0){
+         for(i=1; i<=nlstate;i++)
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+           prlim[i][i]=probs[(int)age][i][ij];
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       }else{ /* mobilav */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+         for(i=1; i<=nlstate;i++)
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+           prlim[i][i]=mobaverage[(int)age][i][ij];
+       }
-         for(theta=1; theta <=npar; theta++){
+     }
-           for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+     /* This for computing probability of death (h=1 means
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+        as a weighted average of prlim.
+     */
-           k=0;
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-           for(i=1; i<= (nlstate); i++){
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-             for(j=1; j<=(nlstate+ndeath);j++){
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-               k=k+1;
+     }
-               gp[k]=pmmij[i][j];
+     /* end probability of death */
-             }
-           }
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-           for(i=1; i<=npar; i++)
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+       for(i=1; i<=nlstate;i++){
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+       }
-           k=0;
+     }
-           for(i=1; i<=(nlstate); i++){
+     fprintf(ficresprobmorprev,"\n");
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+     fprintf(ficresvij,"%.0f ",age );
-               gm[k]=pmmij[i][j];
+     for(i=1; i<=nlstate;i++)
-             }
+       for(j=1; j<=nlstate;j++){
-           }
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+       }
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+     fprintf(ficresvij,"\n");
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+     free_matrix(gp,0,nhstepm,1,nlstate);
-         }
+     free_matrix(gm,0,nhstepm,1,nlstate);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-           for(theta=1; theta <=npar; theta++)
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             trgradg[j][theta]=gradg[theta][j];
+   } /* End age */
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   fprintf(ficgp,"\n set log y; unset log 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); */
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+ /*   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); */
-         k=0;
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-         for(i=1; i<=(nlstate); i++){
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-           for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-             k=k+1;
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-             mu[k][(int) age]=pmmij[i][j];
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-           }
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
-         }
+ */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-             varpij[i][j][(int)age] = doldm[i][j];
+   free_vector(xp,1,npar);
-         /*printf("\n%d ",(int)age);
+   free_matrix(doldm,1,nlstate,1,nlstate);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+   free_matrix(dnewm,1,nlstate,1,npar);
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-           }*/
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         fprintf(ficresprob,"\n%d ",(int)age);
+   fclose(ficresprobmorprev);
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+   fflush(ficgp);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+   fflush(fichtm);
+ }  /* end varevsij */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+ /************ Variance of prevlim ******************/
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+ {
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+   /* Variance of prevalence limit */
-         }
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-         i=0;
+   double **newm;
-         for (k=1; k<=(nlstate);k++){
+   double **dnewm,**doldm;
-           for (l=1; l<=(nlstate+ndeath);l++){
+   int i, j, nhstepm, hstepm;
-             i=i++;
+   int k, cptcode;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+   double *xp;
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+   double *gp, *gm;
-             for (j=1; j<=i;j++){
+   double **gradg, **trgradg;
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+   double age,agelim;
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+   int theta;
-             }
-           }
+   pstamp(ficresvpl);
-         }/* end of loop for state */
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-       } /* end of loop for age */
+   fprintf(ficresvpl,"# Age");
+   for(i=1; i<=nlstate;i++)
-       /* Confidence intervalle of pij  */
+       fprintf(ficresvpl," %1d-%1d",i,i);
-       /*
+   fprintf(ficresvpl,"\n");
-         fprintf(ficgp,"\nset noparametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+   xp=vector(1,npar);
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   dnewm=matrix(1,nlstate,1,npar);
-         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);
+   doldm=matrix(1,nlstate,1,nlstate);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+   hstepm=1*YEARM; /* Every year of age */
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-       */
+   agelim = AGESUP;
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       first1=1;
+     if (stepm >= YEARM) hstepm=1;
-       for (k2=1; k2<=(nlstate);k2++){
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+     gradg=matrix(1,npar,1,nlstate);
-           if(l2==k2) continue;
+     gp=vector(1,nlstate);
-           j=(k2-1)*(nlstate+ndeath)+l2;
+     gm=vector(1,nlstate);
-           for (k1=1; k1<=(nlstate);k1++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+     for(theta=1; theta <=npar; theta++){
-               if(l1==k1) continue;
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-               i=(k1-1)*(nlstate+ndeath)+l1;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-               if(i<=j) continue;
+       }
-               for (age=bage; age<=fage; age ++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-                 if ((int)age %5==0){
+       for(i=1;i<=nlstate;i++)
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+         gp[i] = prlim[i][i];
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+       for(i=1; i<=npar; i++) /* Computes gradient */
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-                   c12=cv12/sqrt(v1*v2);
+       for(i=1;i<=nlstate;i++)
-                   /* Computing eigen value of matrix of covariance */
+         gm[i] = prlim[i][i];
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+       for(i=1;i<=nlstate;i++)
-                   /* Eigen vectors */
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+     } /* End theta */
-                   /*v21=sqrt(1.-v11*v11); *//* error */
-                   v21=(lc1-v1)/cv12*v11;
+     trgradg =matrix(1,nlstate,1,npar);
-                   v12=-v21;
-                   v22=v11;
+     for(j=1; j<=nlstate;j++)
-                   tnalp=v21/v11;
+       for(theta=1; theta <=npar; theta++)
-                   if(first1==1){
+         trgradg[j][theta]=gradg[theta][j];
-                     first1=0;
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+     for(i=1;i<=nlstate;i++)
-                   }
+       varpl[i][(int)age] =0.;
-                   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);
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-                   /*printf(fignu*/
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+     for(i=1;i<=nlstate;i++)
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-                   if(first==1){
-                     first=0;
+     fprintf(ficresvpl,"%.0f ",age );
-                     fprintf(ficgp,"\nset parametric;unset label");
+     for(i=1; i<=nlstate;i++)
-                     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(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     fprintf(ficresvpl,"\n");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+     free_vector(gp,1,nlstate);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+     free_vector(gm,1,nlstate);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+     free_matrix(gradg,1,npar,1,nlstate);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+     free_matrix(trgradg,1,nlstate,1,npar);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   } /* End age */
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   free_vector(xp,1,npar);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   free_matrix(doldm,1,nlstate,1,npar);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+ }
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ /************ Variance of one-step probabilities  ******************/
-                   }else{
+ 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[])
-                     first=0;
+ {
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   int i, j=0,  i1, k1, l1, t, tj;
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   int k2, l2, j1,  z1;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   int k=0,l, cptcode;
-                     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 first=1, first1, first2;
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   double **dnewm,**doldm;
-                   }/* if first */
+   double *xp;
-                 } /* age mod 5 */
+   double *gp, *gm;
-               } /* end loop age */
+   double **gradg, **trgradg;
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   double **mu;
-               first=1;
+   double age,agelim, cov[NCOVMAX+1];
-             } /*l12 */
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-           } /* k12 */
+   int theta;
-         } /*l1 */
+   char fileresprob[FILENAMELENGTH];
-       }/* k1 */
+   char fileresprobcov[FILENAMELENGTH];
-     } /* loop covariates */
+   char fileresprobcor[FILENAMELENGTH];
-   }
+   double ***varpij;
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   strcpy(fileresprob,"prob");
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   strcat(fileresprob,fileres);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-   free_vector(xp,1,npar);
+     printf("Problem with resultfile: %s\n", fileresprob);
-   fclose(ficresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-   fclose(ficresprobcov);
+   }
-   fclose(ficresprobcor);
+   strcpy(fileresprobcov,"probcov");
-   fflush(ficgp);
+   strcat(fileresprobcov,fileres);
-   fflush(fichtmcov);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
- }
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   }
- /******************* Printing html file ***********/
+   strcpy(fileresprobcor,"probcor");
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   strcat(fileresprobcor,fileres);
-                   int lastpass, int stepm, int weightopt, char model[],\
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-                   int popforecast, int estepm ,\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-                   double jprev1, double mprev1,double anprev1, \
+   }
-                   double jprev2, double mprev2,double anprev2){
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   int jj1, k1, i1, cpt;
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- </ul>");
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+   pstamp(ficresprob);
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   fprintf(ficresprob,"# Age");
-    fprintf(fichtm,"\
+   pstamp(ficresprobcov);
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   fprintf(ficresprobcov,"# Age");
-    fprintf(fichtm,"\
+   pstamp(ficresprobcor);
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+   fprintf(ficresprobcor,"# Age");
-    fprintf(fichtm,"\
-  - (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(i=1; i<=nlstate;i++)
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+     for(j=1; j<=(nlstate+ndeath);j++){
-    fprintf(fichtm,"\
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-  - Population projections by age and states: \
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+  /* fprintf(ficresprob,"\n");
+   fprintf(ficresprobcov,"\n");
-  m=cptcoveff;
+   fprintf(ficresprobcor,"\n");
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+  */
+   xp=vector(1,npar);
-  jj1=0;
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-  for(k1=1; k1<=m;k1++){
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-      jj1++;
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-      if (cptcovn > 0) {
+   first=1;
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   fprintf(ficgp,"\n# Routine varprob");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   fprintf(fichtm,"\n");
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-      }
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-      /* Pij */
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
+   file %s<br>\n",optionfilehtmcov);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-      /* Quasi-incidences */
+ and drawn. It helps understanding how is the covariance between two incidences.\
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-        /* Period (stable) prevalence in each health state */
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-        for(cpt=1; cpt<nlstate;cpt++){
+ standard deviations wide on each axis. <br>\
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-        }
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+   cov[1]=1;
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+   /* tj=cptcoveff; */
-      }
+   tj = (int) pow(2,cptcoveff);
-    } /* end i1 */
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-  }/* End k1 */
+   j1=0;
-  fprintf(fichtm,"</ul>");
+   for(j1=1; j1<=tj;j1++){
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+     /*j1++;*/
-  fprintf(fichtm,"\
+       if  (cptcovn>0) {
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+         fprintf(ficresprob, "\n#********** Variable ");
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprob, "**********\n#\n");
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+         fprintf(ficresprobcov, "\n#********** Variable ");
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-  fprintf(fichtm,"\
+         fprintf(ficresprobcov, "**********\n#\n");
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+         fprintf(ficgp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-  fprintf(fichtm,"\
+         fprintf(ficgp, "**********\n#\n");
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-  fprintf(fichtm,"\
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-  - 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): \
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-  fprintf(fichtm,"\
+         fprintf(ficresprobcor, "\n#********** Variable ");
-  - (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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+         fprintf(ficresprobcor, "**********\n#");
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+       }
-  fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), 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",
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-  fprintf(fichtm,"\
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-  - 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",
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+       for (age=bage; age<=fage; age ++){
-  fprintf(fichtm,"\
+         cov[2]=age;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+         for (k=1; k<=cptcovn;k++) {
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+                                                          * 1  1 1 1 1
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+                                                          * 2  2 1 1 1
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+                                                          * 3  1 2 1 1
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+                                                          */
- /*      <br>",fileres,fileres,fileres,fileres); */
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
- /*  else  */
+         }
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-  fflush(fichtm);
+         for (k=1; k<=cptcovprod;k++)
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-  m=cptcoveff;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
-  jj1=0;
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-  for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-      jj1++;
-      if (cptcovn > 0) {
+           k=0;
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+           for(i=1; i<= (nlstate); i++){
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+             for(j=1; j<=(nlstate+ndeath);j++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+               k=k+1;
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+               gp[k]=pmmij[i][j];
-      }
+             }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+           }
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+           for(i=1; i<=npar; i++)
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
- health expectancies in states (1) and (2): %s%d.png<br>\
+           k=0;
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+           for(i=1; i<=(nlstate); i++){
-    } /* end i1 */
+             for(j=1; j<=(nlstate+ndeath);j++){
-  }/* End k1 */
+               k=k+1;
-  fprintf(fichtm,"</ul>");
+               gm[k]=pmmij[i][j];
-  fflush(fichtm);
+             }
- }
+           }
- /******************* Gnuplot file **************/
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         }
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-   int ng;
+           for(theta=1; theta <=npar; theta++)
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+             trgradg[j][theta]=gradg[theta][j];
- /*     printf("Problem with file %s",optionfilegnuplot); */
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+         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);
-   /*#ifdef windows */
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+         k=0;
-   m=pow(2,cptcoveff);
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
-   strcpy(dirfileres,optionfilefiname);
+             k=k+1;
-   strcpy(optfileres,"vpl");
+             mu[k][(int) age]=pmmij[i][j];
-  /* 1eme*/
+           }
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+         }
-    for (k1=1; k1<= m ; k1 ++) {
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+             varpij[i][j][(int)age] = doldm[i][j];
-      fprintf(ficgp,"set xlabel \"Age\" \n\
- set ylabel \"Probability\" \n\
+         /*printf("\n%d ",(int)age);
- set ter png small\n\
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- set size 0.65,0.65\n\
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           }*/
-      for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficresprob,"\n%d ",(int)age);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-      }
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-      for (i=1; i<= nlstate ; i ++) {
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-      }
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-      for (i=1; i<= nlstate ; i ++) {
+         }
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         i=0;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+         for (k=1; k<=(nlstate);k++){
-      }
+           for (l=1; l<=(nlstate+ndeath);l++){
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+             i++;
-    }
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-   }
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   /*2 eme*/
+             for (j=1; j<=i;j++){
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-   for (k1=1; k1<= m ; k1 ++) {
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+             }
+           }
-     for (i=1; i<= nlstate+1 ; i ++) {
+         }/* end of loop for state */
-       k=2*i;
+       } /* end of loop for age */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-       for (j=1; j<= nlstate+1 ; j ++) {
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       /* Confidence intervalle of pij  */
-       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);
+         fprintf(ficgp,"\nunset parametric;unset label");
-       for (j=1; j<= nlstate+1 ; j ++) {
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         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(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-       fprintf(ficgp,"\" t\"\" w l 0,");
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       for (j=1; j<= nlstate+1 ; j ++) {
+       */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       }
+       first1=1;first2=2;
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       for (k2=1; k2<=(nlstate);k2++){
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-     }
+           if(l2==k2) continue;
-   }
+           j=(k2-1)*(nlstate+ndeath)+l2;
+           for (k1=1; k1<=(nlstate);k1++){
-   /*3eme*/
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
+               if(l1==k1) continue;
-   for (k1=1; k1<= m ; k1 ++) {
+               i=(k1-1)*(nlstate+ndeath)+l1;
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+               if(i<=j) continue;
-       /*       k=2+nlstate*(2*cpt-2); */
+               for (age=bage; age<=fage; age ++){
-       k=2+(nlstate+1)*(cpt-1);
+                 if ((int)age %5==0){
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-       fprintf(ficgp,"set ter png small\n\
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
- set size 0.65,0.65\n\
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                   c12=cv12/sqrt(v1*v2);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                   /* Computing eigen value of matrix of covariance */
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                   if ((lc2 <0) || (lc1 <0) ){
+                     if(first2==1){
-       */
+                       first1=0;
-       for (i=1; i< nlstate ; i ++) {
+                     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," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+                     }
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+                     fprintf(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 */
-       }
+                     /* lc2=fabs(lc2); */
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+                   }
-     }
-   }
+                   /* Eigen vectors */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-   /* CV preval stable (period) */
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-   for (k1=1; k1<= m ; k1 ++) {
+                   v21=(lc1-v1)/cv12*v11;
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+                   v12=-v21;
-       k=3;
+                   v22=v11;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+                   tnalp=v21/v11;
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+                   if(first1==1){
- set ter png small\nset size 0.65,0.65\n\
+                     first1=0;
- unset log y\n\
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+                   }
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-       for (i=1; i< nlstate ; i ++)
+                   /*printf(fignu*/
-         fprintf(ficgp,"+$%d",k+i+1);
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                   if(first==1){
-       l=3+(nlstate+ndeath)*cpt;
+                     first=0;
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+                     fprintf(ficgp,"\nset parametric;unset label");
-       for (i=1; i< nlstate ; i ++) {
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-         l=3+(nlstate+ndeath)*cpt;
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-         fprintf(ficgp,"+$%d",l+i+1);
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-       }
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-     }
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-   }
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   /* proba elementaires */
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-   for(i=1,jk=1; i <=nlstate; i++){
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-     for(k=1; k <=(nlstate+ndeath); k++){
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-       if (k != i) {
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-         for(j=1; j <=ncovmodel; j++){
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-           jk++;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-           fprintf(ficgp,"\n");
+                   }else{
-         }
+                     first=0;
-       }
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-     }
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-    }
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     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",\
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-      for(jk=1; jk <=m; jk++) {
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+                   }/* if first */
-        if (ng==2)
+                 } /* age mod 5 */
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+               } /* end loop age */
-        else
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+               first=1;
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+             } /*l12 */
-        i=1;
+           } /* k12 */
-        for(k2=1; k2<=nlstate; k2++) {
+         } /*l1 */
-          k3=i;
+       }/* k1 */
-          for(k=1; k<=(nlstate+ndeath); k++) {
+       /* } /* loop covariates */
-            if (k != k2){
+   }
-              if(ng==2)
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-              else
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-              ij=1;
+   free_vector(xp,1,npar);
-              for(j=3; j <=ncovmodel; j++) {
+   fclose(ficresprob);
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+   fclose(ficresprobcov);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   fclose(ficresprobcor);
-                  ij++;
+   fflush(ficgp);
-                }
+   fflush(fichtmcov);
-                else
+ }
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-              }
-              fprintf(ficgp,")/(1");
+ /******************* Printing html file ***********/
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-              for(k1=1; k1 <=nlstate; k1++){
+                   int lastpass, int stepm, int weightopt, char model[],\
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                ij=1;
+                   int popforecast, int estepm ,\
-                for(j=3; j <=ncovmodel; j++){
+                   double jprev1, double mprev1,double anprev1, \
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                   double jprev2, double mprev2,double anprev2){
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+   int jj1, k1, i1, cpt;
-                    ij++;
-                  }
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-                  else
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+ </ul>");
-                }
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-                fprintf(ficgp,")");
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-              }
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+    fprintf(fichtm,"\
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-              i=i+ncovmodel;
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-            }
+    fprintf(fichtm,"\
-          } /* end k */
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-        } /* end k2 */
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-      } /* end jk */
+    fprintf(fichtm,"\
-    } /* end ng */
+  - (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): \
-    fflush(ficgp);
+    <a href=\"%s\">%s</a> <br>\n",
- }  /* end gnuplot */
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
- /*************** Moving average **************/
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-   int i, cpt, cptcod;
-   int modcovmax =1;
+  m=pow(2,cptcoveff);
-   int mobilavrange, mob;
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   double age;
+  jj1=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+  for(k1=1; k1<=m;k1++){
-                            a covariate has 2 modalities */
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+      jj1++;
+      if (cptcovn > 0) {
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-     if(mobilav==1) mobilavrange=5; /* default */
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-     else mobilavrange=mobilav;
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-     for (age=bage; age<=fage; age++)
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-       for (i=1; i<=nlstate;i++)
+      }
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+      /* Pij */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+      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> \
-     /* We keep the original values on the extreme ages bage, fage and for
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+      /* Quasi-incidences */
-        we use a 5 terms etc. until the borders are no more concerned.
+      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%d_2.png\">%s%d_2.png</a><br> \
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+        /* Period (stable) prevalence in each health state */
-         for (i=1; i<=nlstate;i++){
+        for(cpt=1; cpt<=nlstate;cpt++){
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+          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> \
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+ <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+        }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+      for(cpt=1; cpt<=nlstate;cpt++) {
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+         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> \
-               }
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+      }
-           }
+    } /* end i1 */
-         }
+  }/* End k1 */
-       }/* end age */
+  fprintf(fichtm,"</ul>");
-     }/* end mob */
-   }else return -1;
-   return 0;
+  fprintf(fichtm,"\
- }/* End movingaverage */
+ \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);
- /************** Forecasting ******************/
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- 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){
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-   /* proj1, year, month, day of starting projection
+  fprintf(fichtm,"\
-      agemin, agemax range of age
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-      anproj2 year of en of projection (same day and month as proj1).
-   */
+  fprintf(fichtm,"\
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-   int *popage;
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-   double agec; /* generic age */
+  fprintf(fichtm,"\
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
-   double *popeffectif,*popcount;
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   double ***p3mat;
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-   double ***mobaverage;
+  fprintf(fichtm,"\
-   char fileresf[FILENAMELENGTH];
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   agelim=AGESUP;
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-   strcpy(fileresf,"f");
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-   strcat(fileresf,fileres);
+  fprintf(fichtm,"\
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+  - 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",
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+  fprintf(fichtm,"\
-   }
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-   if (mobilav!=0) {
+ /*      <br>",fileres,fileres,fileres,fileres); */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*  else  */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+  fflush(fichtm);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-     }
-   }
+  m=pow(2,cptcoveff);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=12) stepsize=1;
+  jj1=0;
-   if(estepm < stepm){
+  for(k1=1; k1<=m;k1++){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    for(i1=1; i1<=ncodemax[k1];i1++){
-   }
+      jj1++;
-   else  hstepm=estepm;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   hstepm=hstepm/stepm;
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-                                fractional in yp1 */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   anprojmean=yp;
+      }
-   yp2=modf((yp1*12),&yp);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-   mprojmean=yp;
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-   yp1=modf((yp2*30.5),&yp);
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-   jprojmean=yp;
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-   if(jprojmean==0) jprojmean=1;
+      }
-   if(mprojmean==0) jprojmean=1;
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-   i1=cptcoveff;
+ true period expectancies (those weighted with period prevalences are also\
-   if (cptcovn < 1){i1=1;}
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+    } /* end i1 */
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+  }/* End k1 */
+  fprintf(fichtm,"</ul>");
- /*            if (h==(int)(YEARM*yearp)){ */
+  fflush(fichtm);
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+ }
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       k=k+1;
+ /******************* Gnuplot file **************/
-       fprintf(ficresf,"\n#******");
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   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;
-       fprintf(ficresf,"******\n");
+   int ng=0;
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-       for(j=1; j<=nlstate+ndeath;j++){
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-         for(i=1; i<=nlstate;i++)
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-           fprintf(ficresf," p%d%d",i,j);
+ /*   } */
-         fprintf(ficresf," p.%d",j);
-       }
+   /*#ifdef windows */
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-         fprintf(ficresf,"\n");
+     /*#endif */
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   m=pow(2,cptcoveff);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+   strcpy(dirfileres,optionfilefiname);
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+   strcpy(optfileres,"vpl");
-           nhstepm = nhstepm/hstepm;
+  /* 1eme*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-           oldm=oldms;savm=savms;
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-           for (h=0; h<=nhstepm; h++){
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-             if (h*hstepm/YEARM*stepm ==yearp) {
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-               fprintf(ficresf,"\n");
+ set ylabel \"Probability\" \n\
-               for(j=1;j<=cptcoveff;j++)
+ set ter png small size 320, 240\n\
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-             }
+      for (i=1; i<= nlstate ; i ++) {
-             for(j=1; j<=nlstate+ndeath;j++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-               ppij=0.;
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-               for(i=1; i<=nlstate;i++) {
+      }
-                 if (mobilav==1)
+      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);
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+      for (i=1; i<= nlstate ; i ++) {
-                 else {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-                 }
+      }
-                 if (h*hstepm/YEARM*stepm== yearp) {
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+      for (i=1; i<= nlstate ; i ++) {
-                 }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-               } /* end i */
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-               if (h*hstepm/YEARM*stepm==yearp) {
+      }
-                 fprintf(ficresf," %.3f", ppij);
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-               }
+    }
-             }/* end j */
+   }
-           } /* end h */
+   /*2 eme*/
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-         } /* end agec */
+   for (k1=1; k1<= m ; k1 ++) {
-       } /* end yearp */
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-     } /* end cptcod */
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-   } /* end  cptcov */
+     for (i=1; i<= nlstate+1 ; i ++) {
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       k=2*i;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   fclose(ficresf);
+       for (j=1; j<= nlstate+1 ; j ++) {
- }
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
- /************** 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){
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-   int *popage;
+       for (j=1; j<= nlstate+1 ; j ++) {
-   double calagedatem, agelim, kk1, kk2;
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   double *popeffectif,*popcount;
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-   double ***p3mat,***tabpop,***tabpopprev;
+       }
-   double ***mobaverage;
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-   char filerespop[FILENAMELENGTH];
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-   agelim=AGESUP;
+       }
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     }
+   }
-   strcpy(filerespop,"pop");
+   /*3eme*/
-   strcat(filerespop,fileres);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+   for (k1=1; k1<= m ; k1 ++) {
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+       /*       k=2+nlstate*(2*cpt-2); */
-   }
+       k=2+(nlstate+1)*(cpt-1);
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+       fprintf(ficgp,"set ter png small size 320, 240\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-   if (mobilav!=0) {
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
+       */
-   }
+       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);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-   if (stepm<=12) stepsize=1;
+       }
-   agelim=AGESUP;
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+     }
-   hstepm=1;
+   }
-   hstepm=hstepm/stepm;
+   /* CV preval stable (period) */
-   if (popforecast==1) {
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+       k=3;
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+       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);
-     popage=ivector(0,AGESUP);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-     popeffectif=vector(0,AGESUP);
+ set ter png small size 320, 240\n\
-     popcount=vector(0,AGESUP);
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-     i=1;
+       for (i=1; i<= nlstate ; i ++){
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+         if(i==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
-     imx=i;
+         else
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+           fprintf(ficgp,", '' ");
-   }
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+         for (j=1; j<= (nlstate-1) ; j ++)
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+           fprintf(ficgp,"+$%d",k+l+j);
-       k=k+1;
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-       fprintf(ficrespop,"\n#******");
+       } /* nlstate */
-       for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficgp,"\n");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     } /* end cpt state*/
-       }
+   } /* end covariate */
-       fprintf(ficrespop,"******\n");
-       fprintf(ficrespop,"# Age");
+   /* proba elementaires */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+   for(i=1,jk=1; i <=nlstate; i++){
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
-       for (cpt=0; cpt<=0;cpt++) {
+         for(j=1; j <=ncovmodel; j++){
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+           fprintf(ficgp,"\n");
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+         }
-           nhstepm = nhstepm/hstepm;
+       }
+     }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    }
-           oldm=oldms;savm=savms;
+   /*goto avoid;*/
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
-           for (h=0; h<=nhstepm; h++){
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+        if (ng==2)
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-             }
+        else
-             for(j=1; j<=nlstate+ndeath;j++) {
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-               kk1=0.;kk2=0;
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-               for(i=1; i<=nlstate;i++) {
+        i=1;
-                 if (mobilav==1)
+        for(k2=1; k2<=nlstate; k2++) {
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+          k3=i;
-                 else {
+          for(k=1; k<=(nlstate+ndeath); k++) {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+            if (k != k2){
-                 }
+              if(ng==2)
-               }
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-               if (h==(int)(calagedatem+12*cpt)){
+              else
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-                   /*fprintf(ficrespop," %.3f", kk1);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+              for(j=3; j <=ncovmodel; j++) {
-               }
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-             }
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-             for(i=1; i<=nlstate;i++){
+                /*        ij++; */
-               kk1=0.;
+                /* } */
-                 for(j=1; j<=nlstate;j++){
+                /* else */
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-                 }
+              }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+              fprintf(ficgp,")/(1");
-             }
+              for(k1=1; k1 <=nlstate; k1++){
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+                ij=1;
-           }
+                for(j=3; j <=ncovmodel; j++){
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-         }
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-       }
+                  /*   ij++; */
+                  /* } */
-   /******/
+                  /* else */
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+                }
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+                fprintf(ficgp,")");
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+              }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-           nhstepm = nhstepm/hstepm;
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+              i=i+ncovmodel;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+            }
-           oldm=oldms;savm=savms;
+          } /* end k */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+        } /* end k2 */
-           for (h=0; h<=nhstepm; h++){
+      } /* end jk */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+    } /* end ng */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+  avoid:
-             }
+    fflush(ficgp);
-             for(j=1; j<=nlstate+ndeath;j++) {
+ }  /* end gnuplot */
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*************** Moving average **************/
-               }
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-             }
+   int i, cpt, cptcod;
-           }
+   int modcovmax =1;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int mobilavrange, mob;
-         }
+   double age;
-       }
-    }
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-   }
+                            a covariate has 2 modalities */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-   if (popforecast==1) {
+     if(mobilav==1) mobilavrange=5; /* default */
-     free_ivector(popage,0,AGESUP);
+     else mobilavrange=mobilav;
-     free_vector(popeffectif,0,AGESUP);
+     for (age=bage; age<=fage; age++)
-     free_vector(popcount,0,AGESUP);
+       for (i=1; i<=nlstate;i++)
-   }
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* We keep the original values on the extreme ages bage, fage and for
-   fclose(ficrespop);
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
- } /* End of popforecast */
+        we use a 5 terms etc. until the borders are no more concerned.
+     */
- int fileappend(FILE *fichier, char *optionfich)
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
- {
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+         for (i=1; i<=nlstate;i++){
-     printf("Problem with file: %s\n", optionfich);
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-     return (0);
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-   }
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-   fflush(fichier);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-   return (1);
+               }
- }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+           }
+         }
- /**************** function prwizard **********************/
+       }/* end age */
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+     }/* end mob */
- {
+   }else return -1;
+   return 0;
-   /* Wizard to print covariance matrix template */
+ }/* End movingaverage */
-   char ca[32], cb[32], cc[32];
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+ /************** Forecasting ******************/
-   int numlinepar;
+ 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){
+   /* proj1, year, month, day of starting projection
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+      agemin, agemax range of age
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-   for(i=1; i <=nlstate; i++){
+      anproj2 year of en of projection (same day and month as proj1).
-     jj=0;
+   */
-     for(j=1; j <=nlstate+ndeath; j++){
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-       if(j==i) continue;
+   int *popage;
-       jj++;
+   double agec; /* generic age */
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-       printf("%1d%1d",i,j);
+   double *popeffectif,*popcount;
-       fprintf(ficparo,"%1d%1d",i,j);
+   double ***p3mat;
-       for(k=1; k<=ncovmodel;k++){
+   double ***mobaverage;
-         /*        printf(" %lf",param[i][j][k]); */
+   char fileresf[FILENAMELENGTH];
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-         printf(" 0.");
+   agelim=AGESUP;
-         fprintf(ficparo," 0.");
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-       }
-       printf("\n");
+   strcpy(fileresf,"f");
-       fprintf(ficparo,"\n");
+   strcat(fileresf,fileres);
-     }
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   }
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-   printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   for(i=1; i <=nlstate; i++){
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-       if(j==i) continue;
-       jj++;
+   if (mobilav!=0) {
-       fprintf(ficparo,"%1d%1d",i,j);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       printf("%1d%1d",i,j);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       fflush(stdout);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       for(k=1; k<=ncovmodel;k++){
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-         /*      printf(" %le",delti3[i][j][k]); */
+     }
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+   }
-         printf(" 0.");
-         fprintf(ficparo," 0.");
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-       }
+   if (stepm<=12) stepsize=1;
-       numlinepar++;
+   if(estepm < stepm){
-       printf("\n");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       fprintf(ficparo,"\n");
+   }
-     }
+   else  hstepm=estepm;
-   }
-   printf("# Covariance matrix\n");
+   hstepm=hstepm/stepm;
- /* # 121 Var(a12)\n\ */
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                                fractional in yp1 */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   anprojmean=yp;
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   yp2=modf((yp1*12),&yp);
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+   mprojmean=yp;
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   yp1=modf((yp2*30.5),&yp);
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+   jprojmean=yp;
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   if(jprojmean==0) jprojmean=1;
-   fflush(stdout);
+   if(mprojmean==0) jprojmean=1;
-   fprintf(ficparo,"# Covariance matrix\n");
-   /* # 121 Var(a12)\n\ */
+   i1=cptcoveff;
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   if (cptcovn < 1){i1=1;}
-   /* #   ...\n\ */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   for(itimes=1;itimes<=2;itimes++){
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-     jj=0;
-     for(i=1; i <=nlstate; i++){
+ /*            if (h==(int)(YEARM*yearp)){ */
-       for(j=1; j <=nlstate+ndeath; j++){
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-         if(j==i) continue;
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-         for(k=1; k<=ncovmodel;k++){
+       k=k+1;
-           jj++;
+       fprintf(ficresf,"\n#******");
-           ca[0]= k+'a'-1;ca[1]='\0';
+       for(j=1;j<=cptcoveff;j++) {
-           if(itimes==1){
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-             printf("#%1d%1d%d",i,j,k);
+       }
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+       fprintf(ficresf,"******\n");
-           }else{
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-             printf("%1d%1d%d",i,j,k);
+       for(j=1; j<=nlstate+ndeath;j++){
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+         for(i=1; i<=nlstate;i++)
-             /*  printf(" %.5le",matcov[i][j]); */
+           fprintf(ficresf," p%d%d",i,j);
-           }
+         fprintf(ficresf," p.%d",j);
-           ll=0;
+       }
-           for(li=1;li <=nlstate; li++){
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+         fprintf(ficresf,"\n");
-               if(lj==li) continue;
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-               for(lk=1;lk<=ncovmodel;lk++){
-                 ll++;
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-                 if(ll<=jj){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+           nhstepm = nhstepm/hstepm;
-                   if(ll<jj){
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                     if(itimes==1){
+           oldm=oldms;savm=savms;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                     }else{
+           for (h=0; h<=nhstepm; h++){
-                       printf(" 0.");
+             if (h*hstepm/YEARM*stepm ==yearp) {
-                       fprintf(ficparo," 0.");
+               fprintf(ficresf,"\n");
-                     }
+               for(j=1;j<=cptcoveff;j++)
-                   }else{
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                     if(itimes==1){
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+             }
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+             for(j=1; j<=nlstate+ndeath;j++) {
-                     }else{
+               ppij=0.;
-                       printf(" 0.");
+               for(i=1; i<=nlstate;i++) {
-                       fprintf(ficparo," 0.");
+                 if (mobilav==1)
-                     }
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-                   }
+                 else {
-                 }
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-               } /* end lk */
+                 }
-             } /* end lj */
+                 if (h*hstepm/YEARM*stepm== yearp) {
-           } /* end li */
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-           printf("\n");
+                 }
-           fprintf(ficparo,"\n");
+               } /* end i */
-           numlinepar++;
+               if (h*hstepm/YEARM*stepm==yearp) {
-         } /* end k*/
+                 fprintf(ficresf," %.3f", ppij);
-       } /*end j */
+               }
-     } /* end i */
+             }/* end j */
-   } /* end itimes */
+           } /* end h */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- } /* end of prwizard */
+         } /* end agec */
- /******************* Gompertz Likelihood ******************************/
+       } /* end yearp */
- double gompertz(double x[])
+     } /* end cptcod */
- {
+   } /* end  cptcov */
-   double A,B,L=0.0,sump=0.,num=0.;
-   int i,n=0; /* n is the size of the sample */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   for (i=0;i<=imx-1 ; i++) {
+   fclose(ficresf);
-     sump=sump+weight[i];
+ }
-     /*    sump=sump+1;*/
-     num=num+1;
+ /************** 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 cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   /* for (i=0; i<=imx; i++)
+   int *popage;
-      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]);*/
+   double calagedatem, agelim, kk1, kk2;
+   double *popeffectif,*popcount;
-   for (i=1;i<=imx ; i++)
+   double ***p3mat,***tabpop,***tabpopprev;
-     {
+   double ***mobaverage;
-       if (cens[i] == 1 && wav[i]>1)
+   char filerespop[FILENAMELENGTH];
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (cens[i] == 0 && wav[i]>1)
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   agelim=AGESUP;
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-       if (wav[i] > 1 ) { /* ??? */
-         L=L+A*weight[i];
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+   strcpy(filerespop,"pop");
-       }
+   strcat(filerespop,fileres);
-     }
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
-   return -2*L*num/sump;
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
- }
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
- /******************* Printing html file ***********/
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-                   int lastpass, int stepm, int weightopt, char model[],\
+   if (mobilav!=0) {
-                   int imx,  double p[],double **matcov,double agemortsup){
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int i,k;
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+     }
-   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]));
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   fprintf(fichtm,"</ul>");
+   if (stepm<=12) stepsize=1;
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   agelim=AGESUP;
-  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>");
+   hstepm=1;
+   hstepm=hstepm/stepm;
-  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]);
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   fflush(fichtm);
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- }
+     }
+     popage=ivector(0,AGESUP);
- /******************* Gnuplot file **************/
+     popeffectif=vector(0,AGESUP);
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     popcount=vector(0,AGESUP);
-   char dirfileres[132],optfileres[132];
+     i=1;
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   int ng;
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   /*#ifdef windows */
+   }
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
-   strcpy(dirfileres,optionfilefiname);
+       fprintf(ficrespop,"\n#******");
-   strcpy(optfileres,"vpl");
+       for(j=1;j<=cptcoveff;j++) {
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+       }
-   fprintf(ficgp, "set ter png small\n set log y\n");
+       fprintf(ficrespop,"******\n");
-   fprintf(ficgp, "set size 0.65,0.65\n");
+       fprintf(ficrespop,"# Age");
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
- }
+       for (cpt=0; cpt<=0;cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- /***********************************************/
+           nhstepm = nhstepm/hstepm;
- /**************** Main Program *****************/
- /***********************************************/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
- int main(int argc, char *argv[])
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- {
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+           for (h=0; h<=nhstepm; h++){
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   int linei, month, year,iout;
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   int jj, ll, li, lj, lk, imk;
+             }
-   int numlinepar=0; /* Current linenumber of parameter file */
+             for(j=1; j<=nlstate+ndeath;j++) {
-   int itimes;
+               kk1=0.;kk2=0;
-   int NDIM=2;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
-   char ca[32], cb[32], cc[32];
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   char dummy[]="                         ";
+                 else {
-   /*  FILE *fichtm; *//* Html File */
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-   /* FILE *ficgp;*/ /*Gnuplot File */
+                 }
-   struct stat info;
+               }
-   double agedeb, agefin,hf;
+               if (h==(int)(calagedatem+12*cpt)){
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
-   double fret;
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-   double **xi,tmp,delta;
+               }
+             }
-   double dum; /* Dummy variable */
+             for(i=1; i<=nlstate;i++){
-   double ***p3mat;
+               kk1=0.;
-   double ***mobaverage;
+                 for(j=1; j<=nlstate;j++){
-   int *indx;
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   char line[MAXLINE], linepar[MAXLINE];
+                 }
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   char pathr[MAXLINE], pathimach[MAXLINE];
+             }
-   char **bp, *tok, *val; /* pathtot */
-   int firstobs=1, lastobs=10;
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   int sdeb, sfin; /* Status at beginning and end */
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   int c,  h , cpt,l;
+           }
-   int ju,jl, mi;
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+         }
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+       }
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   int mobilav=0,popforecast=0;
+   /******/
-   int hstepm, nhstepm;
-   int agemortsup;
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   float  sumlpop=0.;
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   double **prlim;
+           oldm=oldms;savm=savms;
-   double *severity;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   double ***param; /* Matrix of parameters */
+           for (h=0; h<=nhstepm; h++){
-   double  *p;
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   double **matcov; /* Matrix of covariance */
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   double ***delti3; /* Scale */
+             }
-   double *delti; /* Scale */
+             for(j=1; j<=nlstate+ndeath;j++) {
-   double ***eij, ***vareij;
+               kk1=0.;kk2=0;
-   double **varpl; /* Variances of prevalence limits by age */
+               for(i=1; i<=nlstate;i++) {
-   double *epj, vepp;
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   double kk1, kk2;
+               }
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   double **ximort;
+             }
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+           }
-   int *dcwave;
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   char z[1]="c", occ;
+       }
+    }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   }
-   char  *strt, strtend[80];
-   char *stratrunc;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int lstra;
+   if (popforecast==1) {
-   long total_usecs;
+     free_ivector(popage,0,AGESUP);
+     free_vector(popeffectif,0,AGESUP);
- /*   setlocale (LC_ALL, ""); */
+     free_vector(popcount,0,AGESUP);
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+   }
- /*   textdomain (PACKAGE); */
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /*   setlocale (LC_CTYPE, ""); */
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- /*   setlocale (LC_MESSAGES, ""); */
+   fclose(ficrespop);
+ } /* End of popforecast */
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   (void) gettimeofday(&start_time,&tzp);
+ int fileappend(FILE *fichier, char *optionfich)
-   curr_time=start_time;
+ {
-   tm = *localtime(&start_time.tv_sec);
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-   tmg = *gmtime(&start_time.tv_sec);
+     printf("Problem with file: %s\n", optionfich);
-   strcpy(strstart,asctime(&tm));
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     return (0);
- /*  printf("Localtime (at start)=%s",strstart); */
+   }
- /*  tp.tv_sec = tp.tv_sec +86400; */
+   fflush(fichier);
- /*  tm = *localtime(&start_time.tv_sec); */
+   return (1);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ }
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
- /*   tp.tv_sec = mktime(&tmg); */
+ /**************** function prwizard **********************/
- /*   strt=asctime(&tmg); */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
- /*   printf("Time(after) =%s",strstart);  */
+ {
- /*  (void) time (&time_value);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+   /* Wizard to print covariance matrix template */
- *  tm = *localtime(&time_value);
- *  strstart=asctime(&tm);
+   char ca[32], cb[32], cc[32];
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
- */
+   int numlinepar;
-   nberr=0; /* Number of errors and warnings */
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   nbwarn=0;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   getcwd(pathcd, size);
+   for(i=1; i <=nlstate; i++){
+     jj=0;
-   printf("\n%s\n%s",version,fullversion);
+     for(j=1; j <=nlstate+ndeath; j++){
-   if(argc <=1){
+       if(j==i) continue;
-     printf("\nEnter the parameter file name: ");
+       jj++;
-     fgets(pathr,FILENAMELENGTH,stdin);
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-     i=strlen(pathr);
+       printf("%1d%1d",i,j);
-     if(pathr[i-1]=='\n')
+       fprintf(ficparo,"%1d%1d",i,j);
-       pathr[i-1]='\0';
+       for(k=1; k<=ncovmodel;k++){
-    for (tok = pathr; tok != NULL; ){
+         /*        printf(" %lf",param[i][j][k]); */
-       printf("Pathr |%s|\n",pathr);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+         printf(" 0.");
-       printf("val= |%s| pathr=%s\n",val,pathr);
+         fprintf(ficparo," 0.");
-       strcpy (pathtot, val);
+       }
-       if(pathr[0] == '\0') break; /* Dirty */
+       printf("\n");
-     }
+       fprintf(ficparo,"\n");
-   }
+     }
-   else{
+   }
-     strcpy(pathtot,argv[1]);
+   printf("# Scales (for hessian or gradient estimation)\n");
-   }
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   /*cygwin_split_path(pathtot,path,optionfile);
+   for(i=1; i <=nlstate; i++){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+     jj=0;
-   /* cutv(path,optionfile,pathtot,'\\');*/
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
-   /* Split argv[0], imach program to get pathimach */
+       jj++;
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+       fprintf(ficparo,"%1d%1d",i,j);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+       printf("%1d%1d",i,j);
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+       fflush(stdout);
-  /*   strcpy(pathimach,argv[0]); */
+       for(k=1; k<=ncovmodel;k++){
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+         /*      printf(" %le",delti3[i][j][k]); */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+         printf(" 0.");
-   chdir(path); /* Can be a relative path */
+         fprintf(ficparo," 0.");
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+       }
-     printf("Current directory %s!\n",pathcd);
+       numlinepar++;
-   strcpy(command,"mkdir ");
+       printf("\n");
-   strcat(command,optionfilefiname);
+       fprintf(ficparo,"\n");
-   if((outcmd=system(command)) != 0){
+     }
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+   }
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+   printf("# Covariance matrix\n");
-     /* fclose(ficlog); */
+ /* # 121 Var(a12)\n\ */
- /*     exit(1); */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   }
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
- /*     perror("mkdir"); */
+ /* # 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\ */
-   /*-------- arguments in the command line --------*/
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
-   /* Log file */
+   fprintf(ficparo,"# Covariance matrix\n");
-   strcat(filelog, optionfilefiname);
+   /* # 121 Var(a12)\n\ */
-   strcat(filelog,".log");    /* */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+   /* #   ...\n\ */
-     printf("Problem with logfile %s\n",filelog);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-     goto end;
-   }
+   for(itimes=1;itimes<=2;itimes++){
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+     jj=0;
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+     for(i=1; i <=nlstate; i++){
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+       for(j=1; j <=nlstate+ndeath; j++){
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+         if(j==i) continue;
-  path=%s \n\
+         for(k=1; k<=ncovmodel;k++){
-  optionfile=%s\n\
+           jj++;
-  optionfilext=%s\n\
+           ca[0]= k+'a'-1;ca[1]='\0';
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+           if(itimes==1){
+             printf("#%1d%1d%d",i,j,k);
-   printf("Local time (at start):%s",strstart);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+           }else{
-   fflush(ficlog);
+             printf("%1d%1d%d",i,j,k);
- /*   (void) gettimeofday(&curr_time,&tzp); */
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
-   /* */
+           ll=0;
-   strcpy(fileres,"r");
+           for(li=1;li <=nlstate; li++){
-   strcat(fileres, optionfilefiname);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-   strcat(fileres,".txt");    /* Other files have txt extension */
+               if(lj==li) continue;
+               for(lk=1;lk<=ncovmodel;lk++){
-   /*---------arguments file --------*/
+                 ll++;
+                 if(ll<=jj){
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-     printf("Problem with optionfile %s\n",optionfile);
+                   if(ll<jj){
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+                     if(itimes==1){
-     fflush(ficlog);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     goto end;
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-   }
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
+                     }
-   strcpy(filereso,"o");
+                   }else{
-   strcat(filereso,fileres);
+                     if(itimes==1){
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-     printf("Problem with Output resultfile: %s\n", filereso);
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+                     }else{
-     fflush(ficlog);
+                       printf(" 0.");
-     goto end;
+                       fprintf(ficparo," 0.");
-   }
+                     }
+                   }
-   /* Reads comments: lines beginning with '#' */
+                 }
-   numlinepar=0;
+               } /* end lk */
-   while((c=getc(ficpar))=='#' && c!= EOF){
+             } /* end lj */
-     ungetc(c,ficpar);
+           } /* end li */
-     fgets(line, MAXLINE, ficpar);
+           printf("\n");
-     numlinepar++;
+           fprintf(ficparo,"\n");
-     puts(line);
+           numlinepar++;
-     fputs(line,ficparo);
+         } /* end k*/
-     fputs(line,ficlog);
+       } /*end j */
-   }
+     } /* end i */
-   ungetc(c,ficpar);
+   } /* end itimes */
-   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);
+ } /* end of prwizard */
-   numlinepar++;
+ /******************* Gompertz Likelihood ******************************/
-   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);
+ double gompertz(double x[])
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+ {
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   double A,B,L=0.0,sump=0.,num=0.;
-   fflush(ficlog);
+   int i,n=0; /* n is the size of the sample */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   for (i=0;i<=imx-1 ; i++) {
-     fgets(line, MAXLINE, ficpar);
+     sump=sump+weight[i];
-     numlinepar++;
+     /*    sump=sump+1;*/
-     puts(line);
+     num=num+1;
-     fputs(line,ficparo);
+   }
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
+   /* 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]);*/
-   covar=matrix(0,NCOVMAX,1,n);
+   for (i=1;i<=imx ; i++)
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+     {
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       if (cens[i] == 0 && wav[i]>1)
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         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);
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   delti=delti3[1][1];
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+       if (wav[i] > 1 ) { /* ??? */
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+         L=L+A*weight[i];
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       }
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     }
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     fclose (ficparo);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     fclose (ficlog);
-     goto end;
+   return -2*L*num/sump;
-     exit(0);
+ }
-   }
-   else if(mle==-3) {
+ #ifdef GSL
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+ /******************* Gompertz_f Likelihood ******************************/
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ double gompertz_f(const gsl_vector *v, void *params)
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+ {
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   double A,B,LL=0.0,sump=0.,num=0.;
-     matcov=matrix(1,npar,1,npar);
+   double *x= (double *) v->data;
-   }
+   int i,n=0; /* n is the size of the sample */
-   else{
-     /* Read guess parameters */
+   for (i=0;i<=imx-1 ; i++) {
-     /* Reads comments: lines beginning with '#' */
+     sump=sump+weight[i];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /*    sump=sump+1;*/
-       ungetc(c,ficpar);
+     num=num+1;
-       fgets(line, MAXLINE, ficpar);
+   }
-       numlinepar++;
-       puts(line);
-       fputs(line,ficparo);
+   /* for (i=0; i<=imx; i++)
-       fputs(line,ficlog);
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-     }
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-     ungetc(c,ficpar);
+   for (i=1;i<=imx ; i++)
+     {
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       if (cens[i] == 1 && wav[i]>1)
-     for(i=1; i <=nlstate; i++){
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-       j=0;
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+       if (cens[i] == 0 && wav[i]>1)
-         if(jj==i) continue;
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-         j++;
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1 != i) && (j1 != j)){
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+       if (wav[i] > 1 ) { /* ??? */
- It might be a problem of design; if ncovcol and the model are correct\n \
+         LL=LL+A*weight[i];
- run imach with mle=-1 to get a correct template of the parameter file.\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);
+       }
-         }
+     }
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         if(mle==1)
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-           printf("%1d%1d",i,j);
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-         fprintf(ficlog,"%1d%1d",i,j);
-         for(k=1; k<=ncovmodel;k++){
+   return -2*LL*num/sump;
-           fscanf(ficpar," %lf",&param[i][j][k]);
+ }
-           if(mle==1){
+ #endif
-             printf(" %lf",param[i][j][k]);
-             fprintf(ficlog," %lf",param[i][j][k]);
+ /******************* Printing html file ***********/
-           }
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-           else
+                   int lastpass, int stepm, int weightopt, char model[],\
-             fprintf(ficlog," %lf",param[i][j][k]);
+                   int imx,  double p[],double **matcov,double agemortsup){
-           fprintf(ficparo," %lf",param[i][j][k]);
+   int i,k;
-         }
-         fscanf(ficpar,"\n");
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-         numlinepar++;
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-         if(mle==1)
+   for (i=1;i<=2;i++)
-           printf("\n");
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-         fprintf(ficlog,"\n");
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-         fprintf(ficparo,"\n");
+   fprintf(fichtm,"</ul>");
-       }
-     }
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-     fflush(ficlog);
+  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>");
-     p=param[1][1];
+  for (k=agegomp;k<(agemortsup-2);k++)
-     /* Reads comments: lines beginning with '#' */
+    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   fflush(fichtm);
-       numlinepar++;
+ }
-       puts(line);
-       fputs(line,ficparo);
+ /******************* Gnuplot file **************/
-       fputs(line,ficlog);
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     }
-     ungetc(c,ficpar);
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-     for(i=1; i <=nlstate; i++){
+   int ng;
-       for(j=1; j <=nlstate+ndeath-1; j++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+   /*#ifdef windows */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-           exit(1);
+     /*#endif */
-         }
-         printf("%1d%1d",i,j);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+   strcpy(dirfileres,optionfilefiname);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+   strcpy(optfileres,"vpl");
-         for(k=1; k<=ncovmodel;k++){
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-           printf(" %le",delti3[i][j][k]);
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-           fprintf(ficparo," %le",delti3[i][j][k]);
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-           fprintf(ficlog," %le",delti3[i][j][k]);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-         }
-         fscanf(ficpar,"\n");
+ }
-         numlinepar++;
-         printf("\n");
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-         fprintf(ficparo,"\n");
+ {
-         fprintf(ficlog,"\n");
-       }
+   /*-------- data file ----------*/
-     }
+   FILE *fic;
-     fflush(ficlog);
+   char dummy[]="                         ";
+   int i, j, n;
-     delti=delti3[1][1];
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[80], strb[80];
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+   char *stratrunc;
+   int lstra;
-     /* Reads comments: lines beginning with '#' */
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-       fgets(line, MAXLINE, ficpar);
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-       numlinepar++;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       puts(line);
+   }
-       fputs(line,ficparo);
-       fputs(line,ficlog);
+   i=1;
-     }
+   linei=0;
-     ungetc(c,ficpar);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
-     matcov=matrix(1,npar,1,npar);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     for(i=1; i <=npar; i++){
+       if(line[j] == '\t')
-       fscanf(ficpar,"%s",&str);
+         line[j] = ' ';
-       if(mle==1)
+     }
-         printf("%s",str);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       fprintf(ficlog,"%s",str);
+       ;
-       fprintf(ficparo,"%s",str);
+     };
-       for(j=1; j <=i; j++){
+     line[j+1]=0;  /* Trims blanks at end of line */
-         fscanf(ficpar," %le",&matcov[i][j]);
+     if(line[0]=='#'){
-         if(mle==1){
+       fprintf(ficlog,"Comment line\n%s\n",line);
-           printf(" %.5le",matcov[i][j]);
+       printf("Comment line\n%s\n",line);
-         }
+       continue;
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     }
-         fprintf(ficparo," %.5le",matcov[i][j]);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-       }
+     for (j=0; line[j]!='\0';j++){
-       fscanf(ficpar,"\n");
+       line[j]=linetmp[j];
-       numlinepar++;
+     }
-       if(mle==1)
-         printf("\n");
-       fprintf(ficlog,"\n");
+     for (j=maxwav;j>=1;j--){
-       fprintf(ficparo,"\n");
+       cutv(stra, strb, line, ' ');
-     }
+       if(strb[0]=='.') { /* Missing status */
-     for(i=1; i <=npar; i++)
+         lval=-1;
-       for(j=i+1;j<=npar;j++)
+       }else{
-         matcov[i][j]=matcov[j][i];
+         errno=0;
+         lval=strtol(strb,&endptr,10);
-     if(mle==1)
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-       printf("\n");
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     fprintf(ficlog,"\n");
+           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);
-     fflush(ficlog);
+           return 1;
+         }
-     /*-------- Rewriting parameter file ----------*/
+       }
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+       s[j][i]=lval;
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     strcat(rfileres,".");    /* */
+       strcpy(line,stra);
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+       cutv(stra, strb,line,' ');
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       }
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     }
+         month=99;
-     fprintf(ficres,"#%s\n",version);
+         year=9999;
-   }    /* End of mle != -3 */
+       }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);
-   /*-------- data file ----------*/
+         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((fic=fopen(datafile,"r"))==NULL)    {
+         return 1;
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+       }
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+       anint[j][i]= (double) year;
-   }
+       mint[j][i]= (double)month;
+       strcpy(line,stra);
-   n= lastobs;
+     } /* ENd Waves */
-   severity = vector(1,maxwav);
-   outcome=imatrix(1,maxwav+1,1,n);
+     cutv(stra, strb,line,' ');
-   num=lvector(1,n);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   moisnais=vector(1,n);
+     }
-   annais=vector(1,n);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-   moisdc=vector(1,n);
+       month=99;
-   andc=vector(1,n);
+       year=9999;
-   agedc=vector(1,n);
+     }else{
-   cod=ivector(1,n);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-   weight=vector(1,n);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+         return 1;
-   mint=matrix(1,maxwav,1,n);
+     }
-   anint=matrix(1,maxwav,1,n);
+     andc[i]=(double) year;
-   s=imatrix(1,maxwav+1,1,n);
+     moisdc[i]=(double) month;
-   tab=ivector(1,NCOVMAX);
+     strcpy(line,stra);
-   ncodemax=ivector(1,8);
+     cutv(stra, strb,line,' ');
-   i=1;
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   linei=0;
+     }
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-     linei=linei+1;
+       month=99;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       year=9999;
-       if(line[j] == '\t')
+     }else{
-         line[j] = ' ';
+       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);
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+         return 1;
-       ;
+     }
-     };
+     if (year==9999) {
-     line[j+1]=0;  /* Trims blanks at end of line */
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-     if(line[0]=='#'){
+       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);
-       fprintf(ficlog,"Comment line\n%s\n",line);
+         return 1;
-       printf("Comment line\n%s\n",line);
-       continue;
+     }
-     }
+     annais[i]=(double)(year);
+     moisnais[i]=(double)(month);
-     for (j=maxwav;j>=1;j--){
+     strcpy(line,stra);
-       cutv(stra, strb,line,' ');
-       errno=0;
+     cutv(stra, strb,line,' ');
-       lval=strtol(strb,&endptr,10);
+     errno=0;
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     dval=strtod(strb,&endptr);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+     if( strb[0]=='\0' || (*endptr != '\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);
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-         exit(1);
+       fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       }
+       fflush(ficlog);
-       s[j][i]=lval;
+       return 1;
+     }
-       strcpy(line,stra);
+     weight[i]=dval;
-       cutv(stra, strb,line,' ');
+     strcpy(line,stra);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       }
+     for (j=ncovcol;j>=1;j--){
-       else  if(iout=sscanf(strb,"%s.") != 0){
+       cutv(stra, strb,line,' ');
-         month=99;
+       if(strb[0]=='.') { /* Missing status */
-         year=9999;
+         lval=-1;
        }else{
-         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);
+         errno=0;
-         exit(1);
+         lval=strtol(strb,&endptr,10);
-       }
+         if( strb[0]=='\0' || (*endptr != '\0')){
-       anint[j][i]= (double) year;
+           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);
-       mint[j][i]= (double)month;
+           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);
-       strcpy(line,stra);
+           return 1;
-     } /* ENd Waves */
+         }
+       }
-     cutv(stra, strb,line,' ');
+       if(lval <-1 || lval >1){
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     }
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-       month=99;
+  For example, for multinomial values like 1, 2 and 3,\n \
-       year=9999;
+  build V1=0 V2=0 for the reference value (1),\n \
-     }else{
+         V1=1 V2=0 for (2) \n \
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       exit(1);
+  output of IMaCh is often meaningless.\n \
-     }
+  Exiting.\n",lval,linei, i,line,j);
-     andc[i]=(double) year;
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     moisdc[i]=(double) month;
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     strcpy(line,stra);
+  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 \
-     cutv(stra, strb,line,' ');
+  build V1=0 V2=0 for the reference value (1),\n \
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         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 \
-     else  if(iout=sscanf(strb,"%s.") != 0){
+  output of IMaCh is often meaningless.\n \
-       month=99;
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       year=9999;
+         return 1;
-     }else{
+       }
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+       covar[j][i]=(double)(lval);
-       exit(1);
+       strcpy(line,stra);
      }
-     annais[i]=(double)(year);
+     lstra=strlen(stra);
-     moisnais[i]=(double)(month);
-     strcpy(line,stra);
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
-     cutv(stra, strb,line,' ');
+       num[i]=atol(stratrunc);
-     errno=0;
+     }
-     dval=strtod(strb,&endptr);
+     else
-     if( strb[0]=='\0' || (*endptr != '\0')){
+       num[i]=atol(stra);
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       exit(1);
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-     }
-     weight[i]=dval;
+     i=i+1;
-     strcpy(line,stra);
+   } /* End loop reading  data */
-     for (j=ncovcol;j>=1;j--){
+   *imax=i-1; /* Number of individuals */
-       cutv(stra, strb,line,' ');
+   fclose(fic);
-       errno=0;
-       lval=strtol(strb,&endptr,10);
+   return (0);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   endread:
-         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);
+     printf("Exiting readdata: ");
-         exit(1);
+     fclose(fic);
-       }
+     return (1);
-       if(lval <-1 || lval >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 \
-  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 \
+ void removespace(char *str) {
-  build V1=0 V2=0 for the reference value (1),\n \
+   char *p1 = str, *p2 = str;
-         V1=1 V2=0 for (2) \n \
+   do
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+     while (*p2 == ' ')
-  output of IMaCh is often meaningless.\n \
+       p2++;
-  Exiting.\n",lval,linei, i,line,j);
+   while (*p1++ = *p2++);
-         exit(1);
+ }
-       }
-       covar[j][i]=(double)(lval);
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-       strcpy(line,stra);
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-     }
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-     lstra=strlen(stra);
+    * - cptcovn or number of covariates k of the models excluding age*products =6
+    * - cptcovage number of covariates with age*products =2
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+    * - cptcovs number of simple covariates
-       stratrunc = &(stra[lstra-9]);
+    * - 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
-       num[i]=atol(stratrunc);
+    *     which is a new column after the 9 (ncovcol) variables.
-     }
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-     else
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-       num[i]=atol(stra);
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-       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;}*/
+  */
+ {
-     i=i+1;
+   int i, j, k, ks;
-   } /* End loop reading  data */
+   int i1, j1, k1, k2;
-   fclose(fic);
+   char modelsav[80];
-   /* printf("ii=%d", ij);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-      scanf("%d",i);*/
-   imx=i-1; /* Number of individuals */
+   /*removespace(model);*/
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-   /* for (i=1; i<=imx; i++){
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     }*/
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-    /*  for (i=1; i<=imx; i++){
+                   /* including age products which are counted in cptcovage.
-      if (s[4][i]==9)  s[4][i]=-1;
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-      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]));}*/
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-   /* for (i=1; i<=imx; i++) */
+     strcpy(modelsav,model);
+     if (strstr(model,"AGE") !=0){
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-      else weight[i]=1;*/
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       return 1;
-   /* Calculation of the number of parameters from char model */
+     }
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+     if (strstr(model,"v") !=0){
-   Tprod=ivector(1,15);
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-   Tvaraff=ivector(1,15);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-   Tvard=imatrix(1,15,1,2);
+       return 1;
-   Tage=ivector(1,15);
+     }
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     /*   Design
-     j=0, j1=0, k1=1, k2=1;
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-     j=nbocc(model,'+'); /* j=Number of '+' */
+      *  <          ncovcol=8                >
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-     cptcovn=j+1;
+      *   k=  1    2      3       4     5       6      7        8
-     cptcovprod=j1; /*Number of products */
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-     strcpy(modelsav,model);
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-       printf("Error. Non available option model=%s ",model);
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+      *  Tage[++cptcovage]=k
-       goto end;
+      *       if products, new covar are created after ncovcol with k1
-     }
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-     /* This loop fills the array Tvar from the string 'model'.*/
+      *  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];
-     for(i=(j+1); i>=1;i--){
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+      *  <          ncovcol=8                >
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-       /*scanf("%d",i);*/
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-       if (strchr(strb,'*')) {  /* Model includes a product */
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+      * p Tprod[1]@2={                         6, 5}
-           cptcovprod--;
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-           cutv(strb,stre,strd,'V');
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           cptcovage++;
+      *How to reorganize?
-             Tage[cptcovage]=i;
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-             /*printf("stre=%s ", stre);*/
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         }
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+      * Struct []
-           cptcovprod--;
+      */
-           cutv(strb,stre,strc,'V');
-           Tvar[i]=atoi(stre);
+     /* This loop fills the array Tvar from the string 'model'.*/
-           cptcovage++;
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-           Tage[cptcovage]=i;
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-         }
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-         else {  /* Age is not in the model */
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-           Tvar[i]=ncovcol+k1;
+     /*  k=1 Tvar[1]=2 (from V2) */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+     /*  k=5 Tvar[5] */
-           Tprod[k1]=i;
+     /* for (k=1; k<=cptcovn;k++) { */
-           Tvard[k1][1]=atoi(strc); /* m*/
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-           Tvard[k1][2]=atoi(stre); /* n */
+     /*  } */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+     /*
-           for (k=1; k<=lastobs;k++)
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-           k1++;
+         Tvar[k]=0;
-           k2=k2+2;
+     cptcovage=0;
-         }
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-       }
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-       else { /* no more sum */
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-        /*  scanf("%d",i);*/
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-       cutv(strd,strc,strb,'V');
+       /*scanf("%d",i);*/
-       Tvar[i]=atoi(strc);
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-       }
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-       strcpy(modelsav,stra);
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+           /* covar is not filled and then is empty */
-         scanf("%d",i);*/
+           cptcovprod--;
-     } /* end of loop + */
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-   } /* end model */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+           /*printf("stre=%s ", stre);*/
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+           cptcovprod--;
-   printf("cptcovprod=%d ", cptcovprod);
+           cutl(stre,strb,strc,'V');
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+           Tvar[k]=atoi(stre);
+           cptcovage++;
-   scanf("%d ",i);*/
+           Tage[cptcovage]=k;
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-     /*  if(mle==1){*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-   if (weightopt != 1) { /* Maximisation without weights*/
+           cptcovn++;
-     for(i=1;i<=n;i++) weight[i]=1.0;
+           cptcovprodnoage++;k1++;
-   }
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-     /*-calculation of age at interview from date of interview and age at death -*/
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-   agev=matrix(1,maxwav,1,imx);
+                                   because this model-covariate is a construction we invent a new column
+                                   ncovcol + k1
-   for (i=1; i<=imx; i++) {
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-     for(m=2; (m<= maxwav); m++) {
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-         anint[m][i]=9999;
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-         s[m][i]=-1;
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-       }
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+           k2=k2+2;
-         nberr++;
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-         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);
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-         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);
+           for (i=1; i<=lastobs;i++){
-         s[m][i]=-1;
+             /* Computes the new covariate which is a product of
-       }
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-         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]);
+         } /* End age is not in the model */
-         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]);
+       } /* End if model includes a product */
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       else { /* no more sum */
-       }
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-     }
+        /*  scanf("%d",i);*/
-   }
+         cutl(strd,strc,strb,'V');
+         ks++; /**< Number of simple covariates */
-   for (i=1; i<=imx; i++)  {
+         cptcovn++;
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+         Tvar[k]=atoi(strd);
-     for(m=firstpass; (m<= lastpass); m++){
+       }
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-         if (s[m][i] >= nlstate+1) {
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-           if(agedc[i]>0)
+         scanf("%d",i);*/
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     } /* end of loop + */
-               agev[m][i]=agedc[i];
+   } /* end model */
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             else {
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-               if ((int)andc[i]!=9999){
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-                 nbwarn++;
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+   printf("cptcovprod=%d ", cptcovprod);
-                 agev[m][i]=-1;
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-               }
-             }
+   scanf("%d ",i);*/
-         }
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a month */
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+   endread:
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+     printf("Exiting decodemodel: ");
-             agev[m][i]=1;
+     return (1);
-           else if(agev[m][i] <agemin){
+ }
-             agemin=agev[m][i];
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-           }
+ {
-           else if(agev[m][i] >agemax){
+   int i, m;
-             agemax=agev[m][i];
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   for (i=1; i<=imx; i++) {
-           }
+     for(m=2; (m<= maxwav); m++) {
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-           /*     agev[m][i] = age[i]+2*m;*/
+         anint[m][i]=9999;
-         }
+         s[m][i]=-1;
-         else { /* =9 */
+       }
-           agev[m][i]=1;
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-           s[m][i]=-1;
+         *nberr++;
-         }
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-       }
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-       else /*= 0 Unknown */
+         s[m][i]=-1;
-         agev[m][i]=1;
+       }
-     }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         *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]);
-   for (i=1; i<=imx; i++)  {
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-     for(m=firstpass; (m<=lastpass); m++){
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       if (s[m][i] > (nlstate+ndeath)) {
+       }
-         nberr++;
+     }
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+   }
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+   for (i=1; i<=imx; i++)  {
-       }
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     }
+     for(m=firstpass; (m<= lastpass); m++){
-   }
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         if (s[m][i] >= nlstate+1) {
-   /*for (i=1; i<=imx; i++){
+           if(agedc[i]>0)
-   for (m=firstpass; (m<lastpass); m++){
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+               agev[m][i]=agedc[i];
- }
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+             else {
- }*/
+               if ((int)andc[i]!=9999){
+                 nbwarn++;
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+                 agev[m][i]=-1;
+               }
-   agegomp=(int)agemin;
+             }
-   free_vector(severity,1,maxwav);
+         }
-   free_imatrix(outcome,1,maxwav+1,1,n);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-   free_vector(moisnais,1,n);
+                                  years but with the precision of a month */
-   free_vector(annais,1,n);
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-   /* free_matrix(mint,1,maxwav,1,n);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-      free_matrix(anint,1,maxwav,1,n);*/
+             agev[m][i]=1;
-   free_vector(moisdc,1,n);
+           else if(agev[m][i] < *agemin){
-   free_vector(andc,1,n);
+             *agemin=agev[m][i];
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+           }
-   wav=ivector(1,imx);
+           else if(agev[m][i] >*agemax){
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+             *agemax=agev[m][i];
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-   /* Concatenates waves */
+           /*     agev[m][i] = age[i]+2*m;*/
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+         }
+         else { /* =9 */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+           agev[m][i]=1;
+           s[m][i]=-1;
-   Tcode=ivector(1,100);
+         }
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+       }
-   ncodemax[1]=1;
+       else /*= 0 Unknown */
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+         agev[m][i]=1;
+     }
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
-                                  the estimations*/
+   }
-   h=0;
+   for (i=1; i<=imx; i++)  {
-   m=pow(2,cptcoveff);
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
-   for(k=1;k<=cptcoveff; k++){
+         *nberr++;
-     for(i=1; i <=(m/pow(2,k));i++){
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-       for(j=1; j <= ncodemax[k]; j++){
+         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);
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+         return 1;
-           h++;
+       }
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+     }
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   }
-         }
-       }
+   /*for (i=1; i<=imx; i++){
-     }
+   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]);
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+ }
-      codtab[1][2]=1;codtab[2][2]=2; */
-   /* for(i=1; i <=m ;i++){
+ }*/
-      for(k=1; k <=cptcovn; k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-      }
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-      printf("\n");
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-      }
-      scanf("%d",i);*/
+   return (0);
+   endread:
-   /*------------ gnuplot -------------*/
+     printf("Exiting calandcheckages: ");
-   strcpy(optionfilegnuplot,optionfilefiname);
+     return (1);
-   if(mle==-3)
+ }
-     strcat(optionfilegnuplot,"-mort");
-   strcat(optionfilegnuplot,".gp");
+ /***********************************************/
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+ /**************** Main Program *****************/
-     printf("Problem with file %s",optionfilegnuplot);
+ /***********************************************/
-   }
-   else{
+ int main(int argc, char *argv[])
-     fprintf(ficgp,"\n# %s\n", version);
+ {
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+ #ifdef GSL
-     fprintf(ficgp,"set missing 'NaNq'\n");
+   const gsl_multimin_fminimizer_type *T;
-   }
+   size_t iteri = 0, it;
-   /*  fclose(ficgp);*/
+   int rval = GSL_CONTINUE;
-   /*--------- index.htm --------*/
+   int status = GSL_SUCCESS;
+   double ssval;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+ #endif
-   if(mle==-3)
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-     strcat(optionfilehtm,"-mort");
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   strcat(optionfilehtm,".htm");
+   int linei, month, year,iout;
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+   int jj, ll, li, lj, lk, imk;
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+   int numlinepar=0; /* Current linenumber of parameter file */
-   }
+   int itimes;
+   int NDIM=2;
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   int vpopbased=0;
-   strcat(optionfilehtmcov,"-cov.htm");
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+   char ca[32], cb[32], cc[32];
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   /*  FILE *fichtm; *//* Html File */
-   }
+   /* FILE *ficgp;*/ /*Gnuplot File */
-   else{
+   struct stat info;
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   double agedeb, agefin,hf;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   double fret;
-   }
+   double **xi,tmp,delta;
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   double dum; /* Dummy variable */
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+   double ***p3mat;
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+   double ***mobaverage;
- \n\
+   int *indx;
- <hr  size=\"2\" color=\"#EC5E5E\">\
+   char line[MAXLINE], linepar[MAXLINE];
-  <ul><li><h4>Parameter files</h4>\n\
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+   char pathr[MAXLINE], pathimach[MAXLINE];
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+   char **bp, *tok, *val; /* pathtot */
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+   int firstobs=1, lastobs=10;
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+   int sdeb, sfin; /* Status at beginning and end */
-  - Date and time at start: %s</ul>\n",\
+   int c,  h , cpt,l;
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+   int ju,jl, mi;
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+   int i1,j1, jk,aa,bb, stepsize, ij;
-           fileres,fileres,\
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   fflush(fichtm);
+   int mobilav=0,popforecast=0;
+   int hstepm, nhstepm;
-   strcpy(pathr,path);
+   int agemortsup;
-   strcat(pathr,optionfilefiname);
+   float  sumlpop=0.;
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+   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;
-   /* Calculates basic frequencies. Computes observed prevalence at single age
-      and prints on file fileres'p'. */
+   double bage, fage, age, agelim, agebase;
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   double ftolpl=FTOL;
+   double **prlim;
-   fprintf(fichtm,"\n");
+   double ***param; /* Matrix of parameters */
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+   double  *p;
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+   double **matcov; /* Matrix of covariance */
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+   double ***delti3; /* Scale */
-           imx,agemin,agemax,jmin,jmax,jmean);
+   double *delti; /* Scale */
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   double ***eij, ***vareij;
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   double **varpl; /* Variances of prevalence limits by age */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   double *epj, vepp;
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   double kk1, kk2;
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double **ximort;
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+   int *dcwave;
-      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) */
+   char z[1]="c", occ;
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /*char  *strt;*/
+   char strtend[80];
-   if (mle==-3){
-     ximort=matrix(1,NDIM,1,NDIM);
+   long total_usecs;
-     cens=ivector(1,n);
-     ageexmed=vector(1,n);
+ /*   setlocale (LC_ALL, ""); */
-     agecens=vector(1,n);
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-     dcwave=ivector(1,n);
+ /*   textdomain (PACKAGE); */
+ /*   setlocale (LC_CTYPE, ""); */
-     for (i=1; i<=imx; i++){
+ /*   setlocale (LC_MESSAGES, ""); */
-       dcwave[i]=-1;
-       for (m=firstpass; m<=lastpass; m++)
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-         if (s[m][i]>nlstate) {
+   rstart_time = time(NULL);
-           dcwave[i]=m;
+   /*  (void) gettimeofday(&start_time,&tzp);*/
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+   start_time = *localtime(&rstart_time);
-           break;
+   curr_time=start_time;
-         }
+   /*tml = *localtime(&start_time.tm_sec);*/
-     }
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
-     for (i=1; i<=imx; i++) {
-       if (wav[i]>0){
+ /*  printf("Localtime (at start)=%s",strstart); */
-         ageexmed[i]=agev[mw[1][i]][i];
+ /*  tp.tm_sec = tp.tm_sec +86400; */
-         j=wav[i];
+ /*  tm = *localtime(&start_time.tm_sec); */
-         agecens[i]=1.;
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-         if (ageexmed[i]> 1 && wav[i] > 0){
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-           agecens[i]=agev[mw[j][i]][i];
+ /*   tp.tm_sec = mktime(&tmg); */
-           cens[i]= 1;
+ /*   strt=asctime(&tmg); */
-         }else if (ageexmed[i]< 1)
+ /*   printf("Time(after) =%s",strstart);  */
-           cens[i]= -1;
+ /*  (void) time (&time_value);
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-           cens[i]=0 ;
+ *  tm = *localtime(&time_value);
-       }
+ *  strstart=asctime(&tm);
-       else cens[i]=-1;
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-     }
+ */
-     for (i=1;i<=NDIM;i++) {
+   nberr=0; /* Number of errors and warnings */
-       for (j=1;j<=NDIM;j++)
+   nbwarn=0;
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   getcwd(pathcd, size);
-     }
+   printf("\n%s\n%s",version,fullversion);
-     p[1]=0.0268; p[NDIM]=0.083;
+   if(argc <=1){
-     /*printf("%lf %lf", p[1], p[2]);*/
+     printf("\nEnter the parameter file name: ");
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     if(pathr[i-1]=='\n')
-     strcpy(filerespow,"pow-mort");
+       pathr[i-1]='\0';
-     strcat(filerespow,fileres);
+     i=strlen(pathr);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-       printf("Problem with resultfile: %s\n", filerespow);
+       pathr[i-1]='\0';
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+    for (tok = pathr; tok != NULL; ){
-     }
+       printf("Pathr |%s|\n",pathr);
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-     /*  for (i=1;i<=nlstate;i++)
+       printf("val= |%s| pathr=%s\n",val,pathr);
-         for(j=1;j<=nlstate+ndeath;j++)
+       strcpy (pathtot, val);
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       if(pathr[0] == '\0') break; /* Dirty */
-     */
+     }
-     fprintf(ficrespow,"\n");
+   }
+   else{
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     strcpy(pathtot,argv[1]);
-     fclose(ficrespow);
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   /*cygwin_split_path(pathtot,path,optionfile);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-     for(i=1; i <=NDIM; i++)
+   /* cutv(path,optionfile,pathtot,'\\');*/
-       for(j=i+1;j<=NDIM;j++)
-         matcov[i][j]=matcov[j][i];
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-     printf("\nCovariance matrix\n ");
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-     for(i=1; i <=NDIM; i++) {
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-       for(j=1;j<=NDIM;j++){
+  /*   strcpy(pathimach,argv[0]); */
-         printf("%f ",matcov[i][j]);
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-       }
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-       printf("\n ");
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-     }
+   chdir(path); /* Can be a relative path */
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     printf("Current directory %s!\n",pathcd);
-     for (i=1;i<=NDIM;i++)
+   strcpy(command,"mkdir ");
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   strcat(command,optionfilefiname);
+   if((outcmd=system(command)) != 0){
-     lsurv=vector(1,AGESUP);
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     lpop=vector(1,AGESUP);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     tpop=vector(1,AGESUP);
+     /* fclose(ficlog); */
-     lsurv[agegomp]=100000;
+ /*     exit(1); */
+   }
-     for (k=agegomp;k<=AGESUP;k++) {
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-       agemortsup=k;
+ /*     perror("mkdir"); */
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+ /*   } */
-     }
+   /*-------- arguments in the command line --------*/
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   /* Log file */
+   strcat(filelog, optionfilefiname);
-     for (k=agegomp;k<agemortsup;k++){
+   strcat(filelog,".log");    /* */
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-       sumlpop=sumlpop+lpop[k];
+     printf("Problem with logfile %s\n",filelog);
-     }
+     goto end;
+   }
-     tpop[agegomp]=sumlpop;
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     for (k=agegomp;k<(agemortsup-3);k++){
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-       /*  tpop[k+1]=2;*/
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-       tpop[k+1]=tpop[k]-lpop[k];
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     }
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     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]);
+   printf("Local time (at start):%s",strstart);
+   fprintf(ficlog,"Local time (at start): %s",strstart);
+   fflush(ficlog);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+   /* */
-                      stepm, weightopt,\
+   strcpy(fileres,"r");
-                      model,imx,p,matcov,agemortsup);
+   strcat(fileres, optionfilefiname);
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     free_vector(lsurv,1,AGESUP);
-     free_vector(lpop,1,AGESUP);
+   /*---------arguments file --------*/
-     free_vector(tpop,1,AGESUP);
-   } /* Endof if mle==-3 */
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-   else{ /* For mle >=1 */
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fflush(ficlog);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     /* goto end; */
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     exit(70);
-     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 */
+   strcpy(filereso,"o");
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   strcat(filereso,fileres);
-     for (k=1; k<=npar;k++)
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-       printf(" %d %8.5f",k,p[k]);
+     printf("Problem with Output resultfile: %s\n", filereso);
-     printf("\n");
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-     if(mle>=1){ /* Could be 1 or 2 */
+     fflush(ficlog);
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     goto end;
-     }
+   }
-     /*--------- results files --------------*/
+   /* Reads comments: lines beginning with '#' */
-     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);
+   numlinepar=0;
+   while((c=getc(ficpar))=='#' && c!= EOF){
+     ungetc(c,ficpar);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fgets(line, MAXLINE, ficpar);
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     numlinepar++;
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fputs(line,stdout);
-     for(i=1,jk=1; i <=nlstate; i++){
+     fputs(line,ficparo);
-       for(k=1; k <=(nlstate+ndeath); k++){
+     fputs(line,ficlog);
-         if (k != i) {
+   }
-           printf("%d%d ",i,k);
+   ungetc(c,ficpar);
-           fprintf(ficlog,"%d%d ",i,k);
-           fprintf(ficres,"%1d%1d ",i,k);
+   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);
-           for(j=1; j <=ncovmodel; j++){
+   numlinepar++;
-             printf("%lf ",p[jk]);
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-             fprintf(ficlog,"%lf ",p[jk]);
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-             fprintf(ficres,"%lf ",p[jk]);
+   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);
-             jk++;
+   fflush(ficlog);
-           }
+   while((c=getc(ficpar))=='#' && c!= EOF){
-           printf("\n");
+     ungetc(c,ficpar);
-           fprintf(ficlog,"\n");
+     fgets(line, MAXLINE, ficpar);
-           fprintf(ficres,"\n");
+     numlinepar++;
-         }
+     fputs(line, stdout);
-       }
+     //puts(line);
-     }
+     fputs(line,ficparo);
-     if(mle!=0){
+     fputs(line,ficlog);
-       /* Computing hessian and covariance matrix */
+   }
-       ftolhess=ftol; /* Usually correct */
+   ungetc(c,ficpar);
-       hesscov(matcov, p, npar, delti, ftolhess, func);
-     }
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-     printf("# Scales (for hessian or gradient estimation)\n");
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-     for(i=1,jk=1; i <=nlstate; i++){
+      v1+v2*age+v2*v3 makes cptcovn = 3
-       for(j=1; j <=nlstate+ndeath; j++){
+   */
-         if (j!=i) {
+   if (strlen(model)>1)
-           fprintf(ficres,"%1d%1d",i,j);
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
-           printf("%1d%1d",i,j);
+   else
-           fprintf(ficlog,"%1d%1d",i,j);
+     ncovmodel=2;
-           for(k=1; k<=ncovmodel;k++){
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-             printf(" %.5e",delti[jk]);
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-             fprintf(ficlog," %.5e",delti[jk]);
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-             fprintf(ficres," %.5e",delti[jk]);
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-             jk++;
+     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,"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);
-           printf("\n");
+     fflush(stdout);
-           fprintf(ficlog,"\n");
+     fclose (ficlog);
-           fprintf(ficres,"\n");
+     goto end;
-         }
+   }
-       }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     }
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     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){ /* Print a wizard for help writing covariance matrix */
-     if(mle>=1)
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-       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");
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     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");
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     /* # 121 Var(a12)\n\ */
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+     fclose (ficparo);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+     fclose (ficlog);
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     goto end;
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     exit(0);
-     /* # 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\ */
+   else if(mle==-3) {
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     /* Just to have a covariance matrix which will be more understandable
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-        even is we still don't want to manage dictionary of variables
+     matcov=matrix(1,npar,1,npar);
-     */
+   }
-     for(itimes=1;itimes<=2;itimes++){
+   else{
-       jj=0;
+     /* Read guessed parameters */
-       for(i=1; i <=nlstate; i++){
+     /* Reads comments: lines beginning with '#' */
-         for(j=1; j <=nlstate+ndeath; j++){
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           if(j==i) continue;
+       ungetc(c,ficpar);
-           for(k=1; k<=ncovmodel;k++){
+       fgets(line, MAXLINE, ficpar);
-             jj++;
+       numlinepar++;
-             ca[0]= k+'a'-1;ca[1]='\0';
+       fputs(line,stdout);
-             if(itimes==1){
+       fputs(line,ficparo);
-               if(mle>=1)
+       fputs(line,ficlog);
-                 printf("#%1d%1d%d",i,j,k);
+     }
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+     ungetc(c,ficpar);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
-             }else{
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-               if(mle>=1)
+     for(i=1; i <=nlstate; i++){
-                 printf("%1d%1d%d",i,j,k);
+       j=0;
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+         if(jj==i) continue;
-             }
+         j++;
-             ll=0;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-             for(li=1;li <=nlstate; li++){
+         if ((i1 != i) && (j1 != j)){
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-                 if(lj==li) continue;
+ It might be a problem of design; if ncovcol and the model are correct\n \
-                 for(lk=1;lk<=ncovmodel;lk++){
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-                   ll++;
+           exit(1);
-                   if(ll<=jj){
+         }
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                     if(ll<jj){
+         if(mle==1)
-                       if(itimes==1){
+           printf("%1d%1d",i,j);
-                         if(mle>=1)
+         fprintf(ficlog,"%1d%1d",i,j);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         for(k=1; k<=ncovmodel;k++){
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           if(mle==1){
-                       }else{
+             printf(" %lf",param[i][j][k]);
-                         if(mle>=1)
+             fprintf(ficlog," %lf",param[i][j][k]);
-                           printf(" %.5e",matcov[jj][ll]);
+           }
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+           else
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+             fprintf(ficlog," %lf",param[i][j][k]);
-                       }
+           fprintf(ficparo," %lf",param[i][j][k]);
-                     }else{
+         }
-                       if(itimes==1){
+         fscanf(ficpar,"\n");
-                         if(mle>=1)
+         numlinepar++;
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+         if(mle==1)
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+           printf("\n");
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+         fprintf(ficlog,"\n");
-                       }else{
+         fprintf(ficparo,"\n");
-                         if(mle>=1)
+       }
-                           printf(" %.5e",matcov[jj][ll]);
+     }
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+     fflush(ficlog);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+     /* Reads scales values */
-                     }
+     p=param[1][1];
-                   }
-                 } /* end lk */
+     /* Reads comments: lines beginning with '#' */
-               } /* end lj */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-             } /* end li */
+       ungetc(c,ficpar);
-             if(mle>=1)
+       fgets(line, MAXLINE, ficpar);
-               printf("\n");
+       numlinepar++;
-             fprintf(ficlog,"\n");
+       fputs(line,stdout);
-             fprintf(ficres,"\n");
+       fputs(line,ficparo);
-             numlinepar++;
+       fputs(line,ficlog);
-           } /* end k*/
+     }
-         } /*end j */
+     ungetc(c,ficpar);
-       } /* end i */
-     } /* end itimes */
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     fflush(ficlog);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     fflush(ficres);
+         if ((i1-i)*(j1-j)!=0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           exit(1);
-       ungetc(c,ficpar);
+         }
-       fgets(line, MAXLINE, ficpar);
+         printf("%1d%1d",i,j);
-       puts(line);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-       fputs(line,ficparo);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-     }
+         for(k=1; k<=ncovmodel;k++){
-     ungetc(c,ficpar);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
-     estepm=0;
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+         }
-     if (fage <= 2) {
+         fscanf(ficpar,"\n");
-       bage = ageminpar;
+         numlinepar++;
-       fage = agemaxpar;
+         printf("\n");
-     }
+         fprintf(ficparo,"\n");
+         fprintf(ficlog,"\n");
-     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);
+     fflush(ficlog);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /* Reads covariance matrix */
-       ungetc(c,ficpar);
+     delti=delti3[1][1];
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
-       fputs(line,ficparo);
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-     }
-     ungetc(c,ficpar);
+     /* Reads comments: lines beginning with '#' */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     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);
+       ungetc(c,ficpar);
-     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);
+       fgets(line, MAXLINE, ficpar);
-     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);
+       numlinepar++;
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       fputs(line,stdout);
-     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);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-       ungetc(c,ficpar);
+     ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+     matcov=matrix(1,npar,1,npar);
-       fputs(line,ficparo);
+     for(i=1; i <=npar; i++)
-     }
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-     ungetc(c,ficpar);
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+       if(mle==1)
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+       fprintf(ficparo,"%s",str);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+       for(j=1; j <=i; j++){
-     fprintf(ficres,"pop_based=%d\n",popbased);
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           printf(" %.5le",matcov[i][j]);
-       ungetc(c,ficpar);
+         }
-       fgets(line, MAXLINE, ficpar);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-       puts(line);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-       fputs(line,ficparo);
+       }
-     }
+       fscanf(ficpar,"\n");
-     ungetc(c,ficpar);
+       numlinepar++;
+       if(mle==1)
-     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);
+         printf("\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(ficlog,"\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(ficparo,"\n");
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     }
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     for(i=1; i <=npar; i++)
-     /* day and month of proj2 are not used but only year anproj2.*/
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
+     if(mle==1)
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+       printf("\n");
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     fprintf(ficlog,"\n");
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     fflush(ficlog);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     /*-------- Rewriting parameter file ----------*/
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-    /*------------ free_vector  -------------*/
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-    /*  chdir(path); */
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     free_ivector(wav,1,imx);
+     }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     fprintf(ficres,"#%s\n",version);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+   }    /* End of mle != -3 */
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     free_lvector(num,1,n);
-     free_vector(agedc,1,n);
+   n= lastobs;
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+   num=lvector(1,n);
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   moisnais=vector(1,n);
-     fclose(ficparo);
+   annais=vector(1,n);
-     fclose(ficres);
+   moisdc=vector(1,n);
+   andc=vector(1,n);
+   agedc=vector(1,n);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   cod=ivector(1,n);
+   weight=vector(1,n);
-     strcpy(filerespl,"pl");
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-     strcat(filerespl,fileres);
+   mint=matrix(1,maxwav,1,n);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+   anint=matrix(1,maxwav,1,n);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   tab=ivector(1,NCOVMAX);
-     }
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   /* Reads data from file datafile */
-     pstamp(ficrespl);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     goto end;
-     fprintf(ficrespl,"#Age ");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   /* Calculation of the number of parameters from char model */
-     fprintf(ficrespl,"\n");
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-     prlim=matrix(1,nlstate,1,nlstate);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     agebase=ageminpar;
+         k=1 Tvar[1]=2 (from V2)
-     agelim=agemaxpar;
+     */
-     ftolpl=1.e-10;
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-     i1=cptcoveff;
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-     if (cptcovn < 1){i1=1;}
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   /* For model-covariate k tells which data-covariate to use but
-         k=k+1;
+     because this model-covariate is a construction we invent a new column
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     ncovcol + k1
-         fprintf(ficrespl,"\n#******");
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-         printf("\n#******");
+     Tvar[3=V1*V4]=4+1 etc */
-         fprintf(ficlog,"\n#******");
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-         for(j=1;j<=cptcoveff;j++) {
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   */
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-         }
+   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
-         fprintf(ficrespl,"******\n");
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-         printf("******\n");
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-         fprintf(ficlog,"******\n");
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+covariates (3 plus signs)
-         for (age=agebase; age<=agelim; age++){
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+                       */
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
+   if(decodemodel(model, lastobs) == 1)
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     goto end;
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-           fprintf(ficrespl,"\n");
+     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);
-     }
+   }
-     fclose(ficrespl);
+     /*  if(mle==1){*/
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     /*------------- h Pij x at various ages ------------*/
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
+   }
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     /*-calculation of age at interview from date of interview and age at death -*/
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+   agev=matrix(1,maxwav,1,imx);
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     goto end;
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+   agegomp=(int)agemin;
-     /*if (stepm<=24) stepsize=2;*/
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
-     agelim=AGESUP;
+   /* free_matrix(mint,1,maxwav,1,n);
-     hstepm=stepsize*YEARM; /* Every year of age */
+      free_matrix(anint,1,maxwav,1,n);*/
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
-     /* hstepm=1;   aff par mois*/
+   /* */
-     pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+   wav=ivector(1,imx);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-         k=k+1;
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-         fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+   /* Concatenates waves */
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-         fprintf(ficrespij,"******\n");
+   /* */
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   ncodemax[1]=1;
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel > 2)
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-           for(i=1; i<=nlstate;i++)
+   h=0;
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
+   /*if (cptcovn > 0) */
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-             for(i=1; i<=nlstate;i++)
+   m=pow(2,cptcoveff);
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-             fprintf(ficrespij,"\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 */
-           }
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-           fprintf(ficrespij,"\n");
+           h++;
-         }
+           if (h>m)
-       }
+             h=1;
-     }
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     h     1     2     3     4
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-     fclose(ficrespij);
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+            *     4     2     2     1     1
-     for(i=1;i<=AGESUP;i++)
+            *     5 i=3 1 i=2 1     2     1
-       for(j=1;j<=NCOVMAX;j++)
+            *     6     2     1     2     1
-         for(k=1;k<=NCOVMAX;k++)
+            *     7 i=4 1     2     2     1
-           probs[i][j][k]=0.;
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
-     /*---------- Forecasting ------------------*/
+            *    10     2     1     1     1
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+            *    11 i=6 1     2     1     1
-     if(prevfcast==1){
+            *    12     2     2     1     1
-       /*    if(stepm ==1){*/
+            *    13 i=7 1 i=4 1     2     1
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+            *    14     2     1     2     1
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+            *    15 i=8 1     2     2     1
-       /*      }  */
+            *    16     2     2     2     1
-       /*      else{ */
+            */
-       /*        erreur=108; */
+           codtab[h][k]=j;
-       /*        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); */
+           /*codtab[h][Tvar[k]]=j;*/
-       /*        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); */
+           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]]);
-       /*      } */
+         }
-     }
+       }
+     }
+   }
-     /*---------- Health expectancies and variances ------------*/
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
-     strcpy(filerest,"t");
+   /* for(i=1; i <=m ;i++){
-     strcat(filerest,fileres);
+      for(k=1; k <=cptcovn; k++){
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+      }
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+      printf("\n");
-     }
+      }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+      scanf("%d",i);*/
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+  free_ivector(Ndum,-1,NCOVMAX);
-     strcpy(filerese,"e");
-     strcat(filerese,fileres);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   /*------------ gnuplot -------------*/
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   strcpy(optionfilegnuplot,optionfilefiname);
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   if(mle==-3)
-     }
+     strcat(optionfilegnuplot,"-mort");
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   strcat(optionfilegnuplot,".gp");
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-     strcpy(fileresstde,"stde");
+     printf("Problem with file %s",optionfilegnuplot);
-     strcat(fileresstde,fileres);
+   }
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   else{
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     fprintf(ficgp,"\n# %s\n", version);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-     }
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   }
+   /*  fclose(ficgp);*/
-     strcpy(filerescve,"cve");
+   /*--------- index.htm --------*/
-     strcat(filerescve,fileres);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   if(mle==-3)
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     strcat(optionfilehtm,"-mort");
-     }
+   strcat(optionfilehtm,".htm");
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
-     strcpy(fileresv,"v");
+   }
-     strcat(fileresv,fileres);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+   strcat(optionfilehtmcov,"-cov.htm");
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-     }
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   }
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   else{
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-     /*  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",\
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+   }
-     */
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     if (mobilav!=0) {
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+ \n\
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+  <ul><li><h4>Parameter files</h4>\n\
-       }
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-     }
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+  - Date and time at start: %s</ul>\n",\
-         k=k+1;
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-         fprintf(ficrest,"\n#****** ");
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-         for(j=1;j<=cptcoveff;j++)
+           fileres,fileres,\
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-         fprintf(ficrest,"******\n");
+   fflush(fichtm);
-         fprintf(ficreseij,"\n#****** ");
+   strcpy(pathr,path);
-         fprintf(ficresstdeij,"\n#****** ");
+   strcat(pathr,optionfilefiname);
-         fprintf(ficrescveij,"\n#****** ");
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      and prints on file fileres'p'. */
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-         }
-         fprintf(ficreseij,"******\n");
+   fprintf(fichtm,"\n");
-         fprintf(ficresstdeij,"******\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-         fprintf(ficrescveij,"******\n");
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-         fprintf(ficresvij,"\n#****** ");
+           imx,agemin,agemax,jmin,jmax,jmean);
-         for(j=1;j<=cptcoveff;j++)
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         fprintf(ficresvij,"******\n");
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-         oldm=oldms;savm=savms;
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+   /* 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] */
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-         oldm=oldms;savm=savms;
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-         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);
+   if (mle==-3){
-         }
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-         pstamp(ficrest);
+     cens=ivector(1,n);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     ageexmed=vector(1,n);
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+     agecens=vector(1,n);
-         fprintf(ficrest,"\n");
+     dcwave=ivector(1,n);
-         epj=vector(1,nlstate+1);
+     for (i=1; i<=imx; i++){
-         for(age=bage; age <=fage ;age++){
+       dcwave[i]=-1;
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       for (m=firstpass; m<=lastpass; m++)
-           if (popbased==1) {
+         if (s[m][i]>nlstate) {
-             if(mobilav ==0){
+           dcwave[i]=m;
-               for(i=1; i<=nlstate;i++)
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-                 prlim[i][i]=probs[(int)age][i][k];
+           break;
-             }else{ /* mobilav */
+         }
-               for(i=1; i<=nlstate;i++)
+     }
-                 prlim[i][i]=mobaverage[(int)age][i][k];
-             }
+     for (i=1; i<=imx; i++) {
-           }
+       if (wav[i]>0){
+         ageexmed[i]=agev[mw[1][i]][i];
-           fprintf(ficrest," %4.0f",age);
+         j=wav[i];
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+         agecens[i]=1.;
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+         if (ageexmed[i]> 1 && wav[i] > 0){
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+           agecens[i]=agev[mw[j][i]][i];
-             }
+           cens[i]= 1;
-             epj[nlstate+1] +=epj[j];
+         }else if (ageexmed[i]< 1)
-           }
+           cens[i]= -1;
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           for(i=1, vepp=0.;i <=nlstate;i++)
+           cens[i]=0 ;
-             for(j=1;j <=nlstate;j++)
+       }
-               vepp += vareij[i][j][(int)age];
+       else cens[i]=-1;
-           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]));
+     for (i=1;i<=NDIM;i++) {
-           }
+       for (j=1;j<=NDIM;j++)
-           fprintf(ficrest,"\n");
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-         }
+     }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-         free_vector(epj,1,nlstate+1);
+     /*printf("%lf %lf", p[1], p[2]);*/
-       }
-     }
-     free_vector(weight,1,n);
+ #ifdef GSL
-     free_imatrix(Tvard,1,15,1,2);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-     free_imatrix(s,1,maxwav+1,1,n);
+ #elsedef
-     free_matrix(anint,1,maxwav,1,n);
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     free_matrix(mint,1,maxwav,1,n);
+ #endif
-     free_ivector(cod,1,n);
+     strcpy(filerespow,"pow-mort");
-     free_ivector(tab,1,NCOVMAX);
+     strcat(filerespow,fileres);
-     fclose(ficreseij);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     fclose(ficresstdeij);
+       printf("Problem with resultfile: %s\n", filerespow);
-     fclose(ficrescveij);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     fclose(ficresvij);
+     }
-     fclose(ficrest);
+ #ifdef GSL
-     fclose(ficpar);
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #elsedef
-     /*------- Variance of period (stable) prevalence------*/
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
-     strcpy(fileresvpl,"vpl");
+     /*  for (i=1;i<=nlstate;i++)
-     strcat(fileresvpl,fileres);
+         for(j=1;j<=nlstate+ndeath;j++)
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+     */
-       exit(0);
+     fprintf(ficrespow,"\n");
-     }
+ #ifdef GSL
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     gsl_multimin_fminimizer *sfm = NULL;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     gsl_vector *ss, *x;
-         k=k+1;
+     gsl_multimin_function minex_func;
-         fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+     /* Initial vertex size vector */
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     ss = gsl_vector_alloc (NDIM);
-         fprintf(ficresvpl,"******\n");
+     if (ss == NULL){
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-         oldm=oldms;savm=savms;
+     }
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+     /* Set all step sizes to 1 */
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     gsl_vector_set_all (ss, 0.001);
-       }
-     }
+     /* Starting point */
-     fclose(ficresvpl);
+     x = gsl_vector_alloc (NDIM);
-     /*---------- End : free ----------------*/
+     if (x == NULL){
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       gsl_vector_free(ss);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
-   }  /* mle==-3 arrives here for freeing */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     /* Initialize method and iterate */
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+ /*     gsl_vector_set(x, 1, 0.083); */
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     gsl_vector_set(x, 0, p[1]);
-     free_matrix(covar,0,NCOVMAX,1,n);
+     gsl_vector_set(x, 1, p[2]);
-     free_matrix(matcov,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+     minex_func.f = &gompertz_f;
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     minex_func.n = NDIM;
-     free_matrix(agev,1,maxwav,1,imx);
+     minex_func.params = (void *)&p; /* ??? */
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-     free_ivector(ncodemax,1,8);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-     free_ivector(Tvar,1,15);
-     free_ivector(Tprod,1,15);
+     printf("Iterations beginning .....\n\n");
-     free_ivector(Tvaraff,1,15);
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-     free_ivector(Tage,1,15);
-     free_ivector(Tcode,1,100);
+     iteri=0;
+     while (rval == GSL_CONTINUE){
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+       iteri++;
-     free_imatrix(codtab,1,100,1,10);
+       status = gsl_multimin_fminimizer_iterate(sfm);
-   fflush(fichtm);
-   fflush(ficgp);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
-   if((nberr >0) || (nbwarn>0)){
+       if (status)
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+         break;
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
-   }else{
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
-     printf("End of Imach\n");
+       ssval = gsl_multimin_fminimizer_size (sfm);
-     fprintf(ficlog,"End of Imach\n");
-   }
+       if (rval == GSL_SUCCESS)
-   printf("See log file on %s\n",filelog);
+         printf ("converged to a local maximum at\n");
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
-   (void) gettimeofday(&end_time,&tzp);
+       printf("%5d ", iteri);
-   tm = *localtime(&end_time.tv_sec);
+       for (it = 0; it < NDIM; it++){
-   tmg = *gmtime(&end_time.tv_sec);
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
-   strcpy(strtend,asctime(&tm));
+       }
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     }
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     gsl_vector_free(x); /* initial values */
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     gsl_vector_free(ss); /* inital step size */
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+     for (it=0; it<NDIM; it++){
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+       p[it+1]=gsl_vector_get(sfm->x,it);
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+       fprintf(ficrespow," %.12lf", p[it]);
-   fclose(fichtm);
+     }
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
-   fclose(fichtmcov);
+ #endif
-   fclose(ficgp);
+ #ifdef POWELL
-   fclose(ficlog);
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-   /*------ End -----------*/
+ #endif
+     fclose(ficrespow);
-    printf("Before Current directory %s!\n",pathcd);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-    if(chdir(pathcd) != 0)
-     printf("Can't move to directory %s!\n",path);
+     for(i=1; i <=NDIM; i++)
-   if(getcwd(pathcd,MAXLINE) > 0)
+       for(j=i+1;j<=NDIM;j++)
-     printf("Current directory %s!\n",pathcd);
+         matcov[i][j]=matcov[j][i];
-   /*strcat(plotcmd,CHARSEPARATOR);*/
-   sprintf(plotcmd,"gnuplot");
+     printf("\nCovariance matrix\n ");
- #ifndef UNIX
+     for(i=1; i <=NDIM; i++) {
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+       for(j=1;j<=NDIM;j++){
- #endif
+         printf("%f ",matcov[i][j]);
-   if(!stat(plotcmd,&info)){
+       }
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       printf("\n ");
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     }
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
-     }else
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-       strcpy(pplotcmd,plotcmd);
+     for (i=1;i<=NDIM;i++)
- #ifdef UNIX
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-     strcpy(plotcmd,GNUPLOTPROGRAM);
-     if(!stat(plotcmd,&info)){
+     lsurv=vector(1,AGESUP);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     lpop=vector(1,AGESUP);
-     }else
+     tpop=vector(1,AGESUP);
-       strcpy(pplotcmd,plotcmd);
+     lsurv[agegomp]=100000;
- #endif
-   }else
+     for (k=agegomp;k<=AGESUP;k++) {
-     strcpy(pplotcmd,plotcmd);
+       agemortsup=k;
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     }
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     for (k=agegomp;k<agemortsup;k++)
-   if((outcmd=system(plotcmd)) != 0){
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-     printf("\n Problem with gnuplot\n");
-   }
+     for (k=agegomp;k<agemortsup;k++){
-   printf(" Wait...");
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
-   while (z[0] != 'q') {
+       sumlpop=sumlpop+lpop[k];
-     /* chdir(path); */
+     }
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
-     scanf("%s",z);
+     tpop[agegomp]=sumlpop;
- /*     if (z[0] == 'c') system("./imach"); */
+     for (k=agegomp;k<(agemortsup-3);k++){
-     if (z[0] == 'e') {
+       /*  tpop[k+1]=2;*/
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       tpop[k+1]=tpop[k]-lpop[k];
-       system(optionfilehtm);
+     }
-     }
-     else if (z[0] == 'g') system(plotcmd);
-     else if (z[0] == 'q') exit(0);
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-   }
+     for (k=agegomp;k<(agemortsup-2);k++)
-   end:
+       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]);
-   while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
-     scanf("%s",z);
+     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.1.161