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 1.157

-version 1.125, 2006/04/04 15:20:31
+version 1.157, 2014/08/27 16:26:55
  Line 1
  /* $Id$
    $State$
    $Log$
+   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> */
+ #include <unistd.h>
- /* #define _(String) gettext (String) */
+ #include <limits.h>
- #define MAXLINE 256
+ #include <sys/types.h>
+ #include <sys/stat.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <errno.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ extern int errno;
- #define FILENAMELENGTH 132
+ /* #ifdef LINUX */
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ /* #include <time.h> */
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ /* #include "timeval.h" */
+ /* #else */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ /* #include <sys/time.h> */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ /* #endif */
- #define NINTERVMAX 8
+ #include <time.h>
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #ifdef GSL
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #include <gsl/gsl_errno.h>
- #define MAXN 20000
+ #include <gsl/gsl_multimin.h>
- #define YEARM 12. /* Number of months per year */
+ #endif
- #define AGESUP 130
- #define AGEBASE 40
+ /* #include <libintl.h> */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ /* #define _(String) gettext (String) */
- #ifdef UNIX
- #define DIRSEPARATOR '/'
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- #define CHARSEPARATOR "/"
- #define ODIRSEPARATOR '\\'
+ #define GNUPLOTPROGRAM "gnuplot"
- #else
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define DIRSEPARATOR '\\'
+ #define FILENAMELENGTH 132
- #define CHARSEPARATOR "\\"
- #define ODIRSEPARATOR '/'
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #endif
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- /* $Id$ */
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
- /* $State$ */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #define NINTERVMAX 8
- char fullversion[]="$Revision$ $Date$";
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- char strstart[80];
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- int nvar;
+ #define MAXN 20000
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #define YEARM 12. /**< Number of months per year */
- int npar=NPARMAX;
+ #define AGESUP 130
- int nlstate=2; /* Number of live states */
+ #define AGEBASE 40
- int ndeath=1; /* Number of dead states */
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ #ifdef _WIN32
- int popbased=0;
+ #define DIRSEPARATOR '\\'
+ #define CHARSEPARATOR "\\"
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define ODIRSEPARATOR '/'
- int maxwav; /* Maxim number of waves */
+ #else
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define DIRSEPARATOR '/'
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #define CHARSEPARATOR "/"
- int gipmx, gsw; /* Global variables on the number of contributions
+ #define ODIRSEPARATOR '\\'
-                    to the likelihood and the sum of weights (done by funcone)*/
+ #endif
- int mle, weightopt;
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ /* $Id$ */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ /* $State$ */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ 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)";
- double jmean; /* Mean space between 2 waves */
+ char fullversion[]="$Revision$ $Date$";
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ char strstart[80];
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- FILE *ficlog, *ficrespow;
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- int globpr; /* Global variable for printing or not */
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- double fretone; /* Only one call to likelihood */
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- long ipmx; /* Number of contributions */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- double sw; /* Sum of weights */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- char filerespow[FILENAMELENGTH];
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- FILE *ficresilk;
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ int cptcov=0; /* Working variable */
- FILE *ficresprobmorprev;
+ int npar=NPARMAX;
- FILE *fichtm, *fichtmcov; /* Html File */
+ int nlstate=2; /* Number of live states */
- FILE *ficreseij;
+ int ndeath=1; /* Number of dead states */
- char filerese[FILENAMELENGTH];
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- FILE *ficresstdeij;
+ int popbased=0;
- char fileresstde[FILENAMELENGTH];
- FILE *ficrescveij;
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char filerescve[FILENAMELENGTH];
+ int maxwav=0; /* Maxim number of waves */
- FILE  *ficresvij;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- char fileresv[FILENAMELENGTH];
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- FILE  *ficresvpl;
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- char fileresvpl[FILENAMELENGTH];
+                    to the likelihood and the sum of weights (done by funcone)*/
- char title[MAXLINE];
+ int mle=1, weightopt=0;
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- char command[FILENAMELENGTH];
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- int  outcmd=0;
+ double jmean=1; /* Mean space between 2 waves */
+ double **matprod2(); /* test */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- char filelog[FILENAMELENGTH]; /* Log file */
+ /*FILE *fic ; */ /* Used in readdata only */
- char filerest[FILENAMELENGTH];
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- char fileregp[FILENAMELENGTH];
+ FILE *ficlog, *ficrespow;
- char popfile[FILENAMELENGTH];
+ int globpr=0; /* Global variable for printing or not */
+ double fretone; /* Only one call to likelihood */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ char filerespow[FILENAMELENGTH];
- struct timezone tzp;
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- extern int gettimeofday();
+ FILE *ficresilk;
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- long time_value;
+ FILE *ficresprobmorprev;
- extern long time();
+ FILE *fichtm, *fichtmcov; /* Html File */
- char strcurr[80], strfor[80];
+ FILE *ficreseij;
+ char filerese[FILENAMELENGTH];
- char *endptr;
+ FILE *ficresstdeij;
- long lval;
+ char fileresstde[FILENAMELENGTH];
- double dval;
+ FILE *ficrescveij;
+ char filerescve[FILENAMELENGTH];
- #define NR_END 1
+ FILE  *ficresvij;
- #define FREE_ARG char*
+ char fileresv[FILENAMELENGTH];
- #define FTOL 1.0e-10
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- #define NRANSI
+ char title[MAXLINE];
- #define ITMAX 200
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- #define TOL 2.0e-4
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- #define CGOLD 0.3819660
+ int  outcmd=0;
- #define ZEPS 1.0e-10
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- #define GOLD 1.618034
+ char filelog[FILENAMELENGTH]; /* Log file */
- #define GLIMIT 100.0
+ char filerest[FILENAMELENGTH];
- #define TINY 1.0e-20
+ char fileregp[FILENAMELENGTH];
+ char popfile[FILENAMELENGTH];
- static double maxarg1,maxarg2;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ /* struct timezone tzp; */
- #define rint(a) floor(a+0.5)
+ /* extern int gettimeofday(); */
+ struct tm tml, *gmtime(), *localtime();
- static double sqrarg;
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ extern time_t time();
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- int agegomp= AGEGOMP;
+ struct tm start_time, end_time, curr_time, last_time, forecast_time;
+ time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
- int imx;
+ struct tm tm;
- int stepm=1;
- /* Stepm, step in month: minimum step interpolation*/
+ char strcurr[80], strfor[80];
- int estepm;
+ char *endptr;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ long lval;
+ double dval;
- int m,nb;
- long *num;
+ #define NR_END 1
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ #define FREE_ARG char*
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ #define FTOL 1.0e-10
- double **pmmij, ***probs;
- double *ageexmed,*agecens;
+ #define NRANSI
- double dateintmean=0;
+ #define ITMAX 200
- double *weight;
+ #define TOL 2.0e-4
- int **s; /* Status */
- double *agedc, **covar, idx;
+ #define CGOLD 0.3819660
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ #define ZEPS 1.0e-10
- double *lsurv, *lpop, *tpop;
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ #define GOLD 1.618034
- double ftolhess; /* Tolerance for computing hessian */
+ #define GLIMIT 100.0
+ #define TINY 1.0e-20
- /**************** split *************************/
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ static double maxarg1,maxarg2;
- {
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   */
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-   char  *ss;                            /* pointer */
+ #define rint(a) floor(a+0.5)
-   int   l1, l2;                         /* length counters */
+ static double sqrarg;
-   l1 = strlen(path );                   /* length of path */
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ int agegomp= AGEGOMP;
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ int imx;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ int stepm=1;
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ /* Stepm, step in month: minimum step interpolation*/
-     /* get current working directory */
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ int estepm;
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-       return( GLOCK_ERROR_GETCWD );
-     }
+ int m,nb;
-     /* got dirc from getcwd*/
+ long *num;
-     printf(" DIRC = %s \n",dirc);
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-   } else {                              /* strip direcotry from path */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-     ss++;                               /* after this, the filename */
+ double **pmmij, ***probs;
-     l2 = strlen( ss );                  /* length of filename */
+ double *ageexmed,*agecens;
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ double dateintmean=0;
-     strcpy( name, ss );         /* save file name */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ double *weight;
-     dirc[l1-l2] = 0;                    /* add zero */
+ int **s; /* Status */
-     printf(" DIRC2 = %s \n",dirc);
+ double *agedc;
-   }
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-   /* We add a separator at the end of dirc if not exists */
+                   * covar=matrix(0,NCOVMAX,1,n);
-   l1 = strlen( dirc );                  /* length of directory */
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ double  idx;
-     dirc[l1] =  DIRSEPARATOR;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-     dirc[l1+1] = 0;
+ int *Ndum; /** Freq of modality (tricode */
-     printf(" DIRC3 = %s \n",dirc);
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   }
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   ss = strrchr( name, '.' );            /* find last / */
+ double *lsurv, *lpop, *tpop;
-   if (ss >0){
-     ss++;
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-     strcpy(ext,ss);                     /* save extension */
+ double ftolhess; /**< Tolerance for computing hessian */
-     l1= strlen( name);
-     l2= strlen(ss)+1;
+ /**************** split *************************/
-     strncpy( finame, name, l1-l2);
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-     finame[l1-l2]= 0;
+ {
-   }
+   /* 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)
-   return( 0 );                          /* we're done */
+   */
- }
+   char  *ss;                            /* pointer */
+   int   l1, l2;                         /* length counters */
- /******************************************/
+   l1 = strlen(path );                   /* length of path */
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- void replace_back_to_slash(char *s, char*t)
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
- {
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-   int i;
+     strcpy( name, path );               /* we got the fullname name because no directory */
-   int lg=0;
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-   i=0;
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   lg=strlen(t);
+     /* get current working directory */
-   for(i=0; i<= lg; i++) {
+     /*    extern  char* getcwd ( char *buf , int len);*/
-     (s[i] = t[i]);
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-     if (t[i]== '\\') s[i]='/';
+       return( GLOCK_ERROR_GETCWD );
-   }
+     }
- }
+     /* got dirc from getcwd*/
+     printf(" DIRC = %s \n",dirc);
- int nbocc(char *s, char occ)
+   } else {                              /* strip direcotry from path */
- {
+     ss++;                               /* after this, the filename */
-   int i,j=0;
+     l2 = strlen( ss );                  /* length of filename */
-   int lg=20;
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   i=0;
+     strcpy( name, ss );         /* save file name */
-   lg=strlen(s);
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-   for(i=0; i<= lg; i++) {
+     dirc[l1-l2] = 0;                    /* add zero */
-   if  (s[i] == occ ) j++;
+     printf(" DIRC2 = %s \n",dirc);
    }
-   return j;
+   /* We add a separator at the end of dirc if not exists */
- }
+   l1 = strlen( dirc );                  /* length of directory */
+   if( dirc[l1-1] != DIRSEPARATOR ){
- void cutv(char *u,char *v, char*t, char occ)
+     dirc[l1] =  DIRSEPARATOR;
- {
+     dirc[l1+1] = 0;
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     printf(" DIRC3 = %s \n",dirc);
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+   }
-      gives u="abcedf" and v="ghi2j" */
+   ss = strrchr( name, '.' );            /* find last / */
-   int i,lg,j,p=0;
+   if (ss >0){
-   i=0;
+     ss++;
-   for(j=0; j<=strlen(t)-1; j++) {
+     strcpy(ext,ss);                     /* save extension */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     l1= strlen( name);
-   }
+     l2= strlen(ss)+1;
+     strncpy( finame, name, l1-l2);
-   lg=strlen(t);
+     finame[l1-l2]= 0;
-   for(j=0; j<p; j++) {
+   }
-     (u[j] = t[j]);
-   }
+   return( 0 );                          /* we're done */
-      u[p]='\0';
+ }
-    for(j=0; j<= lg; j++) {
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ /******************************************/
-   }
- }
+ void replace_back_to_slash(char *s, char*t)
+ {
- /********************** nrerror ********************/
+   int i;
+   int lg=0;
- void nrerror(char error_text[])
+   i=0;
- {
+   lg=strlen(t);
-   fprintf(stderr,"ERREUR ...\n");
+   for(i=0; i<= lg; i++) {
-   fprintf(stderr,"%s\n",error_text);
+     (s[i] = t[i]);
-   exit(EXIT_FAILURE);
+     if (t[i]== '\\') s[i]='/';
- }
+   }
- /*********************** vector *******************/
+ }
- double *vector(int nl, int nh)
- {
+ char *trimbb(char *out, char *in)
-   double *v;
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   char *s;
-   if (!v) nrerror("allocation failure in vector");
+   s=out;
-   return v-nl+NR_END;
+   while (*in != '\0'){
- }
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
+       in++;
- /************************ free vector ******************/
+     }
- void free_vector(double*v, int nl, int nh)
+     *out++ = *in++;
- {
+   }
-   free((FREE_ARG)(v+nl-NR_END));
+   *out='\0';
- }
+   return s;
+ }
- /************************ivector *******************************/
- int *ivector(long nl,long nh)
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
  {
-   int *v;
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   if (!v) nrerror("allocation failure in ivector");
+      gives blocc="abcdef2ghi" and alocc="j".
-   return v-nl+NR_END;
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- }
+   */
+   char *s, *t, *bl;
- /******************free ivector **************************/
+   t=in;s=in;
- void free_ivector(int *v, long nl, long nh)
+   while ((*in != occ) && (*in != '\0')){
- {
+     *alocc++ = *in++;
-   free((FREE_ARG)(v+nl-NR_END));
+   }
- }
+   if( *in == occ){
+     *(alocc)='\0';
- /************************lvector *******************************/
+     s=++in;
- long *lvector(long nl,long nh)
+   }
- {
-   long *v;
+   if (s == t) {/* occ not found */
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+     *(alocc-(in-s))='\0';
-   if (!v) nrerror("allocation failure in ivector");
+     in=s;
-   return v-nl+NR_END;
+   }
- }
+   while ( *in != '\0'){
+     *blocc++ = *in++;
- /******************free lvector **************************/
+   }
- void free_lvector(long *v, long nl, long nh)
- {
+   *blocc='\0';
-   free((FREE_ARG)(v+nl-NR_END));
+   return t;
  }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
- /******************* imatrix *******************************/
+ {
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- {
+      gives blocc="abcdef2ghi" and alocc="j".
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   int **m;
+   */
+   char *s, *t;
-   /* allocate pointers to rows */
+   t=in;s=in;
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   while (*in != '\0'){
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     while( *in == occ){
-   m += NR_END;
+       *blocc++ = *in++;
-   m -= nrl;
+       s=in;
+     }
+     *blocc++ = *in++;
-   /* allocate rows and set pointers to them */
+   }
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   if (s == t) /* occ not found */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+     *(blocc-(in-s))='\0';
-   m[nrl] += NR_END;
+   else
-   m[nrl] -= ncl;
+     *(blocc-(in-s)-1)='\0';
+   in=s;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+   while ( *in != '\0'){
+     *alocc++ = *in++;
-   /* return pointer to array of pointers to rows */
+   }
-   return m;
- }
+   *alocc='\0';
+   return s;
- /****************** free_imatrix *************************/
+ }
- void free_imatrix(m,nrl,nrh,ncl,nch)
-       int **m;
+ int nbocc(char *s, char occ)
-       long nch,ncl,nrh,nrl;
+ {
-      /* free an int matrix allocated by imatrix() */
+   int i,j=0;
- {
+   int lg=20;
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   i=0;
-   free((FREE_ARG) (m+nrl-NR_END));
+   lg=strlen(s);
- }
+   for(i=0; i<= lg; i++) {
+   if  (s[i] == occ ) j++;
- /******************* matrix *******************************/
+   }
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   return j;
- {
+ }
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-   double **m;
+ /* void cutv(char *u,char *v, char*t, char occ) */
+ /* { */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
-   m += NR_END;
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   m -= nrl;
+ /*   int i,lg,j,p=0; */
+ /*   i=0; */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   lg=strlen(t); */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*   for(j=0; j<=lg-1; j++) { */
-   m[nrl] += NR_END;
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   m[nrl] -= ncl;
+ /*   } */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*   for(j=0; j<p; j++) { */
-   return m;
+ /*     (u[j] = t[j]); */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ /*   } */
-    */
+ /*      u[p]='\0'; */
- }
+ /*    for(j=0; j<= lg; j++) { */
- /*************************free matrix ************************/
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ /*   } */
- {
+ /* } */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+ /********************** nrerror ********************/
- }
+ void nrerror(char error_text[])
- /******************* ma3x *******************************/
+ {
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   fprintf(stderr,"ERREUR ...\n");
- {
+   fprintf(stderr,"%s\n",error_text);
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   exit(EXIT_FAILURE);
-   double ***m;
+ }
+ /*********************** vector *******************/
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ double *vector(int nl, int nh)
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ {
-   m += NR_END;
+   double *v;
-   m -= nrl;
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   if (!v) nrerror("allocation failure in vector");
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   return v-nl+NR_END;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ }
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+ /************************ free vector ******************/
+ void free_vector(double*v, int nl, int nh)
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ {
+   free((FREE_ARG)(v+nl-NR_END));
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ }
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   m[nrl][ncl] += NR_END;
+ /************************ivector *******************************/
-   m[nrl][ncl] -= nll;
+ int *ivector(long nl,long nh)
-   for (j=ncl+1; j<=nch; j++)
+ {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   int *v;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   for (i=nrl+1; i<=nrh; i++) {
+   if (!v) nrerror("allocation failure in ivector");
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   return v-nl+NR_END;
-     for (j=ncl+1; j<=nch; j++)
+ }
-       m[i][j]=m[i][j-1]+nlay;
-   }
+ /******************free ivector **************************/
-   return m;
+ void free_ivector(int *v, long nl, long nh)
-   /*  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)
+   free((FREE_ARG)(v+nl-NR_END));
-   */
+ }
- }
+ /************************lvector *******************************/
- /*************************free ma3x ************************/
+ long *lvector(long nl,long nh)
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ {
- {
+   long *v;
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   if (!v) nrerror("allocation failure in ivector");
-   free((FREE_ARG)(m+nrl-NR_END));
+   return v-nl+NR_END;
  }
- /*************** function subdirf ***********/
+ /******************free lvector **************************/
- char *subdirf(char fileres[])
+ 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,"/"); /* Add to the right */
-   strcat(tmpout,fileres);
+ /******************* imatrix *******************************/
-   return tmpout;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
- }
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ {
- /*************** function subdirf2 ***********/
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
- char *subdirf2(char fileres[], char *preop)
+   int **m;
- {
+   /* allocate pointers to rows */
-   /* Caution optionfilefiname is hidden */
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-   strcpy(tmpout,optionfilefiname);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   strcat(tmpout,"/");
+   m += NR_END;
-   strcat(tmpout,preop);
+   m -= nrl;
-   strcat(tmpout,fileres);
-   return tmpout;
- }
+   /* allocate rows and set pointers to them */
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
- /*************** function subdirf3 ***********/
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   m[nrl] += NR_END;
- {
+   m[nrl] -= ncl;
-   /* Caution optionfilefiname is hidden */
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+   /* return pointer to array of pointers to rows */
-   strcat(tmpout,preop);
+   return m;
-   strcat(tmpout,preop2);
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /****************** free_imatrix *************************/
- }
+ void free_imatrix(m,nrl,nrh,ncl,nch)
+       int **m;
- /***************** f1dim *************************/
+       long nch,ncl,nrh,nrl;
- extern int ncom;
+      /* free an int matrix allocated by imatrix() */
- extern double *pcom,*xicom;
+ {
- extern double (*nrfunc)(double []);
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   free((FREE_ARG) (m+nrl-NR_END));
- double f1dim(double x)
+ }
- {
-   int j;
+ /******************* matrix *******************************/
-   double f;
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-   double *xt;
+ {
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-   xt=vector(1,ncom);
+   double **m;
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-   f=(*nrfunc)(xt);
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   free_vector(xt,1,ncom);
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   return f;
+   m += NR_END;
- }
+   m -= nrl;
- /*****************brent *************************/
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- {
+   m[nrl] += NR_END;
-   int iter;
+   m[nrl] -= ncl;
-   double a,b,d,etemp;
-   double fu,fv,fw,fx;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   double ftemp;
+   return m;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
-   double e=0.0;
+ m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+ that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
-   a=(ax < cx ? ax : cx);
+    */
-   b=(ax > cx ? ax : cx);
+ }
-   x=w=v=bx;
-   fw=fv=fx=(*f)(x);
+ /*************************free matrix ************************/
-   for (iter=1;iter<=ITMAX;iter++) {
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-     xm=0.5*(a+b);
+ {
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   free((FREE_ARG)(m+nrl-NR_END));
-     printf(".");fflush(stdout);
+ }
-     fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+ /******************* ma3x *******************************/
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ {
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
- #endif
+   double ***m;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       *xmin=x;
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-       return fx;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     }
+   m += NR_END;
-     ftemp=fu;
+   m -= nrl;
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-       q=(x-v)*(fx-fw);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       p=(x-v)*q-(x-w)*r;
+   m[nrl] += NR_END;
-       q=2.0*(q-r);
+   m[nrl] -= ncl;
-       if (q > 0.0) p = -p;
-       q=fabs(q);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-       etemp=e;
-       e=d;
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   m[nrl][ncl] += NR_END;
-       else {
+   m[nrl][ncl] -= nll;
-         d=p/q;
+   for (j=ncl+1; j<=nch; j++)
-         u=x+d;
+     m[nrl][j]=m[nrl][j-1]+nlay;
-         if (u-a < tol2 || b-u < tol2)
-           d=SIGN(tol1,xm-x);
+   for (i=nrl+1; i<=nrh; i++) {
-       }
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-     } else {
+     for (j=ncl+1; j<=nch; j++)
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+       m[i][j]=m[i][j-1]+nlay;
-     }
+   }
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+   return m;
-     fu=(*f)(u);
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-     if (fu <= fx) {
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-       if (u >= x) a=x; else b=x;
+   */
-       SHFT(v,w,x,u)
+ }
-         SHFT(fv,fw,fx,fu)
-         } else {
+ /*************************free ma3x ************************/
-           if (u < x) a=u; else b=u;
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-           if (fu <= fw || w == x) {
+ {
-             v=w;
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-             w=u;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-             fv=fw;
+   free((FREE_ARG)(m+nrl-NR_END));
-             fw=fu;
+ }
-           } else if (fu <= fv || v == x || v == w) {
-             v=u;
+ /*************** function subdirf ***********/
-             fv=fu;
+ char *subdirf(char fileres[])
-           }
+ {
-         }
+   /* Caution optionfilefiname is hidden */
-   }
+   strcpy(tmpout,optionfilefiname);
-   nrerror("Too many iterations in brent");
+   strcat(tmpout,"/"); /* Add to the right */
-   *xmin=x;
+   strcat(tmpout,fileres);
-   return fx;
+   return tmpout;
  }
- /****************** mnbrak ***********************/
+ /*************** function subdirf2 ***********/
+ char *subdirf2(char fileres[], char *preop)
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+ {
-             double (*func)(double))
- {
+   /* Caution optionfilefiname is hidden */
-   double ulim,u,r,q, dum;
+   strcpy(tmpout,optionfilefiname);
-   double fu;
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
-   *fa=(*func)(*ax);
+   strcat(tmpout,fileres);
-   *fb=(*func)(*bx);
+   return tmpout;
-   if (*fb > *fa) {
+ }
-     SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+ /*************** function subdirf3 ***********/
-       }
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   *cx=(*bx)+GOLD*(*bx-*ax);
+ {
-   *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,"/");
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+   strcat(tmpout,preop);
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+   strcat(tmpout,preop2);
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+   strcat(tmpout,fileres);
-     if ((*bx-u)*(u-*cx) > 0.0) {
+   return tmpout;
-       fu=(*func)(u);
+ }
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       fu=(*func)(u);
+ /***************** f1dim *************************/
-       if (fu < *fc) {
+ extern int ncom;
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ extern double *pcom,*xicom;
-           SHFT(*fb,*fc,fu,(*func)(u))
+ extern double (*nrfunc)(double []);
-           }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+ double f1dim(double x)
-       u=ulim;
+ {
-       fu=(*func)(u);
+   int j;
-     } else {
+   double f;
-       u=(*cx)+GOLD*(*cx-*bx);
+   double *xt;
-       fu=(*func)(u);
-     }
+   xt=vector(1,ncom);
-     SHFT(*ax,*bx,*cx,u)
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-       SHFT(*fa,*fb,*fc,fu)
+   f=(*nrfunc)(xt);
-       }
+   free_vector(xt,1,ncom);
- }
+   return f;
+ }
- /*************** linmin ************************/
+ /*****************brent *************************/
- int ncom;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- double *pcom,*xicom;
+ {
- double (*nrfunc)(double []);
+   int iter;
+   double a,b,d,etemp;
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   double fu,fv,fw,fx;
- {
+   double ftemp;
-   double brent(double ax, double bx, double cx,
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-                double (*f)(double), double tol, double *xmin);
+   double e=0.0;
-   double f1dim(double x);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   a=(ax < cx ? ax : cx);
-               double *fc, double (*func)(double));
+   b=(ax > cx ? ax : cx);
-   int j;
+   x=w=v=bx;
-   double xx,xmin,bx,ax;
+   fw=fv=fx=(*f)(x);
-   double fx,fb,fa;
+   for (iter=1;iter<=ITMAX;iter++) {
+     xm=0.5*(a+b);
-   ncom=n;
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   pcom=vector(1,n);
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-   xicom=vector(1,n);
+     printf(".");fflush(stdout);
-   nrfunc=func;
+     fprintf(ficlog,".");fflush(ficlog);
-   for (j=1;j<=n;j++) {
+ #ifdef DEBUG
-     pcom[j]=p[j];
+     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);
-     xicom[j]=xi[j];
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-   }
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-   ax=0.0;
+ #endif
-   xx=1.0;
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+       *xmin=x;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+       return fx;
- #ifdef DEBUG
+     }
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+     ftemp=fu;
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+     if (fabs(e) > tol1) {
- #endif
+       r=(x-w)*(fx-fv);
-   for (j=1;j<=n;j++) {
+       q=(x-v)*(fx-fw);
-     xi[j] *= xmin;
+       p=(x-v)*q-(x-w)*r;
-     p[j] += xi[j];
+       q=2.0*(q-r);
-   }
+       if (q > 0.0) p = -p;
-   free_vector(xicom,1,n);
+       q=fabs(q);
-   free_vector(pcom,1,n);
+       etemp=e;
- }
+       e=d;
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
- char *asc_diff_time(long time_sec, char ascdiff[])
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
- {
+       else {
-   long sec_left, days, hours, minutes;
+         d=p/q;
-   days = (time_sec) / (60*60*24);
+         u=x+d;
-   sec_left = (time_sec) % (60*60*24);
+         if (u-a < tol2 || b-u < tol2)
-   hours = (sec_left) / (60*60) ;
+           d=SIGN(tol1,xm-x);
-   sec_left = (sec_left) %(60*60);
+       }
-   minutes = (sec_left) /60;
+     } else {
-   sec_left = (sec_left) % (60);
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+     }
-   return ascdiff;
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
- }
+     fu=(*f)(u);
+     if (fu <= fx) {
- /*************** powell ************************/
+       if (u >= x) a=x; else b=x;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+       SHFT(v,w,x,u)
-             double (*func)(double []))
+         SHFT(fv,fw,fx,fu)
- {
+         } else {
-   void linmin(double p[], double xi[], int n, double *fret,
+           if (u < x) a=u; else b=u;
-               double (*func)(double []));
+           if (fu <= fw || w == x) {
-   int i,ibig,j;
+             v=w;
-   double del,t,*pt,*ptt,*xit;
+             w=u;
-   double fp,fptt;
+             fv=fw;
-   double *xits;
+             fw=fu;
-   int niterf, itmp;
+           } else if (fu <= fv || v == x || v == w) {
+             v=u;
-   pt=vector(1,n);
+             fv=fu;
-   ptt=vector(1,n);
+           }
-   xit=vector(1,n);
+         }
-   xits=vector(1,n);
+   }
-   *fret=(*func)(p);
+   nrerror("Too many iterations in brent");
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   *xmin=x;
-   for (*iter=1;;++(*iter)) {
+   return fx;
-     fp=(*fret);
+ }
-     ibig=0;
-     del=0.0;
+ /****************** mnbrak ***********************/
-     last_time=curr_time;
-     (void) gettimeofday(&curr_time,&tzp);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-     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);
+             double (*func)(double))
-     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);
+ {
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+   double ulim,u,r,q, dum;
-    for (i=1;i<=n;i++) {
+   double fu;
-       printf(" %d %.12f",i, p[i]);
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   *fa=(*func)(*ax);
-       fprintf(ficrespow," %.12lf", p[i]);
+   *fb=(*func)(*bx);
-     }
+   if (*fb > *fa) {
-     printf("\n");
+     SHFT(dum,*ax,*bx,dum)
-     fprintf(ficlog,"\n");
+       SHFT(dum,*fb,*fa,dum)
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+       }
-     if(*iter <=3){
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       tm = *localtime(&curr_time.tv_sec);
+   *fc=(*func)(*cx);
-       strcpy(strcurr,asctime(&tm));
+   while (*fb > *fc) {
- /*       asctime_r(&tm,strcurr); */
+     r=(*bx-*ax)*(*fb-*fc);
-       forecast_time=curr_time;
+     q=(*bx-*cx)*(*fb-*fa);
-       itmp = strlen(strcurr);
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-         strcurr[itmp-1]='\0';
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     if ((*bx-u)*(u-*cx) > 0.0) {
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fu=(*func)(u);
-       for(niterf=10;niterf<=30;niterf+=10){
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+       fu=(*func)(u);
-         tmf = *localtime(&forecast_time.tv_sec);
+       if (fu < *fc) {
- /*      asctime_r(&tmf,strfor); */
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         strcpy(strfor,asctime(&tmf));
+           SHFT(*fb,*fc,fu,(*func)(u))
-         itmp = strlen(strfor);
+           }
-         if(strfor[itmp-1]=='\n')
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-         strfor[itmp-1]='\0';
+       u=ulim;
-         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);
+       fu=(*func)(u);
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     } else {
-       }
+       u=(*cx)+GOLD*(*cx-*bx);
-     }
+       fu=(*func)(u);
-     for (i=1;i<=n;i++) {
+     }
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+     SHFT(*ax,*bx,*cx,u)
-       fptt=(*fret);
+       SHFT(*fa,*fb,*fc,fu)
- #ifdef DEBUG
+       }
-       printf("fret=%lf \n",*fret);
+ }
-       fprintf(ficlog,"fret=%lf \n",*fret);
- #endif
+ /*************** linmin ************************/
-       printf("%d",i);fflush(stdout);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+ int ncom;
-       linmin(p,xit,n,fret,func);
+ double *pcom,*xicom;
-       if (fabs(fptt-(*fret)) > del) {
+ double (*nrfunc)(double []);
-         del=fabs(fptt-(*fret));
-         ibig=i;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-       }
+ {
- #ifdef DEBUG
+   double brent(double ax, double bx, double cx,
-       printf("%d %.12e",i,(*fret));
+                double (*f)(double), double tol, double *xmin);
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   double f1dim(double x);
-       for (j=1;j<=n;j++) {
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+               double *fc, double (*func)(double));
-         printf(" x(%d)=%.12e",j,xit[j]);
+   int j;
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   double xx,xmin,bx,ax;
-       }
+   double fx,fb,fa;
-       for(j=1;j<=n;j++) {
-         printf(" p=%.12e",p[j]);
+   ncom=n;
-         fprintf(ficlog," p=%.12e",p[j]);
+   pcom=vector(1,n);
-       }
+   xicom=vector(1,n);
-       printf("\n");
+   nrfunc=func;
-       fprintf(ficlog,"\n");
+   for (j=1;j<=n;j++) {
- #endif
+     pcom[j]=p[j];
-     }
+     xicom[j]=xi[j];
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   }
- #ifdef DEBUG
+   ax=0.0;
-       int k[2],l;
+   xx=1.0;
-       k[0]=1;
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-       k[1]=-1;
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-       printf("Max: %.12e",(*func)(p));
+ #ifdef DEBUG
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       for (j=1;j<=n;j++) {
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-         printf(" %.12e",p[j]);
+ #endif
-         fprintf(ficlog," %.12e",p[j]);
+   for (j=1;j<=n;j++) {
-       }
+     xi[j] *= xmin;
-       printf("\n");
+     p[j] += xi[j];
-       fprintf(ficlog,"\n");
+   }
-       for(l=0;l<=1;l++) {
+   free_vector(xicom,1,n);
-         for (j=1;j<=n;j++) {
+   free_vector(pcom,1,n);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+ }
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ char *asc_diff_time(long time_sec, char ascdiff[])
-         }
+ {
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   long sec_left, days, hours, minutes;
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   days = (time_sec) / (60*60*24);
-       }
+   sec_left = (time_sec) % (60*60*24);
- #endif
+   hours = (sec_left) / (60*60) ;
+   sec_left = (sec_left) %(60*60);
+   minutes = (sec_left) /60;
-       free_vector(xit,1,n);
+   sec_left = (sec_left) % (60);
-       free_vector(xits,1,n);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-       free_vector(ptt,1,n);
+   return ascdiff;
-       free_vector(pt,1,n);
+ }
-       return;
-     }
+ /*************** powell ************************/
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-     for (j=1;j<=n;j++) {
+             double (*func)(double []))
-       ptt[j]=2.0*p[j]-pt[j];
+ {
-       xit[j]=p[j]-pt[j];
+   void linmin(double p[], double xi[], int n, double *fret,
-       pt[j]=p[j];
+               double (*func)(double []));
-     }
+   int i,ibig,j;
-     fptt=(*func)(ptt);
+   double del,t,*pt,*ptt,*xit;
-     if (fptt < fp) {
+   double fp,fptt;
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+   double *xits;
-       if (t < 0.0) {
+   int niterf, itmp;
-         linmin(p,xit,n,fret,func);
-         for (j=1;j<=n;j++) {
+   pt=vector(1,n);
-           xi[j][ibig]=xi[j][n];
+   ptt=vector(1,n);
-           xi[j][n]=xit[j];
+   xit=vector(1,n);
-         }
+   xits=vector(1,n);
- #ifdef DEBUG
+   *fret=(*func)(p);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     rcurr_time = time(NULL);
-         for(j=1;j<=n;j++){
+   for (*iter=1;;++(*iter)) {
-           printf(" %.12e",xit[j]);
+     fp=(*fret);
-           fprintf(ficlog," %.12e",xit[j]);
+     ibig=0;
-         }
+     del=0.0;
-         printf("\n");
+     rlast_time=rcurr_time;
-         fprintf(ficlog,"\n");
+     /* (void) gettimeofday(&curr_time,&tzp); */
- #endif
+     rcurr_time = time(NULL);
-       }
+     curr_time = *localtime(&rcurr_time);
-     }
+     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-   }
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
- }
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+    for (i=1;i<=n;i++) {
- /**** Prevalence limit (stable or period prevalence)  ****************/
+       printf(" %d %.12f",i, p[i]);
+       fprintf(ficlog," %d %.12lf",i, p[i]);
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+       fprintf(ficrespow," %.12lf", p[i]);
- {
+     }
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+     printf("\n");
-      matrix by transitions matrix until convergence is reached */
+     fprintf(ficlog,"\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-   int i, ii,j,k;
+     if(*iter <=3){
-   double min, max, maxmin, maxmax,sumnew=0.;
+       tml = *localtime(&rcurr_time);
-   double **matprod2();
+       strcpy(strcurr,asctime(&tml));
-   double **out, cov[NCOVMAX], **pmij();
+ /*       asctime_r(&tm,strcurr); */
-   double **newm;
+       rforecast_time=rcurr_time;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+       itmp = strlen(strcurr);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+         strcurr[itmp-1]='\0';
-     for (j=1;j<=nlstate+ndeath;j++){
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
-     }
+       for(niterf=10;niterf<=30;niterf+=10){
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-    cov[1]=1.;
+         forecast_time = *localtime(&rforecast_time);
+ /*      asctime_r(&tmf,strfor); */
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+         strcpy(strfor,asctime(&forecast_time));
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+         itmp = strlen(strfor);
-     newm=savm;
+         if(strfor[itmp-1]=='\n')
-     /* Covariates have to be included here again */
+         strfor[itmp-1]='\0';
-      cov[2]=agefin;
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-       for (k=1; k<=cptcovn;k++) {
+       }
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     }
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+     for (i=1;i<=n;i++) {
-       }
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       fptt=(*fret);
-       for (k=1; k<=cptcovprod;k++)
+ #ifdef DEBUG
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       printf("fret=%lf \n",*fret);
+       fprintf(ficlog,"fret=%lf \n",*fret);
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+ #endif
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       printf("%d",i);fflush(stdout);
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+       linmin(p,xit,n,fret,func);
+       if (fabs(fptt-(*fret)) > del) {
-     savm=oldm;
+         del=fabs(fptt-(*fret));
-     oldm=newm;
+         ibig=i;
-     maxmax=0.;
+       }
-     for(j=1;j<=nlstate;j++){
+ #ifdef DEBUG
-       min=1.;
+       printf("%d %.12e",i,(*fret));
-       max=0.;
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       for(i=1; i<=nlstate; i++) {
+       for (j=1;j<=n;j++) {
-         sumnew=0;
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+         printf(" x(%d)=%.12e",j,xit[j]);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-         max=FMAX(max,prlim[i][j]);
+       }
-         min=FMIN(min,prlim[i][j]);
+       for(j=1;j<=n;j++) {
-       }
+         printf(" p=%.12e",p[j]);
-       maxmin=max-min;
+         fprintf(ficlog," p=%.12e",p[j]);
-       maxmax=FMAX(maxmax,maxmin);
+       }
-     }
+       printf("\n");
-     if(maxmax < ftolpl){
+       fprintf(ficlog,"\n");
-       return prlim;
+ #endif
      }
-   }
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- }
+ #ifdef DEBUG
+       int k[2],l;
- /*************** transition probabilities ***************/
+       k[0]=1;
+       k[1]=-1;
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       printf("Max: %.12e",(*func)(p));
- {
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-   double s1, s2;
+       for (j=1;j<=n;j++) {
-   /*double t34;*/
+         printf(" %.12e",p[j]);
-   int i,j,j1, nc, ii, jj;
+         fprintf(ficlog," %.12e",p[j]);
+       }
-     for(i=1; i<= nlstate; i++){
+       printf("\n");
-       for(j=1; j<i;j++){
+       fprintf(ficlog,"\n");
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       for(l=0;l<=1;l++) {
-           /*s2 += param[i][j][nc]*cov[nc];*/
+         for (j=1;j<=n;j++) {
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-         }
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-         ps[i][j]=s2;
+         }
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       }
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       for(j=i+1; j<=nlstate+ndeath;j++){
+       }
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ #endif
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
-         }
+       free_vector(xit,1,n);
-         ps[i][j]=s2;
+       free_vector(xits,1,n);
-       }
+       free_vector(ptt,1,n);
-     }
+       free_vector(pt,1,n);
-     /*ps[3][2]=1;*/
+       return;
+     }
-     for(i=1; i<= nlstate; i++){
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-       s1=0;
+     for (j=1;j<=n;j++) {
-       for(j=1; j<i; j++)
+       ptt[j]=2.0*p[j]-pt[j];
-         s1+=exp(ps[i][j]);
+       xit[j]=p[j]-pt[j];
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       pt[j]=p[j];
-         s1+=exp(ps[i][j]);
+     }
-       ps[i][i]=1./(s1+1.);
+     fptt=(*func)(ptt);
-       for(j=1; j<i; j++)
+     if (fptt < fp) {
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       if (t < 0.0) {
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         linmin(p,xit,n,fret,func);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         for (j=1;j<=n;j++) {
-     } /* end i */
+           xi[j][ibig]=xi[j][n];
+           xi[j][n]=xit[j];
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+         }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+ #ifdef DEBUG
-         ps[ii][jj]=0;
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         ps[ii][ii]=1;
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       }
+         for(j=1;j<=n;j++){
-     }
+           printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
+         }
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+         printf("\n");
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+         fprintf(ficlog,"\n");
- /*         printf("ddd %lf ",ps[ii][jj]); */
+ #endif
- /*       } */
+       }
- /*       printf("\n "); */
+     }
- /*        } */
+   }
- /*        printf("\n ");printf("%lf ",cov[2]); */
+ }
-        /*
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-       goto end;*/
-     return ps;
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
- }
+ {
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
- /**************** Product of 2 matrices ******************/
+      matrix by transitions matrix until convergence is reached */
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+   int i, ii,j,k;
- {
+   double min, max, maxmin, maxmax,sumnew=0.;
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+   /* double **matprod2(); */ /* test */
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+   double **out, cov[NCOVMAX+1], **pmij();
-   /* in, b, out are matrice of pointers which should have been initialized
+   double **newm;
-      before: only the contents of out is modified. The function returns
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-      a pointer to pointers identical to out */
-   long i, j, k;
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-   for(i=nrl; i<= nrh; i++)
+     for (j=1;j<=nlstate+ndeath;j++){
-     for(k=ncolol; k<=ncoloh; k++)
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+     }
-         out[i][k] +=in[i][j]*b[j][k];
+    cov[1]=1.;
-   return out;
- }
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     newm=savm;
- /************* Higher Matrix Product ***************/
+     /* Covariates have to be included here again */
+     cov[2]=agefin;
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
- {
+     for (k=1; k<=cptcovn;k++) {
-   /* Computes the transition matrix starting at age 'age' over
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-      'nhstepm*hstepm*stepm' months (i.e. until
+       /*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]]);*/
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+     }
-      nhstepm*hstepm matrices.
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-      (typically every 2 years instead of every month which is too big
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-      for the memory).
-      Model is determined by parameters x and covariates have to be
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-      included manually here.
+     /*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); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-   int i, j, d, h, k;
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-   double **out, cov[NCOVMAX];
-   double **newm;
+     savm=oldm;
+     oldm=newm;
-   /* Hstepm could be zero and should return the unit matrix */
+     maxmax=0.;
-   for (i=1;i<=nlstate+ndeath;i++)
+     for(j=1;j<=nlstate;j++){
-     for (j=1;j<=nlstate+ndeath;j++){
+       min=1.;
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       max=0.;
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+       for(i=1; i<=nlstate; i++) {
-     }
+         sumnew=0;
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-   for(h=1; h <=nhstepm; h++){
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-     for(d=1; d <=hstepm; d++){
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
-       newm=savm;
+         max=FMAX(max,prlim[i][j]);
-       /* Covariates have to be included here again */
+         min=FMIN(min,prlim[i][j]);
-       cov[1]=1.;
+       }
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       maxmin=max-min;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       maxmax=FMAX(maxmax,maxmin);
-       for (k=1; k<=cptcovage;k++)
+     }
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     if(maxmax < ftolpl){
-       for (k=1; k<=cptcovprod;k++)
+       return prlim;
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     }
+   }
+ }
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+ /*************** transition probabilities ***************/
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-       savm=oldm;
+ {
-       oldm=newm;
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-     }
+      computes the probability to be observed in state j being in state i by appying the
-     for(i=1; i<=nlstate+ndeath; i++)
+      model to the ncovmodel covariates (including constant and age).
-       for(j=1;j<=nlstate+ndeath;j++) {
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
-         po[i][j][h]=newm[i][j];
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+      ncth covariate in the global vector x is given by the formula:
-          */
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-       }
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-   } /* end h */
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-   return po;
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
- }
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
- /*************** log-likelihood *************/
+   double s1, lnpijopii;
- double func( double *x)
+   /*double t34;*/
- {
+   int i,j,j1, nc, ii, jj;
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+     for(i=1; i<= nlstate; i++){
-   double **out;
+       for(j=1; j<i;j++){
-   double sw; /* Sum of weights */
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   double lli; /* Individual log likelihood */
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-   int s1, s2;
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-   double bbh, survp;
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   long ipmx;
+         }
-   /*extern weight */
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   /* We are differentiating ll according to initial status */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+       }
-   /*for(i=1;i<imx;i++)
+       for(j=i+1; j<=nlstate+ndeath;j++){
-     printf(" %d\n",s[4][i]);
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   */
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-   cov[1]=1.;
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   if(mle==1){
+       }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+     for(i=1; i<= nlstate; i++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       s1=0;
-           for (j=1;j<=nlstate+ndeath;j++){
+       for(j=1; j<i; j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-           }
+       }
-         for(d=0; d<dh[mi][i]; d++){
+       for(j=i+1; j<=nlstate+ndeath; j++){
-           newm=savm;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-           for (kk=1; kk<=cptcovage;kk++) {
+       }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-           }
+       ps[i][i]=1./(s1+1.);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       /* Computing other pijs */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       for(j=1; j<i; j++)
-           savm=oldm;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-           oldm=newm;
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         } /* end mult */
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     } /* end i */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+         ps[ii][jj]=0;
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+         ps[ii][ii]=1;
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       }
-          * probability in order to take into account the bias as a fraction of the way
+     }
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-          * For stepm > 1 the results are less biased than in previous versions.
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-          */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         s1=s[mw[mi][i]][i];
+     /*   } */
-         s2=s[mw[mi+1][i]][i];
+     /*   printf("\n "); */
-         bbh=(double)bh[mi][i]/(double)stepm;
+     /* } */
-         /* bias bh is positive if real duration
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-          * is higher than the multiple of stepm and negative otherwise.
+     /*
-          */
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+       goto end;*/
-         if( s2 > nlstate){
+     return ps;
-           /* i.e. if s2 is a death state and if the date of death is known
+ }
-              then the contribution to the likelihood is the probability to
-              die between last step unit time and current  step unit time,
+ /**************** Product of 2 matrices ******************/
-              which is also equal to probability to die before dh
-              minus probability to die before dh-stepm .
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-              In version up to 0.92 likelihood was computed
+ {
-         as if date of death was unknown. Death was treated as any other
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-         health state: the date of the interview describes the actual state
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         and not the date of a change in health state. The former idea was
+   /* in, b, out are matrice of pointers which should have been initialized
-         to consider that at each interview the state was recorded
+      before: only the contents of out is modified. The function returns
-         (healthy, disable or death) and IMaCh was corrected; but when we
+      a pointer to pointers identical to out */
-         introduced the exact date of death then we should have modified
+   int i, j, k;
-         the contribution of an exact death to the likelihood. This new
+   for(i=nrl; i<= nrh; i++)
-         contribution is smaller and very dependent of the step unit
+     for(k=ncolol; k<=ncoloh; k++){
-         stepm. It is no more the probability to die between last interview
+       out[i][k]=0.;
-         and month of death but the probability to survive from last
+       for(j=ncl; j<=nch; j++)
-         interview up to one month before death multiplied by the
+         out[i][k] +=in[i][j]*b[j][k];
-         probability to die within a month. Thanks to Chris
+     }
-         Jackson for correcting this bug.  Former versions increased
+   return out;
-         mortality artificially. The bad side is that we add another loop
+ }
-         which slows down the processing. The difference can be up to 10%
-         lower mortality.
-           */
+ /************* Higher Matrix Product ***************/
-           lli=log(out[s1][s2] - savm[s1][s2]);
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ {
-         } else if  (s2==-2) {
+   /* Computes the transition matrix starting at age 'age' over
-           for (j=1,survp=0. ; j<=nlstate; j++)
+      'nhstepm*hstepm*stepm' months (i.e. until
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-           /*survp += out[s1][j]; */
+      nhstepm*hstepm matrices.
-           lli= log(survp);
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-         }
+      (typically every 2 years instead of every month which is too big
+      for the memory).
-         else if  (s2==-4) {
+      Model is determined by parameters x and covariates have to be
-           for (j=3,survp=0. ; j<=nlstate; j++)
+      included manually here.
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           lli= log(survp);
+      */
-         }
+   int i, j, d, h, k;
-         else if  (s2==-5) {
+   double **out, cov[NCOVMAX+1];
-           for (j=1,survp=0. ; j<=2; j++)
+   double **newm;
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           lli= log(survp);
+   /* Hstepm could be zero and should return the unit matrix */
-         }
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
-         else{
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+     }
-         }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+   for(h=1; h <=nhstepm; h++){
-         /*if(lli ==000.0)*/
+     for(d=1; d <=hstepm; d++){
-         /*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); */
+       newm=savm;
-         ipmx +=1;
+       /* Covariates have to be included here again */
-         sw += weight[i];
+       cov[1]=1.;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       } /* end of wave */
+       for (k=1; k<=cptcovn;k++)
-     } /* end of individual */
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-   }  else if(mle==2){
+       for (k=1; k<=cptcovage;k++)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-       for(mi=1; mi<= wav[i]-1; mi++){
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-           }
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-         for(d=0; d<=dh[mi][i]; d++){
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-           newm=savm;
+       savm=oldm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       oldm=newm;
-           for (kk=1; kk<=cptcovage;kk++) {
+     }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     for(i=1; i<=nlstate+ndeath; i++)
-           }
+       for(j=1;j<=nlstate+ndeath;j++) {
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         po[i][j][h]=newm[i][j];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-           savm=oldm;
+       }
-           oldm=newm;
+     /*printf("h=%d ",h);*/
-         } /* end mult */
+   } /* end h */
+ /*     printf("\n H=%d \n",h); */
-         s1=s[mw[mi][i]][i];
+   return po;
-         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 */
-         ipmx +=1;
+ /*************** log-likelihood *************/
-         sw += weight[i];
+ double func( double *x)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ {
-       } /* end of wave */
+   int i, ii, j, k, mi, d, kk;
-     } /* end of individual */
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+   double **out;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   double sw; /* Sum of weights */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   double lli; /* Individual log likelihood */
-       for(mi=1; mi<= wav[i]-1; mi++){
+   int s1, s2;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   double bbh, survp;
-           for (j=1;j<=nlstate+ndeath;j++){
+   long ipmx;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /*extern weight */
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   /* We are differentiating ll according to initial status */
-           }
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         for(d=0; d<dh[mi][i]; d++){
+   /*for(i=1;i<imx;i++)
-           newm=savm;
+     printf(" %d\n",s[4][i]);
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   */
-           for (kk=1; kk<=cptcovage;kk++) {
+   cov[1]=1.;
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   if(mle==1){
-           savm=oldm;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           oldm=newm;
+       /* Computes the values of the ncovmodel covariates of the model
-         } /* end mult */
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-         s1=s[mw[mi][i]][i];
+          to be observed in j being in i according to the model.
-         s2=s[mw[mi+1][i]][i];
+        */
-         bbh=(double)bh[mi][i]/(double)stepm;
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-         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 */
+         cov[2+k]=covar[Tvar[k]][i];
-         ipmx +=1;
+       }
-         sw += weight[i];
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-       } /* end of wave */
+          has been calculated etc */
-     } /* end of individual */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           for (j=1;j<=nlstate+ndeath;j++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(mi=1; mi<= wav[i]-1; mi++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+           }
-           for (j=1;j<=nlstate+ndeath;j++){
+         for(d=0; d<dh[mi][i]; d++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           newm=savm;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           }
+           for (kk=1; kk<=cptcovage;kk++) {
-         for(d=0; d<dh[mi][i]; d++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-           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];
+           savm=oldm;
-           }
+           oldm=newm;
+         } /* end mult */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-           savm=oldm;
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-           oldm=newm;
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         } /* end mult */
+          * (in months) between two waves is not a multiple of stepm, we rounded to
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-         s1=s[mw[mi][i]][i];
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         s2=s[mw[mi+1][i]][i];
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         if( s2 > nlstate){
+          * probability in order to take into account the bias as a fraction of the way
-           lli=log(out[s1][s2] - savm[s1][s2]);
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         }else{
+          * -stepm/2 to stepm/2 .
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+          * 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.
-         ipmx +=1;
+          */
-         sw += weight[i];
+         s1=s[mw[mi][i]][i];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         s2=s[mw[mi+1][i]][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]); */
+         bbh=(double)bh[mi][i]/(double)stepm;
-       } /* end of wave */
+         /* bias bh is positive if real duration
-     } /* end of individual */
+          * is higher than the multiple of stepm and negative otherwise.
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+          */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         if( s2 > nlstate){
-       for(mi=1; mi<= wav[i]-1; mi++){
+           /* i.e. if s2 is a death state and if the date of death is known
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+              then the contribution to the likelihood is the probability to
-           for (j=1;j<=nlstate+ndeath;j++){
+              die between last step unit time and current  step unit time,
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+              which is also equal to probability to die before dh
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+              minus probability to die before dh-stepm .
-           }
+              In version up to 0.92 likelihood was computed
-         for(d=0; d<dh[mi][i]; d++){
+         as if date of death was unknown. Death was treated as any other
-           newm=savm;
+         health state: the date of the interview describes the actual state
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         and not the date of a change in health state. The former idea was
-           for (kk=1; kk<=cptcovage;kk++) {
+         to consider that at each interview the state was recorded
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         (healthy, disable or death) and IMaCh was corrected; but when we
-           }
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         contribution is smaller and very dependent of the step unit
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         stepm. It is no more the probability to die between last interview
-           savm=oldm;
+         and month of death but the probability to survive from last
-           oldm=newm;
+         interview up to one month before death multiplied by the
-         } /* end mult */
+         probability to die within a month. Thanks to Chris
+         Jackson for correcting this bug.  Former versions increased
-         s1=s[mw[mi][i]][i];
+         mortality artificially. The bad side is that we add another loop
-         s2=s[mw[mi+1][i]][i];
+         which slows down the processing. The difference can be up to 10%
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         lower mortality.
-         ipmx +=1;
+           */
-         sw += weight[i];
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         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 */
+         } else if  (s2==-2) {
-     } /* end of individual */
+           for (j=1,survp=0. ; j<=nlstate; j++)
-   } /* End of if */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+           /*survp += out[s1][j]; */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           lli= log(survp);
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+         }
-   return -l;
- }
+         else if  (s2==-4) {
+           for (j=3,survp=0. ; j<=nlstate; j++)
- /*************** log-likelihood *************/
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- double funcone( double *x)
+           lli= log(survp);
- {
+         }
-   /* Same as likeli but slower because of a lot of printf and if */
-   int i, ii, j, k, mi, d, kk;
+         else if  (s2==-5) {
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+           for (j=1,survp=0. ; j<=2; j++)
-   double **out;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   double lli; /* Individual log likelihood */
+           lli= log(survp);
-   double llt;
+         }
-   int s1, s2;
-   double bbh, survp;
+         else{
-   /*extern weight */
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   /* We are differentiating ll according to initial status */
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         }
-   /*for(i=1;i<imx;i++)
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-     printf(" %d\n",s[4][i]);
+         /*if(lli ==000.0)*/
-   */
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-   cov[1]=1.;
+         ipmx +=1;
+         sw += weight[i];
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     } /* end of individual */
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   }  else if(mle==2){
-     for(mi=1; mi<= wav[i]-1; mi++){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         for (j=1;j<=nlstate+ndeath;j++){
+       for(mi=1; mi<= wav[i]-1; mi++){
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           for (j=1;j<=nlstate+ndeath;j++){
-         }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(d=0; d<dh[mi][i]; d++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         newm=savm;
+           }
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         for(d=0; d<=dh[mi][i]; d++){
-         for (kk=1; kk<=cptcovage;kk++) {
+           newm=savm;
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         }
+           for (kk=1; kk<=cptcovage;kk++) {
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           }
-         savm=oldm;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         oldm=newm;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       } /* end mult */
+           savm=oldm;
+           oldm=newm;
-       s1=s[mw[mi][i]][i];
+         } /* end mult */
-       s2=s[mw[mi+1][i]][i];
-       bbh=(double)bh[mi][i]/(double)stepm;
+         s1=s[mw[mi][i]][i];
-       /* bias is positive if real duration
+         s2=s[mw[mi+1][i]][i];
-        * is higher than the multiple of stepm and negative otherwise.
+         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 */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         ipmx +=1;
-         lli=log(out[s1][s2] - savm[s1][s2]);
+         sw += weight[i];
-       } else if  (s2==-2) {
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         for (j=1,survp=0. ; j<=nlstate; j++)
+       } /* end of wave */
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+     } /* end of individual */
-         lli= log(survp);
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-       }else if (mle==1){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       } else if(mle==2){
+       for(mi=1; mi<= wav[i]-1; mi++){
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       } else if(mle==3){  /* exponential inter-extrapolation */
+           for (j=1;j<=nlstate+ndeath;j++){
-         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 */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli=log(out[s1][s2]); /* Original formula */
+           }
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         for(d=0; d<dh[mi][i]; d++){
-         lli=log(out[s1][s2]); /* Original formula */
+           newm=savm;
-       } /* End of if */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       ipmx +=1;
+           for (kk=1; kk<=cptcovage;kk++) {
-       sw += weight[i];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       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]); */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       if(globpr){
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+           savm=oldm;
-  %11.6f %11.6f %11.6f ", \
+           oldm=newm;
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+         } /* end mult */
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         s1=s[mw[mi][i]][i];
-           llt +=ll[k]*gipmx/gsw;
+         s2=s[mw[mi+1][i]][i];
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         bbh=(double)bh[mi][i]/(double)stepm;
-         }
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-         fprintf(ficresilk," %10.6f\n", -llt);
+         ipmx +=1;
-       }
+         sw += weight[i];
-     } /* end of wave */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   } /* end of individual */
+       } /* end of wave */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+     } /* end of individual */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   if(globpr==0){ /* First time we count the contributions and weights */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     gipmx=ipmx;
+       for(mi=1; mi<= wav[i]-1; mi++){
-     gsw=sw;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+           for (j=1;j<=nlstate+ndeath;j++){
-   return -l;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
- /*************** function likelione ***********/
+           newm=savm;
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- {
+           for (kk=1; kk<=cptcovage;kk++) {
-   /* This routine should help understanding what is done with
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-      the selection of individuals/waves and
+           }
-      to check the exact contribution to the likelihood.
-      Plotting could be done.
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-    */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   int k;
+           savm=oldm;
+           oldm=newm;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+         } /* end mult */
-     strcpy(fileresilk,"ilk");
-     strcat(fileresilk,fileres);
+         s1=s[mw[mi][i]][i];
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+         s2=s[mw[mi+1][i]][i];
-       printf("Problem with resultfile: %s\n", fileresilk);
+         if( s2 > nlstate){
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-     }
+         }else{
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-     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]); */
+         ipmx +=1;
-     for(k=1; k<=nlstate; k++)
+         sw += weight[i];
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-   }
+       } /* end of wave */
+     } /* end of individual */
-   *fretone=(*funcone)(p);
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-   if(*globpri !=0){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     fclose(ficresilk);
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       for(mi=1; mi<= wav[i]-1; mi++){
-     fflush(fichtm);
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   }
+           for (j=1;j<=nlstate+ndeath;j++){
-   return;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
+         for(d=0; d<dh[mi][i]; d++){
- /*********** Maximum Likelihood Estimation ***************/
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+           for (kk=1; kk<=cptcovage;kk++) {
- {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   int i,j, iter;
+           }
-   double **xi;
-   double fret;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   double fretone; /* Only one call to likelihood */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /*  char filerespow[FILENAMELENGTH];*/
+           savm=oldm;
-   xi=matrix(1,npar,1,npar);
+           oldm=newm;
-   for (i=1;i<=npar;i++)
+         } /* end mult */
-     for (j=1;j<=npar;j++)
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         s1=s[mw[mi][i]][i];
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         s2=s[mw[mi+1][i]][i];
-   strcpy(filerespow,"pow");
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   strcat(filerespow,fileres);
+         ipmx +=1;
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         sw += weight[i];
-     printf("Problem with resultfile: %s\n", filerespow);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         /*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 */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     } /* end of individual */
-   for (i=1;i<=nlstate;i++)
+   } /* End of if */
-     for(j=1;j<=nlstate+ndeath;j++)
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   fprintf(ficrespow,"\n");
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   return -l;
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+ }
-   free_matrix(xi,1,npar,1,npar);
+ /*************** log-likelihood *************/
-   fclose(ficrespow);
+ double funcone( double *x)
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+ {
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   /* Same as likeli but slower because of a lot of printf and if */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   int i, ii, j, k, mi, d, kk;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
- }
+   double **out;
+   double lli; /* Individual log likelihood */
- /**** Computes Hessian and covariance matrix ***/
+   double llt;
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+   int s1, s2;
- {
+   double bbh, survp;
-   double  **a,**y,*x,pd;
+   /*extern weight */
-   double **hess;
+   /* We are differentiating ll according to initial status */
-   int i, j,jk;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   int *indx;
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+   */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+   cov[1]=1.;
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-   double gompertz(double p[]);
-   hess=matrix(1,npar,1,npar);
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+     for(mi=1; mi<= wav[i]-1; mi++){
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-   for (i=1;i<=npar;i++){
+         for (j=1;j<=nlstate+ndeath;j++){
-     printf("%d",i);fflush(stdout);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+       for(d=0; d<dh[mi][i]; d++){
+         newm=savm;
-     /*  printf(" %f ",p[i]);
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+         for (kk=1; kk<=cptcovage;kk++) {
-   }
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
-   for (i=1;i<=npar;i++) {
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-     for (j=1;j<=npar;j++)  {
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       if (j>i) {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         printf(".%d%d",i,j);fflush(stdout);
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+         savm=oldm;
+         oldm=newm;
-         hess[j][i]=hess[i][j];
+       } /* end mult */
-         /*printf(" %lf ",hess[i][j]);*/
-       }
+       s1=s[mw[mi][i]][i];
-     }
+       s2=s[mw[mi+1][i]][i];
-   }
+       bbh=(double)bh[mi][i]/(double)stepm;
-   printf("\n");
+       /* bias is positive if real duration
-   fprintf(ficlog,"\n");
+        * is higher than the multiple of stepm and negative otherwise.
+        */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+         lli=log(out[s1][s2] - savm[s1][s2]);
+       } else if  (s2==-2) {
-   a=matrix(1,npar,1,npar);
+         for (j=1,survp=0. ; j<=nlstate; j++)
-   y=matrix(1,npar,1,npar);
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   x=vector(1,npar);
+         lli= log(survp);
-   indx=ivector(1,npar);
+       }else if (mle==1){
-   for (i=1;i<=npar;i++)
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+       } else if(mle==2){
-   ludcmp(a,npar,indx,&pd);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   for (j=1;j<=npar;j++) {
+         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 */
-     for (i=1;i<=npar;i++) x[i]=0;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     x[j]=1;
+         lli=log(out[s1][s2]); /* Original formula */
-     lubksb(a,npar,indx,x);
+       } else{  /* mle=0 back to 1 */
-     for (i=1;i<=npar;i++){
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       matcov[i][j]=x[i];
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-     }
+       } /* End of if */
-   }
+       ipmx +=1;
+       sw += weight[i];
-   printf("\n#Hessian matrix#\n");
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-   for (i=1;i<=npar;i++) {
+       if(globpr){
-     for (j=1;j<=npar;j++) {
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-       printf("%.3e ",hess[i][j]);
+  %11.6f %11.6f %11.6f ", \
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-     }
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     printf("\n");
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-     fprintf(ficlog,"\n");
+           llt +=ll[k]*gipmx/gsw;
-   }
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         }
-   /* Recompute Inverse */
+         fprintf(ficresilk," %10.6f\n", -llt);
-   for (i=1;i<=npar;i++)
+       }
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+     } /* end of wave */
-   ludcmp(a,npar,indx,&pd);
+   } /* end of individual */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   for (j=1;j<=npar;j++) {
+   if(globpr==0){ /* First time we count the contributions and weights */
-     for (i=1;i<=npar;i++) x[i]=0;
+     gipmx=ipmx;
-     x[j]=1;
+     gsw=sw;
-     lubksb(a,npar,indx,x);
+   }
-     for (i=1;i<=npar;i++){
+   return -l;
-       y[i][j]=x[i];
+ }
-       printf("%.3e ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
-     }
+ /*************** function likelione ***********/
-     printf("\n");
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     fprintf(ficlog,"\n");
+ {
-   }
+   /* This routine should help understanding what is done with
-   */
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
-   free_matrix(a,1,npar,1,npar);
+      Plotting could be done.
-   free_matrix(y,1,npar,1,npar);
+    */
-   free_vector(x,1,npar);
+   int k;
-   free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   if(*globpri !=0){ /* Just counts and sums, no printings */
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
- }
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
- /*************** hessian matrix ****************/
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+     }
- {
+     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");
-   int i;
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-   int l=1, lmax=20;
+     /*  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 k1,k2;
+     for(k=1; k<=nlstate; k++)
-   double p2[NPARMAX+1];
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   double res;
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+   }
-   double fx;
-   int k=0,kmax=10;
+   *fretone=(*funcone)(p);
-   double l1;
+   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 (i=1;i<=npar;i++) p2[i]=x[i];
+     fflush(fichtm);
-   for(l=0 ; l <=lmax; l++){
+   }
-     l1=pow(10,l);
+   return;
-     delts=delt;
+ }
-     for(k=1 ; k <kmax; k=k+1){
-       delt = delta*(l1*k);
-       p2[theta]=x[theta] +delt;
+ /*********** Maximum Likelihood Estimation ***************/
-       k1=func(p2)-fx;
-       p2[theta]=x[theta]-delt;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-       k2=func(p2)-fx;
+ {
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   int i,j, iter;
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   double **xi;
+   double fret;
- #ifdef DEBUG
+   double fretone; /* Only one call to likelihood */
-       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);
+   /*  char filerespow[FILENAMELENGTH];*/
-       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);
+   xi=matrix(1,npar,1,npar);
- #endif
+   for (i=1;i<=npar;i++)
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+     for (j=1;j<=npar;j++)
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-         k=kmax;
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-       }
+   strcpy(filerespow,"pow");
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+   strcat(filerespow,fileres);
-         k=kmax; l=lmax*10.;
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-       }
+     printf("Problem with resultfile: %s\n", filerespow);
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-         delts=delt;
+   }
-       }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     }
+   for (i=1;i<=nlstate;i++)
-   }
+     for(j=1;j<=nlstate+ndeath;j++)
-   delti[theta]=delts;
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   return res;
+   fprintf(ficrespow,"\n");
- }
+   powell(p,xi,npar,ftol,&iter,&fret,func);
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+   free_matrix(xi,1,npar,1,npar);
- {
+   fclose(ficrespow);
-   int i;
+   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-   int l=1, l1, lmax=20;
+   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-   double k1,k2,k3,k4,res,fx;
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-   double p2[NPARMAX+1];
-   int k;
+ }
-   fx=func(x);
+ /**** Computes Hessian and covariance matrix ***/
-   for (k=1; k<=2; k++) {
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+ {
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   double  **a,**y,*x,pd;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   double **hess;
-     k1=func(p2)-fx;
+   int i, j,jk;
+   int *indx;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-     k2=func(p2)-fx;
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   double gompertz(double p[]);
-     k3=func(p2)-fx;
+   hess=matrix(1,npar,1,npar);
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-     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 */
+     printf("%d",i);fflush(stdout);
- #ifdef DEBUG
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-     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);
-     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);
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- #endif
-   }
+     /*  printf(" %f ",p[i]);
-   return res;
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
- }
+   }
- /************** Inverse of matrix **************/
+   for (i=1;i<=npar;i++) {
- void ludcmp(double **a, int n, int *indx, double *d)
+     for (j=1;j<=npar;j++)  {
- {
+       if (j>i) {
-   int i,imax,j,k;
+         printf(".%d%d",i,j);fflush(stdout);
-   double big,dum,sum,temp;
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-   double *vv;
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   vv=vector(1,n);
+         hess[j][i]=hess[i][j];
-   *d=1.0;
+         /*printf(" %lf ",hess[i][j]);*/
-   for (i=1;i<=n;i++) {
+       }
-     big=0.0;
+     }
-     for (j=1;j<=n;j++)
+   }
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+   printf("\n");
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+   fprintf(ficlog,"\n");
-     vv[i]=1.0/big;
-   }
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   for (j=1;j<=n;j++) {
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-     for (i=1;i<j;i++) {
-       sum=a[i][j];
+   a=matrix(1,npar,1,npar);
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   y=matrix(1,npar,1,npar);
-       a[i][j]=sum;
+   x=vector(1,npar);
-     }
+   indx=ivector(1,npar);
-     big=0.0;
+   for (i=1;i<=npar;i++)
-     for (i=j;i<=n;i++) {
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-       sum=a[i][j];
+   ludcmp(a,npar,indx,&pd);
-       for (k=1;k<j;k++)
-         sum -= a[i][k]*a[k][j];
+   for (j=1;j<=npar;j++) {
-       a[i][j]=sum;
+     for (i=1;i<=npar;i++) x[i]=0;
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+     x[j]=1;
-         big=dum;
+     lubksb(a,npar,indx,x);
-         imax=i;
+     for (i=1;i<=npar;i++){
-       }
+       matcov[i][j]=x[i];
      }
-     if (j != imax) {
+   }
-       for (k=1;k<=n;k++) {
-         dum=a[imax][k];
+   printf("\n#Hessian matrix#\n");
-         a[imax][k]=a[j][k];
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-         a[j][k]=dum;
+   for (i=1;i<=npar;i++) {
-       }
+     for (j=1;j<=npar;j++) {
-       *d = -(*d);
+       printf("%.3e ",hess[i][j]);
-       vv[imax]=vv[j];
+       fprintf(ficlog,"%.3e ",hess[i][j]);
      }
-     indx[j]=imax;
+     printf("\n");
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+     fprintf(ficlog,"\n");
-     if (j != n) {
+   }
-       dum=1.0/(a[j][j]);
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   /* Recompute Inverse */
-     }
+   for (i=1;i<=npar;i++)
-   }
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-   free_vector(vv,1,n);  /* Doesn't work */
+   ludcmp(a,npar,indx,&pd);
- ;
- }
+   /*  printf("\n#Hessian matrix recomputed#\n");
- void lubksb(double **a, int n, int *indx, double b[])
+   for (j=1;j<=npar;j++) {
- {
+     for (i=1;i<=npar;i++) x[i]=0;
-   int i,ii=0,ip,j;
+     x[j]=1;
-   double sum;
+     lubksb(a,npar,indx,x);
+     for (i=1;i<=npar;i++){
-   for (i=1;i<=n;i++) {
+       y[i][j]=x[i];
-     ip=indx[i];
+       printf("%.3e ",y[i][j]);
-     sum=b[ip];
+       fprintf(ficlog,"%.3e ",y[i][j]);
-     b[ip]=b[i];
+     }
-     if (ii)
+     printf("\n");
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+     fprintf(ficlog,"\n");
-     else if (sum) ii=i;
+   }
-     b[i]=sum;
+   */
-   }
-   for (i=n;i>=1;i--) {
+   free_matrix(a,1,npar,1,npar);
-     sum=b[i];
+   free_matrix(y,1,npar,1,npar);
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   free_vector(x,1,npar);
-     b[i]=sum/a[i][i];
+   free_ivector(indx,1,npar);
-   }
+   free_matrix(hess,1,npar,1,npar);
- }
- void pstamp(FILE *fichier)
+ }
- {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ /*************** hessian matrix ****************/
- }
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+ {
- /************ Frequencies ********************/
+   int i;
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
+   int l=1, lmax=20;
- {  /* Some frequencies */
+   double k1,k2;
+   double p2[MAXPARM+1]; /* identical to x */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   double res;
-   int first;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double ***freq; /* Frequencies */
+   double fx;
-   double *pp, **prop;
+   int k=0,kmax=10;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   double l1;
-   char fileresp[FILENAMELENGTH];
+   fx=func(x);
-   pp=vector(1,nlstate);
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
-   strcpy(fileresp,"p");
+     l1=pow(10,l);
-   strcat(fileresp,fileres);
+     delts=delt;
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+     for(k=1 ; k <kmax; k=k+1){
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+       delt = delta*(l1*k);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+       p2[theta]=x[theta] +delt;
-     exit(0);
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   }
+       p2[theta]=x[theta]-delt;
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+       k2=func(p2)-fx;
-   j1=0;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   j=cptcoveff;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+ #ifdef DEBUGHESS
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   first=1;
+       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
-   for(k1=1; k1<=j;k1++){
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-       j1++;
+         k=kmax;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+       }
-         scanf("%d", i);*/
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-       for (i=-5; i<=nlstate+ndeath; i++)
+         k=kmax; l=lmax*10.;
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+       }
-           for(m=iagemin; m <= iagemax+3; m++)
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-             freq[i][jk][m]=0;
+         delts=delt;
+       }
-     for (i=1; i<=nlstate; i++)
+     }
-       for(m=iagemin; m <= iagemax+3; m++)
+   }
-         prop[i][m]=0;
+   delti[theta]=delts;
+   return res;
-       dateintsum=0;
-       k2cpt=0;
+ }
-       for (i=1; i<=imx; i++) {
-         bool=1;
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-         if  (cptcovn>0) {
+ {
-           for (z1=1; z1<=cptcoveff; z1++)
+   int i;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   int l=1, l1, lmax=20;
-               bool=0;
+   double k1,k2,k3,k4,res,fx;
-         }
+   double p2[MAXPARM+1];
-         if (bool==1){
+   int k;
-           for(m=firstpass; m<=lastpass; m++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+   fx=func(x);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+   for (k=1; k<=2; k++) {
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-               if (m<lastpass) {
+     k1=func(p2)-fx;
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-               }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     k2=func(p2)-fx;
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-                 dateintsum=dateintsum+k2;
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-                 k2cpt++;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-               }
+     k3=func(p2)-fx;
-               /*}*/
-           }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-         }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-       }
+     k4=func(p2)-fx;
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ #ifdef DEBUG
-       pstamp(ficresp);
+     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-       if  (cptcovn>0) {
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-         fprintf(ficresp, "\n#********** Variable ");
+ #endif
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   }
-         fprintf(ficresp, "**********\n#");
+   return res;
-       }
+ }
-       for(i=1; i<=nlstate;i++)
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+ /************** Inverse of matrix **************/
-       fprintf(ficresp, "\n");
+ void ludcmp(double **a, int n, int *indx, double *d)
+ {
-       for(i=iagemin; i <= iagemax+3; i++){
+   int i,imax,j,k;
-         if(i==iagemax+3){
+   double big,dum,sum,temp;
-           fprintf(ficlog,"Total");
+   double *vv;
-         }else{
-           if(first==1){
+   vv=vector(1,n);
-             first=0;
+   *d=1.0;
-             printf("See log file for details...\n");
+   for (i=1;i<=n;i++) {
-           }
+     big=0.0;
-           fprintf(ficlog,"Age %d", i);
+     for (j=1;j<=n;j++)
-         }
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-         for(jk=1; jk <=nlstate ; jk++){
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+     vv[i]=1.0/big;
-             pp[jk] += freq[jk][m][i];
+   }
-         }
+   for (j=1;j<=n;j++) {
-         for(jk=1; jk <=nlstate ; jk++){
+     for (i=1;i<j;i++) {
-           for(m=-1, pos=0; m <=0 ; m++)
+       sum=a[i][j];
-             pos += freq[jk][m][i];
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-           if(pp[jk]>=1.e-10){
+       a[i][j]=sum;
-             if(first==1){
+     }
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     big=0.0;
-             }
+     for (i=j;i<=n;i++) {
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+       sum=a[i][j];
-           }else{
+       for (k=1;k<j;k++)
-             if(first==1)
+         sum -= a[i][k]*a[k][j];
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       a[i][j]=sum;
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-           }
+         big=dum;
-         }
+         imax=i;
+       }
-         for(jk=1; jk <=nlstate ; jk++){
+     }
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+     if (j != imax) {
-             pp[jk] += freq[jk][m][i];
+       for (k=1;k<=n;k++) {
-         }
+         dum=a[imax][k];
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+         a[imax][k]=a[j][k];
-           pos += pp[jk];
+         a[j][k]=dum;
-           posprop += prop[jk][i];
+       }
-         }
+       *d = -(*d);
-         for(jk=1; jk <=nlstate ; jk++){
+       vv[imax]=vv[j];
-           if(pos>=1.e-5){
+     }
-             if(first==1)
+     indx[j]=imax;
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+     if (j != n) {
-           }else{
+       dum=1.0/(a[j][j]);
-             if(first==1)
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+     }
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   }
-           }
+   free_vector(vv,1,n);  /* Doesn't work */
-           if( i <= iagemax){
+ ;
-             if(pos>=1.e-5){
+ }
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+ void lubksb(double **a, int n, int *indx, double b[])
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+ {
-             }
+   int i,ii=0,ip,j;
-             else
+   double sum;
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-           }
+   for (i=1;i<=n;i++) {
-         }
+     ip=indx[i];
+     sum=b[ip];
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+     b[ip]=b[i];
-           for(m=-1; m <=nlstate+ndeath; m++)
+     if (ii)
-             if(freq[jk][m][i] !=0 ) {
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-             if(first==1)
+     else if (sum) ii=i;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+     b[i]=sum;
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+   }
-             }
+   for (i=n;i>=1;i--) {
-         if(i <= iagemax)
+     sum=b[i];
-           fprintf(ficresp,"\n");
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-         if(first==1)
+     b[i]=sum/a[i][i];
-           printf("Others in log...\n");
+   }
-         fprintf(ficlog,"\n");
+ }
-       }
-     }
+ void pstamp(FILE *fichier)
-   }
+ {
-   dateintmean=dateintsum/k2cpt;
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ }
-   fclose(ficresp);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+ /************ Frequencies ********************/
-   free_vector(pp,1,nlstate);
+ 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[])
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+ {  /* Some frequencies */
-   /* End of Freq */
- }
+   int i, m, jk, k1,i1, j1, bool, z1,j;
+   int first;
- /************ Prevalence ********************/
+   double ***freq; /* Frequencies */
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+   double *pp, **prop;
- {
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   char fileresp[FILENAMELENGTH];
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
-      We still use firstpass and lastpass as another selection.
+   pp=vector(1,nlstate);
-   */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   strcpy(fileresp,"p");
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   strcat(fileresp,fileres);
-   double ***freq; /* Frequencies */
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-   double *pp, **prop;
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-   double pos,posprop;
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-   double  y2; /* in fractional years */
+     exit(0);
-   int iagemin, iagemax;
+   }
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-   iagemin= (int) agemin;
+   j1=0;
-   iagemax= (int) agemax;
-   /*pp=vector(1,nlstate);*/
+   j=cptcoveff;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   j1=0;
+   first=1;
-   j=cptcoveff;
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+   /*    j1++;
-   for(k1=1; k1<=j;k1++){
+ */
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-       j1++;
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         scanf("%d", i);*/
-       for (i=1; i<=nlstate; i++)
+       for (i=-5; i<=nlstate+ndeath; i++)
-         for(m=iagemin; m <= iagemax+3; m++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           prop[i][m]=0.0;
+           for(m=iagemin; m <= iagemax+3; m++)
+             freq[i][jk][m]=0;
-       for (i=1; i<=imx; i++) { /* Each individual */
-         bool=1;
+       for (i=1; i<=nlstate; i++)
-         if  (cptcovn>0) {
+         for(m=iagemin; m <= iagemax+3; m++)
-           for (z1=1; z1<=cptcoveff; z1++)
+           prop[i][m]=0;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+       dateintsum=0;
-         }
+       k2cpt=0;
-         if (bool==1) {
+       for (i=1; i<=imx; i++) {
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+         bool=1;
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+           for (z1=1; z1<=cptcoveff; z1++)
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-               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);
+               bool=0;
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-                 /*if(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]]);*/
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-                 prop[s[m][i]][iagemax+3] += weight[i];
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-               }
+             }
-             }
+         }
-           } /* end selection of waves */
-         }
+         if (bool==1){
-       }
+           for(m=firstpass; m<=lastpass; m++){
-       for(i=iagemin; i <= iagemax+3; i++){
+             k2=anint[m][i]+(mint[m][i]/12.);
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-           posprop += prop[jk][i];
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-         }
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+               if (m<lastpass) {
-         for(jk=1; jk <=nlstate ; jk++){
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-           if( i <=  iagemax){
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-             if(posprop>=1.e-5){
+               }
-               probs[i][jk][j1]= prop[jk][i]/posprop;
-             }
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-           }
+                 dateintsum=dateintsum+k2;
-         }/* end jk */
+                 k2cpt++;
-       }/* end i */
+               }
-     } /* end i1 */
+               /*}*/
-   } /* end k1 */
+           }
+         }
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+       } /* end i */
-   /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- }  /* End of prevalence */
+       pstamp(ficresp);
+       if  (cptcovn>0) {
- /************* Waves Concatenation ***************/
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- 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)
+         fprintf(ficresp, "**********\n#");
- {
+         fprintf(ficlog, "\n#********** Variable ");
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      Death is a valid wave (if date is known).
+         fprintf(ficlog, "**********\n#");
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+       }
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+       for(i=1; i<=nlstate;i++)
-      and mw[mi+1][i]. dh depends on stepm.
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-      */
+       fprintf(ficresp, "\n");
-   int i, mi, m;
+       for(i=iagemin; i <= iagemax+3; i++){
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+         if(i==iagemax+3){
-      double sum=0., jmean=0.;*/
+           fprintf(ficlog,"Total");
-   int first;
+         }else{
-   int j, k=0,jk, ju, jl;
+           if(first==1){
-   double sum=0.;
+             first=0;
-   first=0;
+             printf("See log file for details...\n");
-   jmin=1e+5;
+           }
-   jmax=-1;
+           fprintf(ficlog,"Age %d", i);
-   jmean=0.;
+         }
-   for(i=1; i<=imx; i++){
+         for(jk=1; jk <=nlstate ; jk++){
-     mi=0;
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-     m=firstpass;
+             pp[jk] += freq[jk][m][i];
-     while(s[m][i] <= nlstate){
+         }
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+         for(jk=1; jk <=nlstate ; jk++){
-         mw[++mi][i]=m;
+           for(m=-1, pos=0; m <=0 ; m++)
-       if(m >=lastpass)
+             pos += freq[jk][m][i];
-         break;
+           if(pp[jk]>=1.e-10){
-       else
+             if(first==1){
-         m++;
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-     }/* end while */
+             }
-     if (s[m][i] > nlstate){
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       mi++;     /* Death is another wave */
+           }else{
-       /* if(mi==0)  never been interviewed correctly before death */
+             if(first==1)
-          /* Only death is a correct wave */
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-       mw[mi][i]=m;
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-     }
+           }
+         }
-     wav[i]=mi;
-     if(mi==0){
+         for(jk=1; jk <=nlstate ; jk++){
-       nbwarn++;
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-       if(first==0){
+             pp[jk] += freq[jk][m][i];
-         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(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-       }
+           pos += pp[jk];
-       if(first==1){
+           posprop += prop[jk][i];
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         }
-       }
+         for(jk=1; jk <=nlstate ; jk++){
-     } /* end mi==0 */
+           if(pos>=1.e-5){
-   } /* End individuals */
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-   for(i=1; i<=imx; i++){
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-     for(mi=1; mi<wav[i];mi++){
+           }else{
-       if (stepm <=0)
+             if(first==1)
-         dh[mi][i]=1;
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-       else{
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+           }
-           if (agedc[i] < 2*AGESUP) {
+           if( i <= iagemax){
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             if(pos>=1.e-5){
-             if(j==0) j=1;  /* Survives at least one month after exam */
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-             else if(j<0){
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-               nberr++;
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-               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 */
+             else
-               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(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+         }
-             }
-             k=k+1;
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-             if (j >= jmax){
+           for(m=-1; m <=nlstate+ndeath; m++)
-               jmax=j;
+             if(freq[jk][m][i] !=0 ) {
-               ijmax=i;
+             if(first==1)
-             }
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-             if (j <= jmin){
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-               jmin=j;
+             }
-               ijmin=i;
+         if(i <= iagemax)
-             }
+           fprintf(ficresp,"\n");
-             sum=sum+j;
+         if(first==1)
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+           printf("Others in log...\n");
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+         fprintf(ficlog,"\n");
-           }
+       }
-         }
+       /*}*/
-         else{
+   }
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   dateintmean=dateintsum/k2cpt;
- /*        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]); */
+   fclose(ficresp);
-           k=k+1;
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-           if (j >= jmax) {
+   free_vector(pp,1,nlstate);
-             jmax=j;
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-             ijmax=i;
+   /* End of Freq */
-           }
+ }
-           else if (j <= jmin){
-             jmin=j;
+ /************ Prevalence ********************/
-             ijmin=i;
+ 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 (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-           /*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]);*/
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-           if(j<0){
+      We still use firstpass and lastpass as another selection.
-             nberr++;
+   */
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-           }
+   double ***freq; /* Frequencies */
-           sum=sum+j;
+   double *pp, **prop;
-         }
+   double pos,posprop;
-         jk= j/stepm;
+   double  y2; /* in fractional years */
-         jl= j -jk*stepm;
+   int iagemin, iagemax;
-         ju= j -(jk+1)*stepm;
+   int first; /** to stop verbosity which is redirected to log file */
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           if(jl==0){
+   iagemin= (int) agemin;
-             dh[mi][i]=jk;
+   iagemax= (int) agemax;
-             bh[mi][i]=0;
+   /*pp=vector(1,nlstate);*/
-           }else{ /* We want a negative bias in order to only have interpolation ie
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-                   * at the price of an extra matrix product in likelihood */
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-             dh[mi][i]=jk+1;
+   j1=0;
-             bh[mi][i]=ju;
-           }
+   /*j=cptcoveff;*/
-         }else{
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           if(jl <= -ju){
-             dh[mi][i]=jk;
+   first=1;
-             bh[mi][i]=jl;       /* bias is positive if real duration
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-                                  * is higher than the multiple of stepm and negative otherwise.
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-                                  */
+       j1++;*/
-           }
-           else{
+       for (i=1; i<=nlstate; i++)
-             dh[mi][i]=jk+1;
+         for(m=iagemin; m <= iagemax+3; m++)
-             bh[mi][i]=ju;
+           prop[i][m]=0.0;
-           }
-           if(dh[mi][i]==0){
+       for (i=1; i<=imx; i++) { /* Each individual */
-             dh[mi][i]=1; /* At least one step */
+         bool=1;
-             bh[mi][i]=ju; /* At least one step */
+         if  (cptcovn>0) {
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+           for (z1=1; z1<=cptcoveff; z1++)
-           }
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-         } /* end if mle */
+               bool=0;
-       }
+         }
-     } /* end wave */
+         if (bool==1) {
-   }
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-   jmean=sum/k;
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-  }
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
- /*********** Tricode ****************************/
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
- void tricode(int *Tvar, int **nbcode, int imx)
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
- {
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+               }
-   int cptcode=0;
+             }
-   cptcoveff=0;
+           } /* end selection of waves */
+         }
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+       }
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+       for(i=iagemin; i <= iagemax+3; i++){
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+           posprop += prop[jk][i];
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+         }
-                                modality*/
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+         for(jk=1; jk <=nlstate ; jk++){
-       Ndum[ij]++; /*store the modality */
+           if( i <=  iagemax){
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+             if(posprop>=1.e-5){
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-                                        Tvar[j]. If V=sex and male is 0 and
+             } else{
-                                        female is 1, then  cptcode=1.*/
+               if(first==1){
-     }
+                 first=0;
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-     for (i=0; i<=cptcode; i++) {
+               }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+             }
-     }
+           }
+         }/* end jk */
-     ij=1;
+       }/* end i */
-     for (i=1; i<=ncodemax[j]; i++) {
+     /*} *//* end i1 */
-       for (k=0; k<= maxncov; k++) {
+   } /* end j1 */
-         if (Ndum[k] != 0) {
-           nbcode[Tvar[j]][ij]=k;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-           /* 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; */
+   /*free_vector(pp,1,nlstate);*/
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-           ij++;
+ }  /* End of prevalence */
-         }
-         if (ij > ncodemax[j]) break;
+ /************* Waves Concatenation ***************/
-       }
-     }
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
-   }
+ {
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+      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
-  for (i=1; i<=ncovmodel-2; i++) {
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      and mw[mi+1][i]. dh depends on stepm.
-    ij=Tvar[i];
+      */
-    Ndum[ij]++;
-  }
+   int i, mi, m;
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-  ij=1;
+      double sum=0., jmean=0.;*/
-  for (i=1; i<= maxncov; i++) {
+   int first;
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+   int j, k=0,jk, ju, jl;
-      Tvaraff[ij]=i; /*For printing */
+   double sum=0.;
-      ij++;
+   first=0;
-    }
+   jmin=1e+5;
-  }
+   jmax=-1;
+   jmean=0.;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+   for(i=1; i<=imx; i++){
- }
+     mi=0;
+     m=firstpass;
- /*********** Health Expectancies ****************/
+     while(s[m][i] <= nlstate){
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
- 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[] )
+         mw[++mi][i]=m;
+       if(m >=lastpass)
- {
+         break;
-   /* Health expectancies, no variances */
+       else
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+         m++;
-   double age, agelim, hf;
+     }/* end while */
-   double ***p3mat;
+     if (s[m][i] > nlstate){
-   double eip;
+       mi++;     /* Death is another wave */
+       /* if(mi==0)  never been interviewed correctly before death */
-   pstamp(ficreseij);
+          /* Only death is a correct wave */
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+       mw[mi][i]=m;
-   fprintf(ficreseij,"# Age");
+     }
-   for(i=1; i<=nlstate;i++){
-     for(j=1; j<=nlstate;j++){
+     wav[i]=mi;
-       fprintf(ficreseij," e%1d%1d ",i,j);
+     if(mi==0){
-     }
+       nbwarn++;
-     fprintf(ficreseij," e%1d. ",i);
+       if(first==0){
-   }
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-   fprintf(ficreseij,"\n");
+         first=1;
+       }
+       if(first==1){
-   if(estepm < stepm){
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       }
-   }
+     } /* end mi==0 */
-   else  hstepm=estepm;
+   } /* End individuals */
-   /* We compute the life expectancy from trapezoids spaced every estepm months
-    * This is mainly to measure the difference between two models: for example
+   for(i=1; i<=imx; i++){
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+     for(mi=1; mi<wav[i];mi++){
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       if (stepm <=0)
-    * progression in between and thus overestimating or underestimating according
+         dh[mi][i]=1;
-    * to the curvature of the survival function. If, for the same date, we
+       else{
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-    * to compare the new estimate of Life expectancy with the same linear
+           if (agedc[i] < 2*AGESUP) {
-    * hypothesis. A more precise result, taking into account a more precise
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-    * curvature will be obtained if estepm is as small as stepm. */
+             if(j==0) j=1;  /* Survives at least one month after exam */
+             else if(j<0){
-   /* For example we decided to compute the life expectancy with the smallest unit */
+               nberr++;
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+               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]);
-      nhstepm is the number of hstepm from age to agelim
+               j=1; /* Temporary Dangerous patch */
-      nstepm is the number of stepm from age to agelin.
+               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);
-      Look at hpijx to understand the reason of that which relies in memory size
+               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]);
-      and note for a fixed period like estepm months */
+               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);
-   /* 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
+             k=k+1;
-      means that if the survival funtion is printed only each two years of age and if
+             if (j >= jmax){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+               jmax=j;
-      results. So we changed our mind and took the option of the best precision.
+               ijmax=i;
-   */
+             }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+             if (j <= jmin){
+               jmin=j;
-   agelim=AGESUP;
+               ijmin=i;
-   /* If stepm=6 months */
+             }
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+             sum=sum+j;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
- /* nhstepm age range expressed in number of stepm */
+           }
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         }
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         else{
-   /* if (stepm >= YEARM) hstepm=1;*/
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ /*        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]); */
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           k=k+1;
-   for (age=bage; age<=fage; age ++){
+           if (j >= jmax) {
+             jmax=j;
+             ijmax=i;
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+           }
+           else if (j <= jmin){
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+             jmin=j;
+             ijmin=i;
-     printf("%d|",(int)age);fflush(stdout);
+           }
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+           if(j<0){
-     /* Computing expectancies */
+             nberr++;
-     for(i=1; i<=nlstate;i++)
+             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]);
-       for(j=1; j<=nlstate;j++)
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           }
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+           sum=sum+j;
+         }
-           /*if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         jk= j/stepm;
+         jl= j -jk*stepm;
-         }
+         ju= j -(jk+1)*stepm;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-     fprintf(ficreseij,"%3.0f",age );
+           if(jl==0){
-     for(i=1; i<=nlstate;i++){
+             dh[mi][i]=jk;
-       eip=0;
+             bh[mi][i]=0;
-       for(j=1; j<=nlstate;j++){
+           }else{ /* We want a negative bias in order to only have interpolation ie
-         eip +=eij[i][j][(int)age];
+                   * to avoid the price of an extra matrix product in likelihood */
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+             dh[mi][i]=jk+1;
-       }
+             bh[mi][i]=ju;
-       fprintf(ficreseij,"%9.4f", eip );
+           }
-     }
+         }else{
-     fprintf(ficreseij,"\n");
+           if(jl <= -ju){
+             dh[mi][i]=jk;
-   }
+             bh[mi][i]=jl;       /* bias is positive if real duration
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                  * is higher than the multiple of stepm and negative otherwise.
-   printf("\n");
+                                  */
-   fprintf(ficlog,"\n");
+           }
+           else{
- }
+             dh[mi][i]=jk+1;
+             bh[mi][i]=ju;
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+           }
+           if(dh[mi][i]==0){
- {
+             dh[mi][i]=1; /* At least one step */
-   /* Covariances of health expectancies eij and of total life expectancies according
+             bh[mi][i]=ju; /* At least one step */
-    to initial status i, ei. .
+             /*  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);*/
-   */
+           }
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+         } /* end if mle */
-   double age, agelim, hf;
+       }
-   double ***p3matp, ***p3matm, ***varhe;
+     } /* end wave */
-   double **dnewm,**doldm;
+   }
-   double *xp, *xm;
+   jmean=sum/k;
-   double **gp, **gm;
+   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);
-   double ***gradg, ***trgradg;
+   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);
-   int theta;
+  }
-   double eip, vip;
+ /*********** Tricode ****************************/
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+ {
-   xp=vector(1,npar);
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   xm=vector(1,npar);
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+   /* nbcode[Tvar[j]][1]=
-   pstamp(ficresstdeij);
+   */
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   fprintf(ficresstdeij,"# Age");
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   for(i=1; i<=nlstate;i++){
+   int modmaxcovj=0; /* Modality max of covariates j */
-     for(j=1; j<=nlstate;j++)
+   int cptcode=0; /* Modality max of covariates j */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+   int modmincovj=0; /* Modality min of covariates j */
-     fprintf(ficresstdeij," e%1d. ",i);
-   }
-   fprintf(ficresstdeij,"\n");
+   cptcoveff=0;
-   pstamp(ficrescveij);
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   fprintf(ficrescveij,"# Age");
-   for(i=1; i<=nlstate;i++)
+   /* Loop on covariates without age and products */
-     for(j=1; j<=nlstate;j++){
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-       cptj= (j-1)*nlstate+i;
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-       for(i2=1; i2<=nlstate;i2++)
+                                modality of this covariate Vj*/
-         for(j2=1; j2<=nlstate;j2++){
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-           cptj2= (j2-1)*nlstate+i2;
+                                     * If product of Vn*Vm, still boolean *:
-           if(cptj2 <= cptj)
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-         }
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-     }
+                                       modality of the nth covariate of individual i. */
-   fprintf(ficrescveij,"\n");
+       if (ij > modmaxcovj)
+         modmaxcovj=ij;
-   if(estepm < stepm){
+       else if (ij < modmincovj)
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         modmincovj=ij;
-   }
+       if ((ij < -1) && (ij > NCOVMAX)){
-   else  hstepm=estepm;
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+         exit(1);
-    * This is mainly to measure the difference between two models: for example
+       }else
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-    * progression in between and thus overestimating or underestimating according
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-    * to the curvature of the survival function. If, for the same date, we
+       /* getting the maximum value of the modality of the covariate
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-    * to compare the new estimate of Life expectancy with the same linear
+          female is 1, then modmaxcovj=1.*/
-    * hypothesis. A more precise result, taking into account a more precise
+     }
-    * curvature will be obtained if estepm is as small as stepm. */
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+     cptcode=modmaxcovj;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+    /*for (i=0; i<=cptcode; i++) {*/
-      nhstepm is the number of hstepm from age to agelim
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-      nstepm is the number of stepm from age to agelin.
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-      Look at hpijx to understand the reason of that which relies in memory size
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-      and note for a fixed period like estepm months */
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-   /* 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
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-      means that if the survival funtion is printed only each two years of age and if
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     } /* Ndum[-1] number of undefined modalities */
-      results. So we changed our mind and took the option of the best precision.
-   */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-   /* If stepm=6 months */
+        modmincovj=3; modmaxcovj = 7;
-   /* nhstepm age range expressed in number of stepm */
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
-   agelim=AGESUP;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+        variables V1_1 and V1_2.
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+        nbcode[Tvar[j]][ij]=k;
-   /* if (stepm >= YEARM) hstepm=1;*/
+        nbcode[Tvar[j]][1]=0;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+        nbcode[Tvar[j]][2]=1;
+        nbcode[Tvar[j]][3]=2;
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     */
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+         /*recode from 0 */
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   for (age=bage; age<=fage; age ++){
+                                      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; */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           ij++;
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         }
+         if (ij > ncodemax[j]) break;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       }  /* end of loop on */
+     } /* end of loop on modality */
-     /* Computing  Variances of health expectancies */
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-        decrease memory allocation */
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-       }
+    Ndum[ij]++;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+  }
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+  ij=1;
-       for(j=1; j<= nlstate; j++){
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-         for(i=1; i<=nlstate; i++){
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-           for(h=0; h<=nhstepm-1; h++){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+      Tvaraff[ij]=i; /*For printing (unclear) */
-           }
+      ij++;
-         }
+    }else
-       }
+        Tvaraff[ij]=0;
+  }
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+  ij--;
-         for(h=0; h<=nhstepm-1; h++){
+  cptcoveff=ij; /*Number of total covariates*/
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         }
+ }
-     }/* End theta */
+ /*********** Health Expectancies ****************/
-     for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*nlstate;j++)
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
+ {
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   int nhstepma, nstepma; /* Decreasing with age */
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+   double age, agelim, hf;
-         varhe[ij][ji][(int)age] =0.;
+   double ***p3mat;
+   double eip;
-      printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   pstamp(ficreseij);
-      for(h=0;h<=nhstepm-1;h++){
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-       for(k=0;k<=nhstepm-1;k++){
+   fprintf(ficreseij,"# Age");
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+   for(i=1; i<=nlstate;i++){
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+     for(j=1; j<=nlstate;j++){
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+       fprintf(ficreseij," e%1d%1d ",i,j);
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+     }
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+     fprintf(ficreseij," e%1d. ",i);
-       }
+   }
-     }
+   fprintf(ficreseij,"\n");
-     /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   if(estepm < stepm){
-     for(i=1; i<=nlstate;i++)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       for(j=1; j<=nlstate;j++)
+   }
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+   else  hstepm=estepm;
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-           /* 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 stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-         }
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-     fprintf(ficresstdeij,"%3.0f",age );
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-     for(i=1; i<=nlstate;i++){
+    * to compare the new estimate of Life expectancy with the same linear
-       eip=0.;
+    * hypothesis. A more precise result, taking into account a more precise
-       vip=0.;
+    * curvature will be obtained if estepm is as small as stepm. */
-       for(j=1; j<=nlstate;j++){
-         eip += eij[i][j][(int)age];
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+      nhstepm is the number of hstepm from age to agelim
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+      nstepm is the number of stepm from age to agelin.
-       }
+      Look at hpijx to understand the reason of that which relies in memory size
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+      and note for a fixed period like estepm months */
-     }
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     fprintf(ficresstdeij,"\n");
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
-     fprintf(ficrescveij,"%3.0f",age );
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     for(i=1; i<=nlstate;i++)
+      results. So we changed our mind and took the option of the best precision.
-       for(j=1; j<=nlstate;j++){
+   */
-         cptj= (j-1)*nlstate+i;
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(i2=1; i2<=nlstate;i2++)
-           for(j2=1; j2<=nlstate;j2++){
+   agelim=AGESUP;
-             cptj2= (j2-1)*nlstate+i2;
+   /* If stepm=6 months */
-             if(cptj2 <= cptj)
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-           }
-       }
+ /* nhstepm age range expressed in number of stepm */
-     fprintf(ficrescveij,"\n");
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   }
+   /* if (stepm >= YEARM) hstepm=1;*/
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   for (age=bage; age<=fage; age ++){
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   printf("\n");
+     /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficlog,"\n");
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   free_vector(xm,1,npar);
+     /* If stepm=6 months */
-   free_vector(xp,1,npar);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
- }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+     printf("%d|",(int)age);fflush(stdout);
- {
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     /* Computing expectancies */
-   /* double **newm;*/
+     for(i=1; i<=nlstate;i++)
-   double **dnewm,**doldm;
+       for(j=1; j<=nlstate;j++)
-   double **dnewmp,**doldmp;
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   int i, j, nhstepm, hstepm, h, nstepm ;
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-   int k, cptcode;
-   double *xp;
+           /* 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]);*/
-   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg; /*for var eij */
+         }
-   double **gradgp, **trgradgp; /* for var p point j */
-   double *gpp, *gmp; /* for var p point j */
+     fprintf(ficreseij,"%3.0f",age );
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+     for(i=1; i<=nlstate;i++){
-   double ***p3mat;
+       eip=0;
-   double age,agelim, hf;
+       for(j=1; j<=nlstate;j++){
-   double ***mobaverage;
+         eip +=eij[i][j][(int)age];
-   int theta;
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-   char digit[4];
+       }
-   char digitp[25];
+       fprintf(ficreseij,"%9.4f", eip );
+     }
-   char fileresprobmorprev[FILENAMELENGTH];
+     fprintf(ficreseij,"\n");
-   if(popbased==1){
+   }
-     if(mobilav!=0)
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       strcpy(digitp,"-populbased-mobilav-");
+   printf("\n");
-     else strcpy(digitp,"-populbased-nomobil-");
+   fprintf(ficlog,"\n");
-   }
-   else
+ }
-     strcpy(digitp,"-stablbased-");
+ 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[] )
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ {
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   /* Covariances of health expectancies eij and of total life expectancies according
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+    to initial status i, ei. .
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   */
-     }
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   }
+   int nhstepma, nstepma; /* Decreasing with age */
+   double age, agelim, hf;
-   strcpy(fileresprobmorprev,"prmorprev");
+   double ***p3matp, ***p3matm, ***varhe;
-   sprintf(digit,"%-d",ij);
+   double **dnewm,**doldm;
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   double *xp, *xm;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   double **gp, **gm;
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   double ***gradg, ***trgradg;
-   strcat(fileresprobmorprev,fileres);
+   int theta;
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   double eip, vip;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   xp=vector(1,npar);
+   xm=vector(1,npar);
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   pstamp(ficresprobmorprev);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*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);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   pstamp(ficresstdeij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   fprintf(ficresstdeij,"# Age");
-     for(i=1; i<=nlstate;i++)
+   for(i=1; i<=nlstate;i++){
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+     for(j=1; j<=nlstate;j++)
-   }
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   fprintf(ficresprobmorprev,"\n");
+     fprintf(ficresstdeij," e%1d. ",i);
-   fprintf(ficgp,"\n# Routine varevsij");
+   }
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   fprintf(ficresstdeij,"\n");
-   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);
+   pstamp(ficrescveij);
- /*   } */
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   fprintf(ficrescveij,"# Age");
-   pstamp(ficresvij);
+   for(i=1; i<=nlstate;i++)
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+     for(j=1; j<=nlstate;j++){
-   if(popbased==1)
+       cptj= (j-1)*nlstate+i;
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+       for(i2=1; i2<=nlstate;i2++)
-   else
+         for(j2=1; j2<=nlstate;j2++){
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+           cptj2= (j2-1)*nlstate+i2;
-   fprintf(ficresvij,"# Age");
+           if(cptj2 <= cptj)
-   for(i=1; i<=nlstate;i++)
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-     for(j=1; j<=nlstate;j++)
+         }
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+     }
-   fprintf(ficresvij,"\n");
+   fprintf(ficrescveij,"\n");
-   xp=vector(1,npar);
+   if(estepm < stepm){
-   dnewm=matrix(1,nlstate,1,npar);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   doldm=matrix(1,nlstate,1,nlstate);
+   }
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   else  hstepm=estepm;
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-   gpp=vector(nlstate+1,nlstate+ndeath);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   gmp=vector(nlstate+1,nlstate+ndeath);
+    * progression in between and thus overestimating or underestimating according
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   if(estepm < stepm){
+    * to compare the new estimate of Life expectancy with the same linear
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    * hypothesis. A more precise result, taking into account a more precise
-   }
+    * curvature will be obtained if estepm is as small as stepm. */
-   else  hstepm=estepm;
    /* For example we decided to compute the life expectancy with the smallest unit */
    /* 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
       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 k years */
+      and note for a fixed period like estepm months */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
-      means that if the survival funtion is printed every two years of age and if
+      means that if the survival funtion is printed only each two years of age and if
       you sum them up and add 1 year (area under the trapezoids) you won't get the same
       results. So we changed our mind and took the option of the best precision.
    */
    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   /* nhstepm age range expressed in number of stepm */
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   agelim=AGESUP;
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-     gp=matrix(0,nhstepm,1,nlstate);
+   /* if (stepm >= YEARM) hstepm=1;*/
-     gm=matrix(0,nhstepm,1,nlstate);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     for(theta=1; theta <=npar; theta++){
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-       }
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   for (age=bage; age<=fage; age ++){
-       if (popbased==1) {
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-         if(mobilav ==0){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-           for(i=1; i<=nlstate;i++)
+     /* if (stepm >= YEARM) hstepm=1;*/
-             prlim[i][i]=probs[(int)age][i][ij];
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+     /* If stepm=6 months */
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-         }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+     /* Computing  Variances of health expectancies */
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+        decrease memory allocation */
-         }
+     for(theta=1; theta <=npar; theta++){
-       }
+       for(i=1; i<=npar; i++){
-       /* This for computing probability of death (h=1 means
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-          computed over hstepm matrices product = hstepm*stepm months)
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-          as a weighted average of prlim.
+       }
-       */
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+       for(j=1; j<= nlstate; j++){
-       }
+         for(i=1; i<=nlstate; i++){
-       /* end probability of death */
+           for(h=0; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+         }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       if (popbased==1) {
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-         if(mobilav ==0){
+         for(h=0; h<=nhstepm-1; h++){
-           for(i=1; i<=nlstate;i++)
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-             prlim[i][i]=probs[(int)age][i][ij];
+         }
-         }else{ /* mobilav */
+     }/* End theta */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+     for(h=0; h<=nhstepm-1; h++)
-       }
+       for(j=1; j<=nlstate*nlstate;j++)
+         for(theta=1; theta <=npar; theta++)
-       for(j=1; j<= nlstate; j++){
+           trgradg[h][j][theta]=gradg[h][theta][j];
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-         }
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-       }
+         varhe[ij][ji][(int)age] =0.;
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+      printf("%d|",(int)age);fflush(stdout);
-          as a weighted average of prlim.
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       */
+      for(h=0;h<=nhstepm-1;h++){
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for(k=0;k<=nhstepm-1;k++){
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-       }
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-       /* end probability of death */
+           for(ji=1;ji<=nlstate*nlstate;ji++)
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-       for(j=1; j<= nlstate; j++) /* vareij */
+       }
-         for(h=0; h<=nhstepm; h++){
+     }
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         }
+     /* Computing expectancies */
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+     for(i=1; i<=nlstate;i++)
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+       for(j=1; j<=nlstate;j++)
-       }
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-     } /* End theta */
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+         }
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
+     fprintf(ficresstdeij,"%3.0f",age );
-         for(theta=1; theta <=npar; theta++)
+     for(i=1; i<=nlstate;i++){
-           trgradg[h][j][theta]=gradg[h][theta][j];
+       eip=0.;
+       vip=0.;
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(j=1; j<=nlstate;j++){
-       for(theta=1; theta <=npar; theta++)
+         eip += eij[i][j][(int)age];
-         trgradgp[j][theta]=gradgp[theta][j];
+         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]) );
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       }
-     for(i=1;i<=nlstate;i++)
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-       for(j=1;j<=nlstate;j++)
+     }
-         vareij[i][j][(int)age] =0.;
+     fprintf(ficresstdeij,"\n");
-     for(h=0;h<=nhstepm;h++){
+     fprintf(ficrescveij,"%3.0f",age );
-       for(k=0;k<=nhstepm;k++){
+     for(i=1; i<=nlstate;i++)
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+       for(j=1; j<=nlstate;j++){
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+         cptj= (j-1)*nlstate+i;
-         for(i=1;i<=nlstate;i++)
+         for(i2=1; i2<=nlstate;i2++)
-           for(j=1;j<=nlstate;j++)
+           for(j2=1; j2<=nlstate;j2++){
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+             cptj2= (j2-1)*nlstate+i2;
-       }
+             if(cptj2 <= cptj)
-     }
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
-     /* pptj */
+       }
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+     fprintf(ficrescveij,"\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++)
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-         varppt[j][i]=doldmp[j][i];
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-     /* end ppptj */
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-     /*  x centered again */
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
-     if (popbased==1) {
+   fprintf(ficlog,"\n");
-       if(mobilav ==0){
-         for(i=1; i<=nlstate;i++)
+   free_vector(xm,1,npar);
-           prlim[i][i]=probs[(int)age][i][ij];
+   free_vector(xp,1,npar);
-       }else{ /* mobilav */
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-         for(i=1; i<=nlstate;i++)
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-       }
+ }
-     }
+ /************ Variance ******************/
-     /* This for computing probability of death (h=1 means
+ 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[])
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+ {
-        as a weighted average of prlim.
+   /* Variance of health expectancies */
-     */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   /* double **newm;*/
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   double **dnewm,**doldm;
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   double **dnewmp,**doldmp;
-     }
+   int i, j, nhstepm, hstepm, h, nstepm ;
-     /* end probability of death */
+   int k, cptcode;
+   double *xp;
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+   double **gp, **gm;  /* for var eij */
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   double ***gradg, ***trgradg; /*for var eij */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   double **gradgp, **trgradgp; /* for var p point j */
-       for(i=1; i<=nlstate;i++){
+   double *gpp, *gmp; /* for var p point j */
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-       }
+   double ***p3mat;
-     }
+   double age,agelim, hf;
-     fprintf(ficresprobmorprev,"\n");
+   double ***mobaverage;
+   int theta;
-     fprintf(ficresvij,"%.0f ",age );
+   char digit[4];
-     for(i=1; i<=nlstate;i++)
+   char digitp[25];
-       for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+   char fileresprobmorprev[FILENAMELENGTH];
-       }
-     fprintf(ficresvij,"\n");
+   if(popbased==1){
-     free_matrix(gp,0,nhstepm,1,nlstate);
+     if(mobilav!=0)
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       strcpy(digitp,"-populbased-mobilav-");
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     else strcpy(digitp,"-populbased-nomobil-");
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   }
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   else
-   } /* End age */
+     strcpy(digitp,"-stablbased-");
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) {
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+     }
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+   }
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+   strcpy(fileresprobmorprev,"prmorprev");
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+   sprintf(digit,"%-d",ij);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   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);
+   strcat(fileresprobmorprev,fileres);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
- */
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   }
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   free_matrix(dnewm,1,nlstate,1,npar);
+   pstamp(ficresprobmorprev);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   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);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   fclose(ficresprobmorprev);
+     for(i=1; i<=nlstate;i++)
-   fflush(ficgp);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   fflush(fichtm);
+   }
- }  /* end varevsij */
+   fprintf(ficresprobmorprev,"\n");
+   fprintf(ficgp,"\n# Routine varevsij");
- /************ Variance of prevlim ******************/
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+   fprintf(fichtm,"\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);
-   /* Variance of prevalence limit */
+ /*   } */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   double **newm;
+   pstamp(ficresvij);
-   double **dnewm,**doldm;
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   int i, j, nhstepm, hstepm;
+   if(popbased==1)
-   int k, cptcode;
+     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);
-   double *xp;
+   else
-   double *gp, *gm;
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   double **gradg, **trgradg;
+   fprintf(ficresvij,"# Age");
-   double age,agelim;
+   for(i=1; i<=nlstate;i++)
-   int theta;
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   pstamp(ficresvpl);
+   fprintf(ficresvij,"\n");
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   xp=vector(1,npar);
-   for(i=1; i<=nlstate;i++)
+   dnewm=matrix(1,nlstate,1,npar);
-       fprintf(ficresvpl," %1d-%1d",i,i);
+   doldm=matrix(1,nlstate,1,nlstate);
-   fprintf(ficresvpl,"\n");
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   doldm=matrix(1,nlstate,1,nlstate);
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-   hstepm=1*YEARM; /* Every year of age */
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+   if(estepm < stepm){
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   }
-     if (stepm >= YEARM) hstepm=1;
+   else  hstepm=estepm;
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     gradg=matrix(1,npar,1,nlstate);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     gp=vector(1,nlstate);
+      nhstepm is the number of hstepm from age to agelim
-     gm=vector(1,nlstate);
+      nstepm is the number of stepm from age to agelin.
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-     for(theta=1; theta <=npar; theta++){
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+      survival function given by stepm (the optimization length). Unfortunately it
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+      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
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      results. So we changed our mind and took the option of the best precision.
-       for(i=1;i<=nlstate;i++)
+   */
-         gp[i] = prlim[i][i];
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim = AGESUP;
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     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);
-         gm[i] = prlim[i][i];
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+     gp=matrix(0,nhstepm,1,nlstate);
-       for(i=1;i<=nlstate;i++)
+     gm=matrix(0,nhstepm,1,nlstate);
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-     } /* End theta */
+     for(theta=1; theta <=npar; theta++){
-     trgradg =matrix(1,nlstate,1,npar);
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     for(j=1; j<=nlstate;j++)
+       }
-       for(theta=1; theta <=npar; theta++)
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         trgradg[j][theta]=gradg[theta][j];
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-     for(i=1;i<=nlstate;i++)
+       if (popbased==1) {
-       varpl[i][(int)age] =0.;
+         if(mobilav ==0){
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+           for(i=1; i<=nlstate;i++)
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+             prlim[i][i]=probs[(int)age][i][ij];
-     for(i=1;i<=nlstate;i++)
+         }else{ /* mobilav */
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-     fprintf(ficresvpl,"%.0f ",age );
+         }
-     for(i=1; i<=nlstate;i++)
+       }
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-     fprintf(ficresvpl,"\n");
+       for(j=1; j<= nlstate; j++){
-     free_vector(gp,1,nlstate);
+         for(h=0; h<=nhstepm; h++){
-     free_vector(gm,1,nlstate);
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-     free_matrix(gradg,1,npar,1,nlstate);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-     free_matrix(trgradg,1,nlstate,1,npar);
+         }
-   } /* End age */
+       }
+       /* This for computing probability of death (h=1 means
-   free_vector(xp,1,npar);
+          computed over hstepm matrices product = hstepm*stepm months)
-   free_matrix(doldm,1,nlstate,1,npar);
+          as a weighted average of prlim.
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
- }
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
- /************ Variance of one-step probabilities  ******************/
+       }
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+       /* end probability of death */
- {
-   int i, j=0,  i1, k1, l1, t, tj;
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-   int k2, l2, j1,  z1;
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   int k=0,l, cptcode;
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-   int first=1, first1;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+       if (popbased==1) {
-   double *xp;
+         if(mobilav ==0){
-   double *gp, *gm;
+           for(i=1; i<=nlstate;i++)
-   double **gradg, **trgradg;
+             prlim[i][i]=probs[(int)age][i][ij];
-   double **mu;
+         }else{ /* mobilav */
-   double age,agelim, cov[NCOVMAX];
+           for(i=1; i<=nlstate;i++)
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-   int theta;
+         }
-   char fileresprob[FILENAMELENGTH];
+       }
-   char fileresprobcov[FILENAMELENGTH];
-   char fileresprobcor[FILENAMELENGTH];
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+         for(h=0; h<=nhstepm; h++){
-   double ***varpij;
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   strcpy(fileresprob,"prob");
+         }
-   strcat(fileresprob,fileres);
+       }
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+       /* This for computing probability of death (h=1 means
-     printf("Problem with resultfile: %s\n", fileresprob);
+          computed over hstepm matrices product = hstepm*stepm months)
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+          as a weighted average of prlim.
-   }
+       */
-   strcpy(fileresprobcov,"probcov");
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   strcat(fileresprobcov,fileres);
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+       }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+       /* end probability of death */
-   }
-   strcpy(fileresprobcor,"probcor");
+       for(j=1; j<= nlstate; j++) /* vareij */
-   strcat(fileresprobcor,fileres);
+         for(h=0; h<=nhstepm; h++){
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+         }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+       }
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+     } /* End theta */
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+     for(h=0; h<=nhstepm; h++) /* veij */
-   fprintf(ficresprob,"# Age");
+       for(j=1; j<=nlstate;j++)
-   pstamp(ficresprobcov);
+         for(theta=1; theta <=npar; theta++)
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   fprintf(ficresprobcov,"# Age");
-   pstamp(ficresprobcor);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+       for(theta=1; theta <=npar; theta++)
-   fprintf(ficresprobcor,"# Age");
+         trgradgp[j][theta]=gradgp[theta][j];
-   for(i=1; i<=nlstate;i++)
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     for(j=1; j<=(nlstate+ndeath);j++){
+     for(i=1;i<=nlstate;i++)
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       for(j=1;j<=nlstate;j++)
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+         vareij[i][j][(int)age] =0.;
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+     for(h=0;h<=nhstepm;h++){
-  /* fprintf(ficresprob,"\n");
+       for(k=0;k<=nhstepm;k++){
-   fprintf(ficresprobcov,"\n");
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-   fprintf(ficresprobcor,"\n");
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-  */
+         for(i=1;i<=nlstate;i++)
-  xp=vector(1,npar);
+           for(j=1;j<=nlstate;j++)
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+       }
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     }
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   first=1;
+     /* pptj */
-   fprintf(ficgp,"\n# Routine varprob");
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-   fprintf(fichtm,"\n");
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+         varppt[j][i]=doldmp[j][i];
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+     /* end ppptj */
-   file %s<br>\n",optionfilehtmcov);
+     /*  x centered again */
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
- and drawn. It helps understanding how is the covariance between two incidences.\
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+     if (popbased==1) {
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+       if(mobilav ==0){
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+         for(i=1; i<=nlstate;i++)
- standard deviations wide on each axis. <br>\
+           prlim[i][i]=probs[(int)age][i][ij];
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+       }else{ /* mobilav */
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+         for(i=1; i<=nlstate;i++)
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+           prlim[i][i]=mobaverage[(int)age][i][ij];
+       }
-   cov[1]=1;
+     }
-   tj=cptcoveff;
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     /* This for computing probability of death (h=1 means
-   j1=0;
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-   for(t=1; t<=tj;t++){
+        as a weighted average of prlim.
-     for(i1=1; i1<=ncodemax[t];i1++){
+     */
-       j1++;
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-       if  (cptcovn>0) {
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-         fprintf(ficresprob, "\n#********** Variable ");
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     }
-         fprintf(ficresprob, "**********\n#\n");
+     /* end probability of death */
-         fprintf(ficresprobcov, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-         fprintf(ficresprobcov, "**********\n#\n");
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-         fprintf(ficgp, "\n#********** Variable ");
+       for(i=1; i<=nlstate;i++){
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-         fprintf(ficgp, "**********\n#\n");
+       }
+     }
+     fprintf(ficresprobmorprev,"\n");
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     fprintf(ficresvij,"%.0f ",age );
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-         fprintf(ficresprobcor, "\n#********** Variable ");
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       }
-         fprintf(ficresprobcor, "**********\n#");
+     fprintf(ficresvij,"\n");
-       }
+     free_matrix(gp,0,nhstepm,1,nlstate);
+     free_matrix(gm,0,nhstepm,1,nlstate);
-       for (age=bage; age<=fage; age ++){
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-         cov[2]=age;
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-         for (k=1; k<=cptcovn;k++) {
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   } /* End age */
-         }
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-         for (k=1; k<=cptcovprod;k++)
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         for(theta=1; theta <=npar; theta++){
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-           for(i=1; i<=npar; i++)
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
-           k=0;
+ */
-           for(i=1; i<= (nlstate); i++){
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-             for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-               k=k+1;
-               gp[k]=pmmij[i][j];
+   free_vector(xp,1,npar);
-             }
+   free_matrix(doldm,1,nlstate,1,nlstate);
-           }
+   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           for(i=1; i<=npar; i++)
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   fclose(ficresprobmorprev);
-           k=0;
+   fflush(ficgp);
-           for(i=1; i<=(nlstate); i++){
+   fflush(fichtm);
-             for(j=1; j<=(nlstate+ndeath);j++){
+ }  /* end varevsij */
-               k=k+1;
-               gm[k]=pmmij[i][j];
+ /************ Variance of prevlim ******************/
-             }
+ 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[])
-           }
+ {
+   /* Variance of prevalence limit */
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+   double **newm;
-         }
+   double **dnewm,**doldm;
+   int i, j, nhstepm, hstepm;
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+   int k, cptcode;
-           for(theta=1; theta <=npar; theta++)
+   double *xp;
-             trgradg[j][theta]=gradg[theta][j];
+   double *gp, *gm;
+   double **gradg, **trgradg;
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+   double age,agelim;
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+   int theta;
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   pstamp(ficresvpl);
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   fprintf(ficresvpl,"# Age");
+   for(i=1; i<=nlstate;i++)
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+       fprintf(ficresvpl," %1d-%1d",i,i);
+   fprintf(ficresvpl,"\n");
-         k=0;
-         for(i=1; i<=(nlstate); i++){
+   xp=vector(1,npar);
-           for(j=1; j<=(nlstate+ndeath);j++){
+   dnewm=matrix(1,nlstate,1,npar);
-             k=k+1;
+   doldm=matrix(1,nlstate,1,nlstate);
-             mu[k][(int) age]=pmmij[i][j];
-           }
+   hstepm=1*YEARM; /* Every year of age */
-         }
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   agelim = AGESUP;
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-             varpij[i][j][(int)age] = doldm[i][j];
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     if (stepm >= YEARM) hstepm=1;
-         /*printf("\n%d ",(int)age);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+     gradg=matrix(1,npar,1,nlstate);
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+     gp=vector(1,nlstate);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+     gm=vector(1,nlstate);
-           }*/
+     for(theta=1; theta <=npar; theta++){
-         fprintf(ficresprob,"\n%d ",(int)age);
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+       }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+       for(i=1;i<=nlstate;i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+         gp[i] = prlim[i][i];
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+       for(i=1; i<=npar; i++) /* Computes gradient */
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-         }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         i=0;
+       for(i=1;i<=nlstate;i++)
-         for (k=1; k<=(nlstate);k++){
+         gm[i] = prlim[i][i];
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
+       for(i=1;i<=nlstate;i++)
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     } /* End theta */
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+     trgradg =matrix(1,nlstate,1,npar);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
+     for(j=1; j<=nlstate;j++)
-           }
+       for(theta=1; theta <=npar; theta++)
-         }/* end of loop for state */
+         trgradg[j][theta]=gradg[theta][j];
-       } /* end of loop for age */
+     for(i=1;i<=nlstate;i++)
-       /* Confidence intervalle of pij  */
+       varpl[i][(int)age] =0.;
-       /*
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-         fprintf(ficgp,"\nset noparametric;unset label");
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     for(i=1;i<=nlstate;i++)
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-         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(ficresvpl,"%.0f ",age );
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+     for(i=1; i<=nlstate;i++)
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-       */
+     fprintf(ficresvpl,"\n");
+     free_vector(gp,1,nlstate);
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+     free_vector(gm,1,nlstate);
-       first1=1;
+     free_matrix(gradg,1,npar,1,nlstate);
-       for (k2=1; k2<=(nlstate);k2++){
+     free_matrix(trgradg,1,nlstate,1,npar);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+   } /* End age */
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
+   free_vector(xp,1,npar);
-           for (k1=1; k1<=(nlstate);k1++){
+   free_matrix(doldm,1,nlstate,1,npar);
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+ }
-               if(i<=j) continue;
-               for (age=bage; age<=fage; age ++){
+ /************ Variance of one-step probabilities  ******************/
-                 if ((int)age %5==0){
+ 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[])
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+ {
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   int i, j=0,  i1, k1, l1, t, tj;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   int k2, l2, j1,  z1;
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+   int k=0,l, cptcode;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+   int first=1, first1, first2;
-                   c12=cv12/sqrt(v1*v2);
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-                   /* Computing eigen value of matrix of covariance */
+   double **dnewm,**doldm;
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   double *xp;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   double *gp, *gm;
-                   /* Eigen vectors */
+   double **gradg, **trgradg;
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+   double **mu;
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+   double age,agelim, cov[NCOVMAX+1];
-                   v21=(lc1-v1)/cv12*v11;
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-                   v12=-v21;
+   int theta;
-                   v22=v11;
+   char fileresprob[FILENAMELENGTH];
-                   tnalp=v21/v11;
+   char fileresprobcov[FILENAMELENGTH];
-                   if(first1==1){
+   char fileresprobcor[FILENAMELENGTH];
-                     first1=0;
+   double ***varpij;
-                     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);
-                   }
+   strcpy(fileresprob,"prob");
-                   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);
+   strcat(fileresprob,fileres);
-                   /*printf(fignu*/
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+     printf("Problem with resultfile: %s\n", fileresprob);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-                   if(first==1){
+   }
-                     first=0;
+   strcpy(fileresprobcov,"probcov");
-                     fprintf(ficgp,"\nset parametric;unset label");
+   strcat(fileresprobcov,fileres);
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+   }
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+   strcpy(fileresprobcor,"probcor");
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   strcat(fileresprobcor,fileres);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   }
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-                     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",\
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-                   }else{
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-                     first=0;
+   pstamp(ficresprob);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fprintf(ficresprob,"# Age");
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   pstamp(ficresprobcov);
-                     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",\
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   fprintf(ficresprobcov,"# Age");
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   pstamp(ficresprobcor);
-                   }/* if first */
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-                 } /* age mod 5 */
+   fprintf(ficresprobcor,"# Age");
-               } /* end loop age */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-               first=1;
+   for(i=1; i<=nlstate;i++)
-             } /*l12 */
+     for(j=1; j<=(nlstate+ndeath);j++){
-           } /* k12 */
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-         } /*l1 */
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       }/* k1 */
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     } /* loop covariates */
+     }
-   }
+  /* fprintf(ficresprob,"\n");
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   fprintf(ficresprobcov,"\n");
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   fprintf(ficresprobcor,"\n");
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+  */
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   xp=vector(1,npar);
-   free_vector(xp,1,npar);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   fclose(ficresprob);
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   fclose(ficresprobcov);
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   fclose(ficresprobcor);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   fflush(ficgp);
+   first=1;
-   fflush(fichtmcov);
+   fprintf(ficgp,"\n# Routine varprob");
- }
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   fprintf(fichtm,"\n");
- /******************* Printing html file ***********/
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-                   int lastpass, int stepm, int weightopt, char model[],\
+   file %s<br>\n",optionfilehtmcov);
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-                   int popforecast, int estepm ,\
+ and drawn. It helps understanding how is the covariance between two incidences.\
-                   double jprev1, double mprev1,double anprev1, \
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-                   double jprev2, double mprev2,double anprev2){
+   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. \
-   int jj1, k1, i1, cpt;
+ 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 \
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+ standard deviations wide on each axis. <br>\
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- </ul>");
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+   cov[1]=1;
-    fprintf(fichtm,"\
+   /* tj=cptcoveff; */
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+   tj = (int) pow(2,cptcoveff);
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-    fprintf(fichtm,"\
+   j1=0;
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+   for(j1=1; j1<=tj;j1++){
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
-    fprintf(fichtm,"\
+     /*j1++;*/
-  - (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): \
+       if  (cptcovn>0) {
-    <a href=\"%s\">%s</a> <br>\n",
+         fprintf(ficresprob, "\n#********** Variable ");
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    fprintf(fichtm,"\
+         fprintf(ficresprob, "**********\n#\n");
-  - Population projections by age and states: \
+         fprintf(ficresprobcov, "\n#********** Variable ");
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#\n");
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+         fprintf(ficgp, "\n#********** Variable ");
-  m=cptcoveff;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+         fprintf(ficgp, "**********\n#\n");
-  jj1=0;
-  for(k1=1; k1<=m;k1++){
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-    for(i1=1; i1<=ncodemax[k1];i1++){
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      jj1++;
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-      if (cptcovn > 0) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         fprintf(ficresprobcor, "\n#********** Variable ");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+         fprintf(ficresprobcor, "**********\n#");
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+       }
-      }
-      /* Pij */
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-      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> \
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-      /* Quasi-incidences */
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+       for (age=bage; age<=fage; age ++){
-  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> \
+         cov[2]=age;
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+         for (k=1; k<=cptcovn;k++) {
-        /* Period (stable) prevalence in each health state */
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-        for(cpt=1; cpt<nlstate;cpt++){
+                                                          * 1  1 1 1 1
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+                                                          * 2  2 1 1 1
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+                                                          * 3  1 2 1 1
-        }
+                                                          */
-      for(cpt=1; cpt<=nlstate;cpt++) {
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+         }
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-      }
+         for (k=1; k<=cptcovprod;k++)
-    } /* end i1 */
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-  }/* End k1 */
-  fprintf(fichtm,"</ul>");
+         for(theta=1; theta <=npar; theta++){
+           for(i=1; i<=npar; i++)
-  fprintf(fichtm,"\
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
- \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);
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+           k=0;
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+           for(i=1; i<= (nlstate); i++){
-  fprintf(fichtm,"\
+             for(j=1; j<=(nlstate+ndeath);j++){
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+               k=k+1;
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+               gp[k]=pmmij[i][j];
+             }
-  fprintf(fichtm,"\
+           }
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+           for(i=1; i<=npar; i++)
-  fprintf(fichtm,"\
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-  - 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): \
-    <a href=\"%s\">%s</a> <br>\n</li>",
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+           k=0;
-  fprintf(fichtm,"\
+           for(i=1; i<=(nlstate); i++){
-  - (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(j=1; j<=(nlstate+ndeath);j++){
-    <a href=\"%s\">%s</a> <br>\n</li>",
+               k=k+1;
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+               gm[k]=pmmij[i][j];
-  fprintf(fichtm,"\
+             }
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+           }
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-  fprintf(fichtm,"\
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-  - 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",
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+         }
-  fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+           for(theta=1; theta <=npar; theta++)
+             trgradg[j][theta]=gradg[theta][j];
- /*  if(popforecast==1) fprintf(fichtm,"\n */
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
- /*      <br>",fileres,fileres,fileres,fileres); */
- /*  else  */
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-  fflush(fichtm);
+         k=0;
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
-  m=cptcoveff;
+             k=k+1;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+             mu[k][(int) age]=pmmij[i][j];
+           }
-  jj1=0;
+         }
-  for(k1=1; k1<=m;k1++){
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-    for(i1=1; i1<=ncodemax[k1];i1++){
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-      jj1++;
+             varpij[i][j][(int)age] = doldm[i][j];
-      if (cptcovn > 0) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         /*printf("\n%d ",(int)age);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-      }
+           }*/
-      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+         fprintf(ficresprob,"\n%d ",(int)age);
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+         fprintf(ficresprobcov,"\n%d ",(int)age);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-      }
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
- health expectancies in states (1) and (2): %s%d.png<br>\
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-    } /* end i1 */
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-  }/* End k1 */
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-  fprintf(fichtm,"</ul>");
+         }
-  fflush(fichtm);
+         i=0;
- }
+         for (k=1; k<=(nlstate);k++){
+           for (l=1; l<=(nlstate+ndeath);l++){
- /******************* Gnuplot file **************/
+             i++;
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   char dirfileres[132],optfileres[132];
+             for (j=1; j<=i;j++){
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-   int ng;
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
- /*     printf("Problem with file %s",optionfilegnuplot); */
+             }
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+           }
- /*   } */
+         }/* end of loop for state */
+       } /* end of loop for age */
-   /*#ifdef windows */
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-     /*#endif */
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   m=pow(2,cptcoveff);
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   strcpy(dirfileres,optionfilefiname);
+       /* Confidence intervalle of pij  */
-   strcpy(optfileres,"vpl");
+       /*
-  /* 1eme*/
+         fprintf(ficgp,"\nunset parametric;unset label");
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-    for (k1=1; k1<= m ; k1 ++) {
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
- set ylabel \"Probability\" \n\
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
- set ter png small\n\
+       */
- set size 0.65,0.65\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+       first1=1;first2=2;
-      for (i=1; i<= nlstate ; i ++) {
+       for (k2=1; k2<=(nlstate);k2++){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+           if(l2==k2) continue;
-      }
+           j=(k2-1)*(nlstate+ndeath)+l2;
-      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 (k1=1; k1<=(nlstate);k1++){
-      for (i=1; i<= nlstate ; i ++) {
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+               if(l1==k1) continue;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+               i=(k1-1)*(nlstate+ndeath)+l1;
-      }
+               if(i<=j) continue;
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+               for (age=bage; age<=fage; age ++){
-      for (i=1; i<= nlstate ; i ++) {
+                 if ((int)age %5==0){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-      }
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-    }
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-   }
+                   c12=cv12/sqrt(v1*v2);
-   /*2 eme*/
+                   /* Computing eigen value of matrix of covariance */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-   for (k1=1; k1<= m ; k1 ++) {
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+                   if ((lc2 <0) || (lc1 <0) ){
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+                     if(first2==1){
+                       first1=0;
-     for (i=1; i<= nlstate+1 ; 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);
-       k=2*i;
+                     }
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                     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);
-       for (j=1; j<= nlstate+1 ; j ++) {
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                     /* lc2=fabs(lc2); */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   }
-       }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+                   /* Eigen vectors */
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-       for (j=1; j<= nlstate+1 ; j ++) {
+                   v21=(lc1-v1)/cv12*v11;
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                   v12=-v21;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   v22=v11;
-       }
+                   tnalp=v21/v11;
-       fprintf(ficgp,"\" t\"\" w l 0,");
+                   if(first1==1){
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                     first1=0;
-       for (j=1; j<= nlstate+1 ; j ++) {
+                     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);
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                   }
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-       }
+                   /*printf(fignu*/
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-     }
+                   if(first==1){
-   }
+                     first=0;
+                     fprintf(ficgp,"\nset parametric;unset label");
-   /*3eme*/
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-   for (k1=1; k1<= m ; k1 ++) {
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-       /*       k=2+nlstate*(2*cpt-2); */
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-       k=2+(nlstate+1)*(cpt-1);
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       fprintf(ficgp,"set ter png small\n\
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- set size 0.65,0.65\n\
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                   }else{
+                     first=0;
-       */
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-       for (i=1; i< nlstate ; i ++) {
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-         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,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-         /*      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(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-       }
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(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);
+                   }/* if first */
-     }
+                 } /* age mod 5 */
-   }
+               } /* end loop age */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   /* CV preval stable (period) */
+               first=1;
-   for (k1=1; k1<= m ; k1 ++) {
+             } /*l12 */
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+           } /* k12 */
-       k=3;
+         } /*l1 */
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       }/* k1 */
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+       /* } /* loop covariates */
- set ter png small\nset size 0.65,0.65\n\
+   }
- unset log y\n\
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-       for (i=1; i< nlstate ; i ++)
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-         fprintf(ficgp,"+$%d",k+i+1);
+   free_vector(xp,1,npar);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+   fclose(ficresprob);
+   fclose(ficresprobcov);
-       l=3+(nlstate+ndeath)*cpt;
+   fclose(ficresprobcor);
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+   fflush(ficgp);
-       for (i=1; i< nlstate ; i ++) {
+   fflush(fichtmcov);
-         l=3+(nlstate+ndeath)*cpt;
+ }
-         fprintf(ficgp,"+$%d",l+i+1);
-       }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+ /******************* Printing html file ***********/
-     }
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-   }
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-   /* proba elementaires */
+                   int popforecast, int estepm ,\
-   for(i=1,jk=1; i <=nlstate; i++){
+                   double jprev1, double mprev1,double anprev1, \
-     for(k=1; k <=(nlstate+ndeath); k++){
+                   double jprev2, double mprev2,double anprev2){
-       if (k != i) {
+   int jj1, k1, i1, cpt;
-         for(j=1; j <=ncovmodel; j++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-           jk++;
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-           fprintf(ficgp,"\n");
+ </ul>");
-         }
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-       }
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-     }
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-    }
+    fprintf(fichtm,"\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-      for(jk=1; jk <=m; jk++) {
+    fprintf(fichtm,"\
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-        if (ng==2)
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+    fprintf(fichtm,"\
-        else
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+    <a href=\"%s\">%s</a> <br>\n",
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-        i=1;
+    fprintf(fichtm,"\
-        for(k2=1; k2<=nlstate; k2++) {
+  - Population projections by age and states: \
-          k3=i;
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-          for(k=1; k<=(nlstate+ndeath); k++) {
-            if (k != k2){
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-              if(ng==2)
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+  m=pow(2,cptcoveff);
-              else
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
+  jj1=0;
-              for(j=3; j <=ncovmodel; j++) {
+  for(k1=1; k1<=m;k1++){
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+    for(i1=1; i1<=ncodemax[k1];i1++){
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+      jj1++;
-                  ij++;
+      if (cptcovn > 0) {
-                }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-                else
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-              }
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-              fprintf(ficgp,")/(1");
+      }
+      /* Pij */
-              for(k1=1; k1 <=nlstate; k1++){
+      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> \
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                ij=1;
+      /* Quasi-incidences */
-                for(j=3; j <=ncovmodel; j++){
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                    ij++;
+        /* Period (stable) prevalence in each health state */
-                  }
+        for(cpt=1; cpt<=nlstate;cpt++){
-                  else
+          fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+ <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-                }
+        }
-                fprintf(ficgp,")");
+      for(cpt=1; cpt<=nlstate;cpt++) {
-              }
+         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+ <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+      }
-              i=i+ncovmodel;
+    } /* end i1 */
-            }
+  }/* End k1 */
-          } /* end k */
+  fprintf(fichtm,"</ul>");
-        } /* end k2 */
-      } /* end jk */
-    } /* end ng */
+  fprintf(fichtm,"\
-    fflush(ficgp);
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- }  /* end gnuplot */
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- /*************** Moving average **************/
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+  fprintf(fichtm,"\
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-   int i, cpt, cptcod;
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-   int modcovmax =1;
-   int mobilavrange, mob;
+  fprintf(fichtm,"\
-   double age;
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+  fprintf(fichtm,"\
-                            a covariate has 2 modalities */
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+  fprintf(fichtm,"\
-     if(mobilav==1) mobilavrange=5; /* default */
+  - (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): \
-     else mobilavrange=mobilav;
+    <a href=\"%s\">%s</a> <br>\n</li>",
-     for (age=bage; age<=fage; age++)
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-       for (i=1; i<=nlstate;i++)
+  fprintf(fichtm,"\
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+  - 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",
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-     /* We keep the original values on the extreme ages bage, fage and for
+  fprintf(fichtm,"\
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+  - 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",
-        we use a 5 terms etc. until the borders are no more concerned.
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-     */
+  fprintf(fichtm,"\
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-         for (i=1; i<=nlstate;i++){
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+ /*      <br>",fileres,fileres,fileres,fileres); */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+ /*  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); */
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+  fflush(fichtm);
-           }
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-         }
-       }/* end age */
+  m=pow(2,cptcoveff);
-     }/* end mob */
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-   }else return -1;
-   return 0;
+  jj1=0;
- }/* End movingaverage */
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
+      jj1++;
- /************** Forecasting ******************/
+      if (cptcovn > 0) {
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   /* proj1, year, month, day of starting projection
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-      agemin, agemax range of age
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-      anproj2 year of en of projection (same day and month as proj1).
+      }
-   */
+      for(cpt=1; cpt<=nlstate;cpt++) {
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-   int *popage;
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
-   double agec; /* generic age */
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+      }
-   double *popeffectif,*popcount;
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   double ***p3mat;
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-   double ***mobaverage;
+ true period expectancies (those weighted with period prevalences are also\
-   char fileresf[FILENAMELENGTH];
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
-   agelim=AGESUP;
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+    } /* end i1 */
+  }/* End k1 */
-   strcpy(fileresf,"f");
+  fprintf(fichtm,"</ul>");
-   strcat(fileresf,fileres);
+  fflush(fichtm);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+ }
-     printf("Problem with forecast resultfile: %s\n", fileresf);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+ /******************* Gnuplot file **************/
-   }
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   char dirfileres[132],optfileres[132];
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   int ng=0;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-   if (mobilav!=0) {
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*   } */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   /*#ifdef windows */
-     }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   }
+     /*#endif */
+   m=pow(2,cptcoveff);
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (stepm<=12) stepsize=1;
+   strcpy(dirfileres,optionfilefiname);
-   if(estepm < stepm){
+   strcpy(optfileres,"vpl");
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+  /* 1eme*/
-   }
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
-   else  hstepm=estepm;
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-   hstepm=hstepm/stepm;
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-                                fractional in yp1 */
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-   anprojmean=yp;
+ set ylabel \"Probability\" \n\
-   yp2=modf((yp1*12),&yp);
+ set ter png small size 320, 240\n\
-   mprojmean=yp;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
+      for (i=1; i<= nlstate ; i ++) {
-   if(jprojmean==0) jprojmean=1;
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   if(mprojmean==0) jprojmean=1;
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-   i1=cptcoveff;
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-   if (cptcovn < 1){i1=1;}
+      for (i=1; i<= nlstate ; i ++) {
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
- /*            if (h==(int)(YEARM*yearp)){ */
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      }
-       k=k+1;
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-       fprintf(ficresf,"\n#******");
+    }
-       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]]);
+   /*2 eme*/
-       }
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
-       fprintf(ficresf,"******\n");
+   for (k1=1; k1<= m ; k1 ++) {
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-       for(j=1; j<=nlstate+ndeath;j++){
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
-         for(i=1; i<=nlstate;i++)
-           fprintf(ficresf," p%d%d",i,j);
+     for (i=1; i<= nlstate+1 ; i ++) {
-         fprintf(ficresf," p.%d",j);
+       k=2*i;
-       }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       for (j=1; j<= nlstate+1 ; j ++) {
-         fprintf(ficresf,"\n");
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-           nhstepm = nhstepm/hstepm;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (j=1; j<= nlstate+1 ; j ++) {
-           oldm=oldms;savm=savms;
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-           for (h=0; h<=nhstepm; h++){
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-             if (h*hstepm/YEARM*stepm ==yearp) {
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-               fprintf(ficresf,"\n");
+       for (j=1; j<= nlstate+1 ; j ++) {
-               for(j=1;j<=cptcoveff;j++)
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+       }
-             }
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-             for(j=1; j<=nlstate+ndeath;j++) {
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-               ppij=0.;
+     }
-               for(i=1; i<=nlstate;i++) {
+   }
-                 if (mobilav==1)
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+   /*3eme*/
-                 else {
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+   for (k1=1; k1<= m ; k1 ++) {
-                 }
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-                 if (h*hstepm/YEARM*stepm== yearp) {
+       /*       k=2+nlstate*(2*cpt-2); */
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+       k=2+(nlstate+1)*(cpt-1);
-                 }
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-               } /* end i */
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-               if (h*hstepm/YEARM*stepm==yearp) {
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-                 fprintf(ficresf," %.3f", ppij);
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-               }
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-             }/* end j */
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-           } /* end h */
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         } /* end agec */
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       } /* end yearp */
-     } /* end cptcod */
+       */
-   } /* end  cptcov */
+       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);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         /*      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);*/
-   fclose(ficresf);
+       }
- }
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+     }
- /************** 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){
+   /* CV preval stable (period) */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
-   int *popage;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-   double calagedatem, agelim, kk1, kk2;
+       k=3;
-   double *popeffectif,*popcount;
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
-   double ***p3mat,***tabpop,***tabpopprev;
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-   double ***mobaverage;
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-   char filerespop[FILENAMELENGTH];
+ set ter png small size 320, 240\n\
+ unset log y\n\
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for (i=1; i<= nlstate ; i ++){
-   agelim=AGESUP;
+         if(i==1)
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+         else
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-   strcpy(filerespop,"pop");
+         for (j=1; j<= (nlstate-1) ; j ++)
-   strcat(filerespop,fileres);
+           fprintf(ficgp,"+$%d",k+l+j);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+       } /* nlstate */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+       fprintf(ficgp,"\n");
-   }
+     } /* end cpt state*/
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   } /* end covariate */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   /* proba elementaires */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
-   if (mobilav!=0) {
+       if (k != i) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(j=1; j <=ncovmodel; j++){
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           jk++;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+           fprintf(ficgp,"\n");
-     }
+         }
-   }
+       }
+     }
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+    }
-   if (stepm<=12) stepsize=1;
+   /*goto avoid;*/
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   agelim=AGESUP;
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-   hstepm=1;
+        if (ng==2)
-   hstepm=hstepm/stepm;
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
-   if (popforecast==1) {
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-       printf("Problem with population file : %s\n",popfile);exit(0);
+        i=1;
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+        for(k2=1; k2<=nlstate; k2++) {
-     }
+          k3=i;
-     popage=ivector(0,AGESUP);
+          for(k=1; k<=(nlstate+ndeath); k++) {
-     popeffectif=vector(0,AGESUP);
+            if (k != k2){
-     popcount=vector(0,AGESUP);
+              if(ng==2)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-     i=1;
+              else
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-     imx=i;
+              for(j=3; j <=ncovmodel; j++) {
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+                /* 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]]]);*\/ */
+                /*        ij++; */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+                /* } */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+                /* else */
-       k=k+1;
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       fprintf(ficrespop,"\n#******");
+              }
-       for(j=1;j<=cptcoveff;j++) {
+              fprintf(ficgp,")/(1");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+              for(k1=1; k1 <=nlstate; k1++){
-       fprintf(ficrespop,"******\n");
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-       fprintf(ficrespop,"# Age");
+                ij=1;
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+                for(j=3; j <=ncovmodel; j++){
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+                  /* 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]]]); */
-       for (cpt=0; cpt<=0;cpt++) {
+                  /*   ij++; */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+                  /* } */
+                  /* else */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+                }
-           nhstepm = nhstepm/hstepm;
+                fprintf(ficgp,")");
+              }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-           oldm=oldms;savm=savms;
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+              i=i+ncovmodel;
+            }
-           for (h=0; h<=nhstepm; h++){
+          } /* end k */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+        } /* end k2 */
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+      } /* end jk */
-             }
+    } /* end ng */
-             for(j=1; j<=nlstate+ndeath;j++) {
+  avoid:
-               kk1=0.;kk2=0;
+    fflush(ficgp);
-               for(i=1; i<=nlstate;i++) {
+ }  /* end gnuplot */
-                 if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
+ /*************** Moving average **************/
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-                 }
-               }
+   int i, cpt, cptcod;
-               if (h==(int)(calagedatem+12*cpt)){
+   int modcovmax =1;
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+   int mobilavrange, mob;
-                   /*fprintf(ficrespop," %.3f", kk1);
+   double age;
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-             }
+                            a covariate has 2 modalities */
-             for(i=1; i<=nlstate;i++){
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-               kk1=0.;
-                 for(j=1; j<=nlstate;j++){
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+     if(mobilav==1) mobilavrange=5; /* default */
-                 }
+     else mobilavrange=mobilav;
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+     for (age=bage; age<=fage; age++)
-             }
+       for (i=1; i<=nlstate;i++)
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+     /* We keep the original values on the extreme ages bage, fage and for
-           }
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+        we use a 5 terms etc. until the borders are no more concerned.
-         }
+     */
-       }
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-   /******/
+         for (i=1; i<=nlstate;i++){
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-           nhstepm = nhstepm/hstepm;
+               }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           }
-           oldm=oldms;savm=savms;
+         }
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       }/* end age */
-           for (h=0; h<=nhstepm; h++){
+     }/* end mob */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   }else return -1;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   return 0;
-             }
+ }/* End movingaverage */
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
+ /************** Forecasting ******************/
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ 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
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+      agemin, agemax range of age
-             }
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-           }
+      anproj2 year of en of projection (same day and month as proj1).
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   */
-         }
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-       }
+   int *popage;
-    }
+   double agec; /* generic age */
-   }
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double ***p3mat;
+   double ***mobaverage;
-   if (popforecast==1) {
+   char fileresf[FILENAMELENGTH];
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
+   agelim=AGESUP;
-     free_vector(popcount,0,AGESUP);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   strcpy(fileresf,"f");
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   strcat(fileresf,fileres);
-   fclose(ficrespop);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
- } /* End of popforecast */
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
- int fileappend(FILE *fichier, char *optionfich)
+   }
- {
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-     printf("Problem with file: %s\n", optionfich);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     return (0);
-   }
+   if (mobilav!=0) {
-   fflush(fichier);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   return (1);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- }
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
- /**************** function prwizard **********************/
+   }
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
- {
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   /* Wizard to print covariance matrix template */
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   char ca[32], cb[32], cc[32];
+   }
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   else  hstepm=estepm;
-   int numlinepar;
+   hstepm=hstepm/stepm;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+                                fractional in yp1 */
-   for(i=1; i <=nlstate; i++){
+   anprojmean=yp;
-     jj=0;
+   yp2=modf((yp1*12),&yp);
-     for(j=1; j <=nlstate+ndeath; j++){
+   mprojmean=yp;
-       if(j==i) continue;
+   yp1=modf((yp2*30.5),&yp);
-       jj++;
+   jprojmean=yp;
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+   if(jprojmean==0) jprojmean=1;
-       printf("%1d%1d",i,j);
+   if(mprojmean==0) jprojmean=1;
-       fprintf(ficparo,"%1d%1d",i,j);
-       for(k=1; k<=ncovmodel;k++){
+   i1=cptcoveff;
-         /*        printf(" %lf",param[i][j][k]); */
+   if (cptcovn < 1){i1=1;}
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-         printf(" 0.");
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-         fprintf(ficparo," 0.");
-       }
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-       printf("\n");
-       fprintf(ficparo,"\n");
+ /*            if (h==(int)(YEARM*yearp)){ */
-     }
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-   }
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-   printf("# Scales (for hessian or gradient estimation)\n");
+       k=k+1;
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+       fprintf(ficresf,"\n#******");
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       for(j=1;j<=cptcoveff;j++) {
-   for(i=1; i <=nlstate; i++){
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     jj=0;
+       }
-     for(j=1; j <=nlstate+ndeath; j++){
+       fprintf(ficresf,"******\n");
-       if(j==i) continue;
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       jj++;
+       for(j=1; j<=nlstate+ndeath;j++){
-       fprintf(ficparo,"%1d%1d",i,j);
+         for(i=1; i<=nlstate;i++)
-       printf("%1d%1d",i,j);
+           fprintf(ficresf," p%d%d",i,j);
-       fflush(stdout);
+         fprintf(ficresf," p.%d",j);
-       for(k=1; k<=ncovmodel;k++){
+       }
-         /*      printf(" %le",delti3[i][j][k]); */
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         fprintf(ficresf,"\n");
-         printf(" 0.");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-         fprintf(ficparo," 0.");
-       }
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-       numlinepar++;
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-       printf("\n");
+           nhstepm = nhstepm/hstepm;
-       fprintf(ficparo,"\n");
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     }
+           oldm=oldms;savm=savms;
-   }
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-   printf("# Covariance matrix\n");
- /* # 121 Var(a12)\n\ */
+           for (h=0; h<=nhstepm; h++){
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+             if (h*hstepm/YEARM*stepm ==yearp) {
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+               fprintf(ficresf,"\n");
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+               for(j=1;j<=cptcoveff;j++)
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
- /* # 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" */
+             for(j=1; j<=nlstate+ndeath;j++) {
-   fflush(stdout);
+               ppij=0.;
-   fprintf(ficparo,"# Covariance matrix\n");
+               for(i=1; i<=nlstate;i++) {
-   /* # 121 Var(a12)\n\ */
+                 if (mobilav==1)
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-   /* #   ...\n\ */
+                 else {
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 }
-   for(itimes=1;itimes<=2;itimes++){
+                 if (h*hstepm/YEARM*stepm== yearp) {
-     jj=0;
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-     for(i=1; i <=nlstate; i++){
+                 }
-       for(j=1; j <=nlstate+ndeath; j++){
+               } /* end i */
-         if(j==i) continue;
+               if (h*hstepm/YEARM*stepm==yearp) {
-         for(k=1; k<=ncovmodel;k++){
+                 fprintf(ficresf," %.3f", ppij);
-           jj++;
+               }
-           ca[0]= k+'a'-1;ca[1]='\0';
+             }/* end j */
-           if(itimes==1){
+           } /* end h */
-             printf("#%1d%1d%d",i,j,k);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+         } /* end agec */
-           }else{
+       } /* end yearp */
-             printf("%1d%1d%d",i,j,k);
+     } /* end cptcod */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+   } /* end  cptcov */
-             /*  printf(" %.5le",matcov[i][j]); */
-           }
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-           ll=0;
-           for(li=1;li <=nlstate; li++){
+   fclose(ficresf);
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+ }
-               if(lj==li) continue;
-               for(lk=1;lk<=ncovmodel;lk++){
+ /************** Forecasting *****not tested NB*************/
-                 ll++;
+ 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(ll<=jj){
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-                   if(ll<jj){
+   int *popage;
-                     if(itimes==1){
+   double calagedatem, agelim, kk1, kk2;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   double *popeffectif,*popcount;
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   double ***p3mat,***tabpop,***tabpopprev;
-                     }else{
+   double ***mobaverage;
-                       printf(" 0.");
+   char filerespop[FILENAMELENGTH];
-                       fprintf(ficparo," 0.");
-                     }
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                   }else{
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                     if(itimes==1){
+   agelim=AGESUP;
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-                     }else{
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-                       printf(" 0.");
-                       fprintf(ficparo," 0.");
-                     }
+   strcpy(filerespop,"pop");
-                   }
+   strcat(filerespop,fileres);
-                 }
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-               } /* end lk */
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-             } /* end lj */
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-           } /* end li */
+   }
-           printf("\n");
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-           fprintf(ficparo,"\n");
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-           numlinepar++;
-         } /* end k*/
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-       } /*end j */
-     } /* end i */
+   if (mobilav!=0) {
-   } /* end itimes */
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- } /* end of prwizard */
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- /******************* Gompertz Likelihood ******************************/
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
- double gompertz(double x[])
+     }
- {
+   }
-   double A,B,L=0.0,sump=0.,num=0.;
-   int i,n=0; /* n is the size of the sample */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   for (i=0;i<=imx-1 ; i++) {
-     sump=sump+weight[i];
+   agelim=AGESUP;
-     /*    sump=sump+1;*/
-     num=num+1;
+   hstepm=1;
-   }
+   hstepm=hstepm/stepm;
+   if (popforecast==1) {
-   /* for (i=0; i<=imx; i++)
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-      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("Problem with population file : %s\n",popfile);exit(0);
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   for (i=1;i<=imx ; i++)
+     }
-     {
+     popage=ivector(0,AGESUP);
-       if (cens[i] == 1 && wav[i]>1)
+     popeffectif=vector(0,AGESUP);
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+     popcount=vector(0,AGESUP);
-       if (cens[i] == 0 && wav[i]>1)
+     i=1;
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+     imx=i;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-       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]);*/
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-       }
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-     }
+       k=k+1;
+       fprintf(ficrespop,"\n#******");
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   return -2*L*num/sump;
+       }
- }
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
- /******************* Printing html file ***********/
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,  double p[],double **matcov,double agemortsup){
+       for (cpt=0; cpt<=0;cpt++) {
-   int i,k;
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   for (i=1;i<=2;i++)
+           nhstepm = nhstepm/hstepm;
-     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\">");
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(fichtm,"</ul>");
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+           for (h=0; h<=nhstepm; h++){
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+             if (h==(int) (calagedatem+YEARM*cpt)) {
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*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]);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
+               for(i=1; i<=nlstate;i++) {
-   fflush(fichtm);
+                 if (mobilav==1)
- }
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 else {
- /******************* Gnuplot file **************/
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+                 }
+               }
-   char dirfileres[132],optfileres[132];
+               if (h==(int)(calagedatem+12*cpt)){
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   int ng;
+                   /*fprintf(ficrespop," %.3f", kk1);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
-   /*#ifdef windows */
+             }
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+             for(i=1; i<=nlstate;i++){
-     /*#endif */
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   strcpy(dirfileres,optionfilefiname);
+                 }
-   strcpy(optfileres,"vpl");
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+             }
-   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");
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   fprintf(ficgp, "set size 0.65,0.65\n");
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- }
+         }
+       }
+   /******/
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
- /***********************************************/
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- /**************** Main Program *****************/
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- /***********************************************/
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
- int main(int argc, char *argv[])
- {
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+           oldm=oldms;savm=savms;
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-   int linei, month, year,iout;
+           for (h=0; h<=nhstepm; h++){
-   int jj, ll, li, lj, lk, imk;
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   int numlinepar=0; /* Current linenumber of parameter file */
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-   int itimes;
+             }
-   int NDIM=2;
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   char ca[32], cb[32], cc[32];
+               for(i=1; i<=nlstate;i++) {
-   char dummy[]="                         ";
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-   /*  FILE *fichtm; *//* Html File */
+               }
-   /* FILE *ficgp;*/ /*Gnuplot File */
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   struct stat info;
+             }
-   double agedeb, agefin,hf;
+           }
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   double fret;
+       }
-   double **xi,tmp,delta;
+    }
+   }
-   double dum; /* Dummy variable */
-   double ***p3mat;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double ***mobaverage;
-   int *indx;
+   if (popforecast==1) {
-   char line[MAXLINE], linepar[MAXLINE];
+     free_ivector(popage,0,AGESUP);
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+     free_vector(popeffectif,0,AGESUP);
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     free_vector(popcount,0,AGESUP);
-   char **bp, *tok, *val; /* pathtot */
+   }
-   int firstobs=1, lastobs=10;
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int sdeb, sfin; /* Status at beginning and end */
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   int c,  h , cpt,l;
+   fclose(ficrespop);
-   int ju,jl, mi;
+ } /* End of popforecast */
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+ int fileappend(FILE *fichier, char *optionfich)
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+ {
-   int mobilav=0,popforecast=0;
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-   int hstepm, nhstepm;
+     printf("Problem with file: %s\n", optionfich);
-   int agemortsup;
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-   float  sumlpop=0.;
+     return (0);
-   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;
+   fflush(fichier);
+   return (1);
-   double bage, fage, age, agelim, agebase;
+ }
-   double ftolpl=FTOL;
-   double **prlim;
-   double *severity;
+ /**************** function prwizard **********************/
-   double ***param; /* Matrix of parameters */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   double  *p;
+ {
-   double **matcov; /* Matrix of covariance */
-   double ***delti3; /* Scale */
+   /* Wizard to print covariance matrix template */
-   double *delti; /* Scale */
-   double ***eij, ***vareij;
+   char ca[32], cb[32], cc[32];
-   double **varpl; /* Variances of prevalence limits by age */
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   double *epj, vepp;
+   int numlinepar;
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   double **ximort;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   for(i=1; i <=nlstate; i++){
-   int *dcwave;
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-   char z[1]="c", occ;
+       if(j==i) continue;
+       jj++;
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   char  *strt, strtend[80];
+       printf("%1d%1d",i,j);
-   char *stratrunc;
+       fprintf(ficparo,"%1d%1d",i,j);
-   int lstra;
+       for(k=1; k<=ncovmodel;k++){
+         /*        printf(" %lf",param[i][j][k]); */
-   long total_usecs;
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
- /*   setlocale (LC_ALL, ""); */
+         fprintf(ficparo," 0.");
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       }
- /*   textdomain (PACKAGE); */
+       printf("\n");
- /*   setlocale (LC_CTYPE, ""); */
+       fprintf(ficparo,"\n");
- /*   setlocale (LC_MESSAGES, ""); */
+     }
+   }
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   printf("# Scales (for hessian or gradient estimation)\n");
-   (void) gettimeofday(&start_time,&tzp);
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   curr_time=start_time;
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   tm = *localtime(&start_time.tv_sec);
+   for(i=1; i <=nlstate; i++){
-   tmg = *gmtime(&start_time.tv_sec);
+     jj=0;
-   strcpy(strstart,asctime(&tm));
+     for(j=1; j <=nlstate+ndeath; j++){
+       if(j==i) continue;
- /*  printf("Localtime (at start)=%s",strstart); */
+       jj++;
- /*  tp.tv_sec = tp.tv_sec +86400; */
+       fprintf(ficparo,"%1d%1d",i,j);
- /*  tm = *localtime(&start_time.tv_sec); */
+       printf("%1d%1d",i,j);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+       fflush(stdout);
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       for(k=1; k<=ncovmodel;k++){
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+         /*      printf(" %le",delti3[i][j][k]); */
- /*   tp.tv_sec = mktime(&tmg); */
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
- /*   strt=asctime(&tmg); */
+         printf(" 0.");
- /*   printf("Time(after) =%s",strstart);  */
+         fprintf(ficparo," 0.");
- /*  (void) time (&time_value);
+       }
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+       numlinepar++;
- *  tm = *localtime(&time_value);
+       printf("\n");
- *  strstart=asctime(&tm);
+       fprintf(ficparo,"\n");
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+     }
- */
+   }
+   printf("# Covariance matrix\n");
-   nberr=0; /* Number of errors and warnings */
+ /* # 121 Var(a12)\n\ */
-   nbwarn=0;
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   getcwd(pathcd, size);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-   printf("\n%s\n%s",version,fullversion);
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-   if(argc <=1){
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     printf("\nEnter the parameter file name: ");
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-     fgets(pathr,FILENAMELENGTH,stdin);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-     i=strlen(pathr);
+   fflush(stdout);
-     if(pathr[i-1]=='\n')
+   fprintf(ficparo,"# Covariance matrix\n");
-       pathr[i-1]='\0';
+   /* # 121 Var(a12)\n\ */
-    for (tok = pathr; tok != NULL; ){
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-       printf("Pathr |%s|\n",pathr);
+   /* #   ...\n\ */
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-       printf("val= |%s| pathr=%s\n",val,pathr);
-       strcpy (pathtot, val);
+   for(itimes=1;itimes<=2;itimes++){
-       if(pathr[0] == '\0') break; /* Dirty */
+     jj=0;
-     }
+     for(i=1; i <=nlstate; i++){
-   }
+       for(j=1; j <=nlstate+ndeath; j++){
-   else{
+         if(j==i) continue;
-     strcpy(pathtot,argv[1]);
+         for(k=1; k<=ncovmodel;k++){
-   }
+           jj++;
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+           ca[0]= k+'a'-1;ca[1]='\0';
-   /*cygwin_split_path(pathtot,path,optionfile);
+           if(itimes==1){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+             printf("#%1d%1d%d",i,j,k);
-   /* cutv(path,optionfile,pathtot,'\\');*/
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
-   /* Split argv[0], imach program to get pathimach */
+             printf("%1d%1d%d",i,j,k);
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+             /*  printf(" %.5le",matcov[i][j]); */
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+           }
-  /*   strcpy(pathimach,argv[0]); */
+           ll=0;
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+           for(li=1;li <=nlstate; li++){
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+               if(lj==li) continue;
-   chdir(path); /* Can be a relative path */
+               for(lk=1;lk<=ncovmodel;lk++){
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+                 ll++;
-     printf("Current directory %s!\n",pathcd);
+                 if(ll<=jj){
-   strcpy(command,"mkdir ");
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-   strcat(command,optionfilefiname);
+                   if(ll<jj){
-   if((outcmd=system(command)) != 0){
+                     if(itimes==1){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     /* fclose(ficlog); */
+                     }else{
- /*     exit(1); */
+                       printf(" 0.");
-   }
+                       fprintf(ficparo," 0.");
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+                     }
- /*     perror("mkdir"); */
+                   }else{
- /*   } */
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-   /*-------- arguments in the command line --------*/
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+                     }else{
-   /* Log file */
+                       printf(" 0.");
-   strcat(filelog, optionfilefiname);
+                       fprintf(ficparo," 0.");
-   strcat(filelog,".log");    /* */
+                     }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+                   }
-     printf("Problem with logfile %s\n",filelog);
+                 }
-     goto end;
+               } /* end lk */
-   }
+             } /* end lj */
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+           } /* end li */
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+           printf("\n");
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+           fprintf(ficparo,"\n");
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+           numlinepar++;
-  path=%s \n\
+         } /* end k*/
-  optionfile=%s\n\
+       } /*end j */
-  optionfilext=%s\n\
+     } /* end i */
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   } /* end itimes */
-   printf("Local time (at start):%s",strstart);
+ } /* end of prwizard */
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+ /******************* Gompertz Likelihood ******************************/
-   fflush(ficlog);
+ double gompertz(double x[])
- /*   (void) gettimeofday(&curr_time,&tzp); */
+ {
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
-   /* */
-   strcpy(fileres,"r");
+   for (i=0;i<=imx-1 ; i++) {
-   strcat(fileres, optionfilefiname);
+     sump=sump+weight[i];
-   strcat(fileres,".txt");    /* Other files have txt extension */
+     /*    sump=sump+1;*/
+     num=num+1;
-   /*---------arguments file --------*/
+   }
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
+   /* for (i=0; i<=imx; i++)
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+      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]);*/
-     fflush(ficlog);
-     goto end;
+   for (i=1;i<=imx ; i++)
-   }
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   strcpy(filereso,"o");
+       if (cens[i] == 0 && wav[i]>1)
-   strcat(filereso,fileres);
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-     printf("Problem with Output resultfile: %s\n", filereso);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     fflush(ficlog);
+       if (wav[i] > 1 ) { /* ??? */
-     goto end;
+         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]);*/
+       }
-   /* Reads comments: lines beginning with '#' */
+     }
-   numlinepar=0;
-   while((c=getc(ficpar))=='#' && c!= EOF){
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
+   return -2*L*num/sump;
-     numlinepar++;
+ }
-     puts(line);
-     fputs(line,ficparo);
+ #ifdef GSL
-     fputs(line,ficlog);
+ /******************* Gompertz_f Likelihood ******************************/
-   }
+ double gompertz_f(const gsl_vector *v, void *params)
-   ungetc(c,ficpar);
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   double *x= (double *) v->data;
-   numlinepar++;
+   int i,n=0; /* n is the size of the sample */
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   for (i=0;i<=imx-1 ; i++) {
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+     sump=sump+weight[i];
-   fflush(ficlog);
+     /*    sump=sump+1;*/
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     num=num+1;
-     ungetc(c,ficpar);
+   }
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
-     puts(line);
+   /* for (i=0; i<=imx; i++)
-     fputs(line,ficparo);
+      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]);*/
-     fputs(line,ficlog);
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-   }
+   for (i=1;i<=imx ; i++)
-   ungetc(c,ficpar);
+     {
+       if (cens[i] == 1 && wav[i]>1)
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-   covar=matrix(0,NCOVMAX,1,n);
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       if (cens[i] == 0 && wav[i]>1)
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+       if (wav[i] > 1 ) { /* ??? */
+         LL=LL+A*weight[i];
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+         /*      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]);*/
-   delti=delti3[1][1];
+       }
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+     }
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-     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);
+   return -2*LL*num/sump;
-     fclose (ficparo);
+ }
-     fclose (ficlog);
+ #endif
-     goto end;
-     exit(0);
+ /******************* Printing html file ***********/
-   }
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   else if(mle==-3) {
+                   int lastpass, int stepm, int weightopt, char model[],\
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+                   int imx,  double p[],double **matcov,double agemortsup){
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+   int i,k;
-     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);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     matcov=matrix(1,npar,1,npar);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   }
+   for (i=1;i<=2;i++)
-   else{
+     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]));
-     /* Read guess parameters */
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     /* Reads comments: lines beginning with '#' */
+   fprintf(fichtm,"</ul>");
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-       fgets(line, MAXLINE, ficpar);
-       numlinepar++;
+  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>");
-       puts(line);
-       fputs(line,ficparo);
+  for (k=agegomp;k<(agemortsup-2);k++)
-       fputs(line,ficlog);
+    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]);
-     }
-     ungetc(c,ficpar);
+   fflush(fichtm);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ }
-     for(i=1; i <=nlstate; i++){
-       j=0;
+ /******************* Gnuplot file **************/
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-         if(jj==i) continue;
-         j++;
+   char dirfileres[132],optfileres[132];
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-         if ((i1 != i) && (j1 != j)){
+   int ng;
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
- It might be a problem of design; if ncovcol and the model are correct\n \
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+   /*#ifdef windows */
-           exit(1);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-         }
+     /*#endif */
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         if(mle==1)
-           printf("%1d%1d",i,j);
+   strcpy(dirfileres,optionfilefiname);
-         fprintf(ficlog,"%1d%1d",i,j);
+   strcpy(optfileres,"vpl");
-         for(k=1; k<=ncovmodel;k++){
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-           fscanf(ficpar," %lf",&param[i][j][k]);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-           if(mle==1){
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-             printf(" %lf",param[i][j][k]);
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
-             fprintf(ficlog," %lf",param[i][j][k]);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-           }
-           else
+ }
-             fprintf(ficlog," %lf",param[i][j][k]);
-           fprintf(ficparo," %lf",param[i][j][k]);
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-         }
+ {
-         fscanf(ficpar,"\n");
-         numlinepar++;
+   /*-------- data file ----------*/
-         if(mle==1)
+   FILE *fic;
-           printf("\n");
+   char dummy[]="                         ";
-         fprintf(ficlog,"\n");
+   int i, j, n;
-         fprintf(ficparo,"\n");
+   int linei, month, year,iout;
-       }
+   char line[MAXLINE], linetmp[MAXLINE];
-     }
+   char stra[80], strb[80];
-     fflush(ficlog);
+   char *stratrunc;
+   int lstra;
-     p=param[1][1];
-     /* Reads comments: lines beginning with '#' */
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-       ungetc(c,ficpar);
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       fgets(line, MAXLINE, ficpar);
+   }
-       numlinepar++;
-       puts(line);
+   i=1;
-       fputs(line,ficparo);
+   linei=0;
-       fputs(line,ficlog);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     }
+     linei=linei+1;
-     ungetc(c,ficpar);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+       if(line[j] == '\t')
-     for(i=1; i <=nlstate; i++){
+         line[j] = ' ';
-       for(j=1; j <=nlstate+ndeath-1; j++){
+     }
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-         if ((i1-i)*(j1-j)!=0){
+       ;
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+     };
-           exit(1);
+     line[j+1]=0;  /* Trims blanks at end of line */
-         }
+     if(line[0]=='#'){
-         printf("%1d%1d",i,j);
+       fprintf(ficlog,"Comment line\n%s\n",line);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       printf("Comment line\n%s\n",line);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       continue;
-         for(k=1; k<=ncovmodel;k++){
+     }
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-           printf(" %le",delti3[i][j][k]);
+     for (j=0; line[j]!='\0';j++){
-           fprintf(ficparo," %le",delti3[i][j][k]);
+       line[j]=linetmp[j];
-           fprintf(ficlog," %le",delti3[i][j][k]);
+     }
-         }
-         fscanf(ficpar,"\n");
-         numlinepar++;
+     for (j=maxwav;j>=1;j--){
-         printf("\n");
+       cutv(stra, strb, line, ' ');
-         fprintf(ficparo,"\n");
+       if(strb[0]=='.') { /* Missing status */
-         fprintf(ficlog,"\n");
+         lval=-1;
-       }
+       }else{
-     }
+         errno=0;
-     fflush(ficlog);
+         lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     delti=delti3[1][1];
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           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);
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+           return 1;
+         }
-     /* Reads comments: lines beginning with '#' */
+       }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       s[j][i]=lval;
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+       strcpy(line,stra);
-       numlinepar++;
+       cutv(stra, strb,line,' ');
-       puts(line);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       fputs(line,ficparo);
+       }
-       fputs(line,ficlog);
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     }
+         month=99;
-     ungetc(c,ficpar);
+         year=9999;
+       }else{
-     matcov=matrix(1,npar,1,npar);
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     for(i=1; i <=npar; i++){
+         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);
-       fscanf(ficpar,"%s",&str);
+         return 1;
-       if(mle==1)
+       }
-         printf("%s",str);
+       anint[j][i]= (double) year;
-       fprintf(ficlog,"%s",str);
+       mint[j][i]= (double)month;
-       fprintf(ficparo,"%s",str);
+       strcpy(line,stra);
-       for(j=1; j <=i; j++){
+     } /* ENd Waves */
-         fscanf(ficpar," %le",&matcov[i][j]);
-         if(mle==1){
+     cutv(stra, strb,line,' ');
-           printf(" %.5le",matcov[i][j]);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-         }
+     }
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-         fprintf(ficparo," %.5le",matcov[i][j]);
+       month=99;
-       }
+       year=9999;
-       fscanf(ficpar,"\n");
+     }else{
-       numlinepar++;
+       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);
-       if(mle==1)
+         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);
-         printf("\n");
+         return 1;
-       fprintf(ficlog,"\n");
+     }
-       fprintf(ficparo,"\n");
+     andc[i]=(double) year;
-     }
+     moisdc[i]=(double) month;
-     for(i=1; i <=npar; i++)
+     strcpy(line,stra);
-       for(j=i+1;j<=npar;j++)
-         matcov[i][j]=matcov[j][i];
+     cutv(stra, strb,line,' ');
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     if(mle==1)
+     }
-       printf("\n");
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-     fprintf(ficlog,"\n");
+       month=99;
+       year=9999;
-     fflush(ficlog);
+     }else{
+       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);
-     /*-------- Rewriting parameter file ----------*/
+       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);
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+         return 1;
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     }
-     strcat(rfileres,".");    /* */
+     if (year==9999) {
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+       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((ficres =fopen(rfileres,"w"))==NULL) {
+       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);
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+         return 1;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
      }
-     fprintf(ficres,"#%s\n",version);
+     annais[i]=(double)(year);
-   }    /* End of mle != -3 */
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+     cutv(stra, strb,line,' ');
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+     errno=0;
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+     dval=strtod(strb,&endptr);
-   }
+     if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-   n= lastobs;
+       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);
-   severity = vector(1,maxwav);
+       fflush(ficlog);
-   outcome=imatrix(1,maxwav+1,1,n);
+       return 1;
-   num=lvector(1,n);
+     }
-   moisnais=vector(1,n);
+     weight[i]=dval;
-   annais=vector(1,n);
+     strcpy(line,stra);
-   moisdc=vector(1,n);
-   andc=vector(1,n);
+     for (j=ncovcol;j>=1;j--){
-   agedc=vector(1,n);
+       cutv(stra, strb,line,' ');
-   cod=ivector(1,n);
+       if(strb[0]=='.') { /* Missing status */
-   weight=vector(1,n);
+         lval=-1;
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+       }else{
-   mint=matrix(1,maxwav,1,n);
+         errno=0;
-   anint=matrix(1,maxwav,1,n);
+         lval=strtol(strb,&endptr,10);
-   s=imatrix(1,maxwav+1,1,n);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   tab=ivector(1,NCOVMAX);
+           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);
-   ncodemax=ivector(1,8);
+           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);
+           return 1;
-   i=1;
+         }
-   linei=0;
+       }
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+       if(lval <-1 || lval >1){
-     linei=linei+1;
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-       if(line[j] == '\t')
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-         line[j] = ' ';
+  For example, for multinomial values like 1, 2 and 3,\n \
-     }
+  build V1=0 V2=0 for the reference value (1),\n \
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+         V1=1 V2=0 for (2) \n \
-       ;
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     };
+  output of IMaCh is often meaningless.\n \
-     line[j+1]=0;  /* Trims blanks at end of line */
+  Exiting.\n",lval,linei, i,line,j);
-     if(line[0]=='#'){
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-       fprintf(ficlog,"Comment line\n%s\n",line);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-       printf("Comment line\n%s\n",line);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-       continue;
+  For example, for multinomial values like 1, 2 and 3,\n \
-     }
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
-     for (j=maxwav;j>=1;j--){
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       cutv(stra, strb,line,' ');
+  output of IMaCh is often meaningless.\n \
-       errno=0;
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       lval=strtol(strb,&endptr,10);
+         return 1;
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+       }
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       covar[j][i]=(double)(lval);
-         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);
+       strcpy(line,stra);
-         exit(1);
+     }
-       }
+     lstra=strlen(stra);
-       s[j][i]=lval;
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       strcpy(line,stra);
+       stratrunc = &(stra[lstra-9]);
-       cutv(stra, strb,line,' ');
+       num[i]=atol(stratrunc);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
-       }
+     else
-       else  if(iout=sscanf(strb,"%s.") != 0){
+       num[i]=atol(stra);
-         month=99;
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-         year=9999;
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-       }else{
-         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);
+     i=i+1;
-         exit(1);
+   } /* End loop reading  data */
-       }
-       anint[j][i]= (double) year;
+   *imax=i-1; /* Number of individuals */
-       mint[j][i]= (double)month;
+   fclose(fic);
-       strcpy(line,stra);
-     } /* ENd Waves */
+   return (0);
+   endread:
-     cutv(stra, strb,line,' ');
+     printf("Exiting readdata: ");
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     fclose(fic);
-     }
+     return (1);
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-       month=99;
-       year=9999;
-     }else{
+ }
-       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);
+ void removespace(char *str) {
-       exit(1);
+   char *p1 = str, *p2 = str;
-     }
+   do
-     andc[i]=(double) year;
+     while (*p2 == ' ')
-     moisdc[i]=(double) month;
+       p2++;
-     strcpy(line,stra);
+   while (*p1++ = *p2++);
+ }
-     cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-     }
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-     else  if(iout=sscanf(strb,"%s.") != 0){
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-       month=99;
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-       year=9999;
+    * - cptcovage number of covariates with age*products =2
-     }else{
+    * - cptcovs number of simple covariates
-       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);
+    * - 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
-       exit(1);
+    *     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
-     annais[i]=(double)(year);
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-     moisnais[i]=(double)(month);
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-     strcpy(line,stra);
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+  */
-     cutv(stra, strb,line,' ');
+ {
-     errno=0;
+   int i, j, k, ks;
-     dval=strtod(strb,&endptr);
+   int i1, j1, k1, k2;
-     if( strb[0]=='\0' || (*endptr != '\0')){
+   char modelsav[80];
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-       exit(1);
-     }
+   /*removespace(model);*/
-     weight[i]=dval;
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-     strcpy(line,stra);
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-     for (j=ncovcol;j>=1;j--){
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-       cutv(stra, strb,line,' ');
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-       errno=0;
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-       lval=strtol(strb,&endptr,10);
+                   /* including age products which are counted in cptcovage.
-       if( strb[0]=='\0' || (*endptr != '\0')){
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-         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);
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-         exit(1);
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-       }
+     strcpy(modelsav,model);
-       if(lval <-1 || lval >1){
+     if (strstr(model,"AGE") !=0){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+       return 1;
-  For example, for multinomial values like 1, 2 and 3,\n \
+     }
-  build V1=0 V2=0 for the reference value (1),\n \
+     if (strstr(model,"v") !=0){
-         V1=1 V2=0 for (2) \n \
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-  output of IMaCh is often meaningless.\n \
+       return 1;
-  Exiting.\n",lval,linei, i,line,j);
+     }
-         exit(1);
-       }
+     /*   Design
-       covar[j][i]=(double)(lval);
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-       strcpy(line,stra);
+      *  <          ncovcol=8                >
-     }
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-     lstra=strlen(stra);
+      *   k=  1    2      3       4     5       6      7        8
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-       stratrunc = &(stra[lstra-9]);
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-       num[i]=atol(stratrunc);
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-     }
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-     else
+      *  Tage[++cptcovage]=k
-       num[i]=atol(stra);
+      *       if products, new covar are created after ncovcol with k1
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-       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;}*/
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+      *  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
-     i=i+1;
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-   } /* End loop reading  data */
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-   fclose(fic);
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-   /* printf("ii=%d", ij);
+      *  <          ncovcol=8                >
-      scanf("%d",i);*/
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-   imx=i-1; /* Number of individuals */
+      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-   /* for (i=1; i<=imx; i++){
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+      * p Tprod[1]@2={                         6, 5}
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-     }*/
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-    /*  for (i=1; i<=imx; i++){
+      *How to reorganize?
-      if (s[4][i]==9)  s[4][i]=-1;
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-      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]));}*/
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-   /* for (i=1; i<=imx; i++) */
+      * Struct []
+      */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
+     /* This loop fills the array Tvar from the string 'model'.*/
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-   /* Calculation of the number of parameters from char model */
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-   Tprod=ivector(1,15);
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-   Tvaraff=ivector(1,15);
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-   Tvard=imatrix(1,15,1,2);
+     /*  k=1 Tvar[1]=2 (from V2) */
-   Tage=ivector(1,15);
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-     j=0, j1=0, k1=1, k2=1;
+     /*  } */
-     j=nbocc(model,'+'); /* j=Number of '+' */
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     /*
-     cptcovn=j+1;
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-     cptcovprod=j1; /*Number of products */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
-     strcpy(modelsav,model);
+     cptcovage=0;
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-       printf("Error. Non available option model=%s ",model);
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-       goto end;
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-     }
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       /*scanf("%d",i);*/
-     /* This loop fills the array Tvar from the string 'model'.*/
+       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 */
-     for(i=(j+1); i>=1;i--){
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+           /* covar is not filled and then is empty */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+           cptcovprod--;
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-       /*scanf("%d",i);*/
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-       if (strchr(strb,'*')) {  /* Model includes a product */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+           /*printf("stre=%s ", stre);*/
-           cptcovprod--;
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cutv(strb,stre,strd,'V');
+           cptcovprod--;
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+           cutl(stre,strb,strc,'V');
-           cptcovage++;
+           Tvar[k]=atoi(stre);
-             Tage[cptcovage]=i;
+           cptcovage++;
-             /*printf("stre=%s ", stre);*/
+           Tage[cptcovage]=k;
-         }
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-           cptcovprod--;
+           cptcovn++;
-           cutv(strb,stre,strc,'V');
+           cptcovprodnoage++;k1++;
-           Tvar[i]=atoi(stre);
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-           cptcovage++;
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-           Tage[cptcovage]=i;
+                                   because this model-covariate is a construction we invent a new column
-         }
+                                   ncovcol + k1
-         else {  /* Age is not in the model */
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-           Tvar[i]=ncovcol+k1;
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-           Tprod[k1]=i;
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-           Tvard[k1][1]=atoi(strc); /* m*/
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-           Tvard[k1][2]=atoi(stre); /* n */
+           k2=k2+2;
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-           for (k=1; k<=lastobs;k++)
+           for (i=1; i<=lastobs;i++){
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+             /* Computes the new covariate which is a product of
-           k1++;
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-           k2=k2+2;
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-         }
+           }
-       }
+         } /* End age is not in the model */
-       else { /* no more sum */
+       } /* End if model includes a product */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       else { /* no more sum */
-        /*  scanf("%d",i);*/
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       cutv(strd,strc,strb,'V');
+        /*  scanf("%d",i);*/
-       Tvar[i]=atoi(strc);
+         cutl(strd,strc,strb,'V');
-       }
+         ks++; /**< Number of simple covariates */
-       strcpy(modelsav,stra);
+         cptcovn++;
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         Tvar[k]=atoi(strd);
-         scanf("%d",i);*/
+       }
-     } /* end of loop + */
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   } /* end model */
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+         scanf("%d",i);*/
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+     } /* end of loop + */
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   } /* end model */
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-   printf("cptcovprod=%d ", cptcovprod);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   scanf("%d ",i);*/
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-     /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+   scanf("%d ",i);*/
-     for(i=1;i<=n;i++) weight[i]=1.0;
-   }
-     /*-calculation of age at interview from date of interview and age at death -*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-   agev=matrix(1,maxwav,1,imx);
+   endread:
+     printf("Exiting decodemodel: ");
-   for (i=1; i<=imx; i++) {
+     return (1);
-     for(m=2; (m<= maxwav); m++) {
+ }
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-         anint[m][i]=9999;
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-         s[m][i]=-1;
+ {
-       }
+   int i, m;
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         nberr++;
+   for (i=1; i<=imx; i++) {
-         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);
+     for(m=2; (m<= maxwav); m++) {
-         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);
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-         s[m][i]=-1;
+         anint[m][i]=9999;
-       }
+         s[m][i]=-1;
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+       }
-         nberr++;
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         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]);
+         *nberr++;
-         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]);
+         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);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
-       }
+         s[m][i]=-1;
-     }
+       }
-   }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         *nberr++;
-   for (i=1; i<=imx; i++)  {
+         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]);
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[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] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+       }
-         if (s[m][i] >= nlstate+1) {
+     }
-           if(agedc[i]>0)
+   }
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-               agev[m][i]=agedc[i];
+   for (i=1; i<=imx; i++)  {
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-             else {
+     for(m=firstpass; (m<= lastpass); m++){
-               if ((int)andc[i]!=9999){
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-                 nbwarn++;
+         if (s[m][i] >= nlstate+1) {
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+           if(agedc[i]>0)
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-                 agev[m][i]=-1;
+               agev[m][i]=agedc[i];
-               }
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-             }
+             else {
-         }
+               if ((int)andc[i]!=9999){
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                 nbwarn++;
-                                  years but with the precision of a month */
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+                 agev[m][i]=-1;
-             agev[m][i]=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);*/
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-           }
+                                  years but with the precision of a month */
-           else if(agev[m][i] >agemax){
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-             agemax=agev[m][i];
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+             agev[m][i]=1;
-           }
+           else if(agev[m][i] < *agemin){
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+             *agemin=agev[m][i];
-           /*     agev[m][i] = age[i]+2*m;*/
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-         }
+           }
-         else { /* =9 */
+           else if(agev[m][i] >*agemax){
-           agev[m][i]=1;
+             *agemax=agev[m][i];
-           s[m][i]=-1;
+             /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
-         }
+           }
-       }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-       else /*= 0 Unknown */
+           /*     agev[m][i] = age[i]+2*m;*/
-         agev[m][i]=1;
+         }
-     }
+         else { /* =9 */
+           agev[m][i]=1;
-   }
+           s[m][i]=-1;
-   for (i=1; i<=imx; i++)  {
+         }
-     for(m=firstpass; (m<=lastpass); m++){
+       }
-       if (s[m][i] > (nlstate+ndeath)) {
+       else /*= 0 Unknown */
-         nberr++;
+         agev[m][i]=1;
-         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++)  {
-     }
+     for(m=firstpass; (m<=lastpass); m++){
-   }
+       if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
-   /*for (i=1; i<=imx; 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 (m=firstpass; (m<lastpass); m++){
+         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);
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+         return 1;
- }
+       }
+     }
- }*/
+   }
+   /*for (i=1; i<=imx; i++){
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   for (m=firstpass; (m<lastpass); m++){
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ }
-   agegomp=(int)agemin;
-   free_vector(severity,1,maxwav);
+ }*/
-   free_imatrix(outcome,1,maxwav+1,1,n);
-   free_vector(moisnais,1,n);
-   free_vector(annais,1,n);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-   /* free_matrix(mint,1,maxwav,1,n);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-      free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
+   return (0);
-   free_vector(andc,1,n);
+   endread:
+     printf("Exiting calandcheckages: ");
+     return (1);
-   wav=ivector(1,imx);
+ }
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+ /***********************************************/
+ /**************** Main Program *****************/
-   /* Concatenates waves */
+ /***********************************************/
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+ int main(int argc, char *argv[])
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+ {
+ #ifdef GSL
-   Tcode=ivector(1,100);
+   const gsl_multimin_fminimizer_type *T;
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   size_t iteri = 0, it;
-   ncodemax[1]=1;
+   int rval = GSL_CONTINUE;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   int status = GSL_SUCCESS;
+   double ssval;
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+ #endif
-                                  the estimations*/
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   h=0;
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   m=pow(2,cptcoveff);
+   int linei, month, year,iout;
+   int jj, ll, li, lj, lk, imk;
-   for(k=1;k<=cptcoveff; k++){
+   int numlinepar=0; /* Current linenumber of parameter file */
-     for(i=1; i <=(m/pow(2,k));i++){
+   int itimes;
-       for(j=1; j <= ncodemax[k]; j++){
+   int NDIM=2;
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   int vpopbased=0;
-           h++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   char ca[32], cb[32], cc[32];
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   /*  FILE *fichtm; *//* Html File */
-         }
+   /* FILE *ficgp;*/ /*Gnuplot File */
-       }
+   struct stat info;
-     }
+   double agedeb, agefin,hf;
-   }
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-      codtab[1][2]=1;codtab[2][2]=2; */
+   double fret;
-   /* for(i=1; i <=m ;i++){
+   double **xi,tmp,delta;
-      for(k=1; k <=cptcovn; k++){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   double dum; /* Dummy variable */
-      }
+   double ***p3mat;
-      printf("\n");
+   double ***mobaverage;
-      }
+   int *indx;
-      scanf("%d",i);*/
+   char line[MAXLINE], linepar[MAXLINE];
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   /*------------ gnuplot -------------*/
+   char pathr[MAXLINE], pathimach[MAXLINE];
-   strcpy(optionfilegnuplot,optionfilefiname);
+   char **bp, *tok, *val; /* pathtot */
-   if(mle==-3)
+   int firstobs=1, lastobs=10;
-     strcat(optionfilegnuplot,"-mort");
+   int sdeb, sfin; /* Status at beginning and end */
-   strcat(optionfilegnuplot,".gp");
+   int c,  h , cpt,l;
+   int ju,jl, mi;
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   int i1,j1, jk,aa,bb, stepsize, ij;
-     printf("Problem with file %s",optionfilegnuplot);
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-   }
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   else{
+   int mobilav=0,popforecast=0;
-     fprintf(ficgp,"\n# %s\n", version);
+   int hstepm, nhstepm;
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   int agemortsup;
-     fprintf(ficgp,"set missing 'NaNq'\n");
+   float  sumlpop=0.;
-   }
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-   /*  fclose(ficgp);*/
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-   /*--------- index.htm --------*/
+   double bage, fage, age, agelim, agebase;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   double ftolpl=FTOL;
-   if(mle==-3)
+   double **prlim;
-     strcat(optionfilehtm,"-mort");
+   double ***param; /* Matrix of parameters */
-   strcat(optionfilehtm,".htm");
+   double  *p;
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+   double **matcov; /* Matrix of covariance */
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+   double ***delti3; /* Scale */
-   }
+   double *delti; /* Scale */
+   double ***eij, ***vareij;
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   double **varpl; /* Variances of prevalence limits by age */
-   strcat(optionfilehtmcov,"-cov.htm");
+   double *epj, vepp;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+   double kk1, kk2;
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   }
+   double **ximort;
-   else{
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   int *dcwave;
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+   char z[1]="c", occ;
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-   }
+   /*char  *strt;*/
+   char strtend[80];
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+   long total_usecs;
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
- \n\
+ /*   setlocale (LC_ALL, ""); */
- <hr  size=\"2\" color=\"#EC5E5E\">\
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-  <ul><li><h4>Parameter files</h4>\n\
+ /*   textdomain (PACKAGE); */
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+ /*   setlocale (LC_CTYPE, ""); */
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+ /*   setlocale (LC_MESSAGES, ""); */
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-  - Date and time at start: %s</ul>\n",\
+   rstart_time = time(NULL);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+   /*  (void) gettimeofday(&start_time,&tzp);*/
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+   start_time = *localtime(&rstart_time);
-           fileres,fileres,\
+   curr_time=start_time;
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+   /*tml = *localtime(&start_time.tm_sec);*/
-   fflush(fichtm);
+   /* strcpy(strstart,asctime(&tml)); */
+   strcpy(strstart,asctime(&start_time));
-   strcpy(pathr,path);
-   strcat(pathr,optionfilefiname);
+ /*  printf("Localtime (at start)=%s",strstart); */
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
+ /*  tm = *localtime(&start_time.tm_sec); */
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-      and prints on file fileres'p'. */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /*   tp.tm_sec = mktime(&tmg); */
-   fprintf(fichtm,"\n");
+ /*   strt=asctime(&tmg); */
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ /*   printf("Time(after) =%s",strstart);  */
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ /*  (void) time (&time_value);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-           imx,agemin,agemax,jmin,jmax,jmean);
+ *  tm = *localtime(&time_value);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ *  strstart=asctime(&tm);
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
+   getcwd(pathcd, size);
-   /* 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] */
+   printf("\n%s\n%s",version,fullversion);
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   if(argc <=1){
+     printf("\nEnter the parameter file name: ");
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+     fgets(pathr,FILENAMELENGTH,stdin);
+     i=strlen(pathr);
-   if (mle==-3){
+     if(pathr[i-1]=='\n')
-     ximort=matrix(1,NDIM,1,NDIM);
+       pathr[i-1]='\0';
-     cens=ivector(1,n);
+     i=strlen(pathr);
-     ageexmed=vector(1,n);
+     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
-     agecens=vector(1,n);
+       pathr[i-1]='\0';
-     dcwave=ivector(1,n);
+    for (tok = pathr; tok != NULL; ){
+       printf("Pathr |%s|\n",pathr);
-     for (i=1; i<=imx; i++){
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-       dcwave[i]=-1;
+       printf("val= |%s| pathr=%s\n",val,pathr);
-       for (m=firstpass; m<=lastpass; m++)
+       strcpy (pathtot, val);
-         if (s[m][i]>nlstate) {
+       if(pathr[0] == '\0') break; /* Dirty */
-           dcwave[i]=m;
+     }
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+   }
-           break;
+   else{
-         }
+     strcpy(pathtot,argv[1]);
-     }
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-     for (i=1; i<=imx; i++) {
+   /*cygwin_split_path(pathtot,path,optionfile);
-       if (wav[i]>0){
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-         ageexmed[i]=agev[mw[1][i]][i];
+   /* cutv(path,optionfile,pathtot,'\\');*/
-         j=wav[i];
-         agecens[i]=1.;
+   /* Split argv[0], imach program to get pathimach */
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-         if (ageexmed[i]> 1 && wav[i] > 0){
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           agecens[i]=agev[mw[j][i]][i];
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           cens[i]= 1;
+  /*   strcpy(pathimach,argv[0]); */
-         }else if (ageexmed[i]< 1)
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-           cens[i]= -1;
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           cens[i]=0 ;
+   chdir(path); /* Can be a relative path */
-       }
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-       else cens[i]=-1;
+     printf("Current directory %s!\n",pathcd);
-     }
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
-     for (i=1;i<=NDIM;i++) {
+   if((outcmd=system(command)) != 0){
-       for (j=1;j<=NDIM;j++)
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     }
+     /* fclose(ficlog); */
+ /*     exit(1); */
-     p[1]=0.0268; p[NDIM]=0.083;
+   }
-     /*printf("%lf %lf", p[1], p[2]);*/
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
+ /*     perror("mkdir"); */
+ /*   } */
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     strcpy(filerespow,"pow-mort");
+   /*-------- arguments in the command line --------*/
-     strcat(filerespow,fileres);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   /* Log file */
-       printf("Problem with resultfile: %s\n", filerespow);
+   strcat(filelog, optionfilefiname);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   strcat(filelog,".log");    /* */
-     }
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     printf("Problem with logfile %s\n",filelog);
-     /*  for (i=1;i<=nlstate;i++)
+     goto end;
-         for(j=1;j<=nlstate+ndeath;j++)
+   }
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     */
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-     fprintf(ficrespow,"\n");
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+  path=%s \n\
-     fclose(ficrespow);
+  optionfile=%s\n\
+  optionfilext=%s\n\
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     for(i=1; i <=NDIM; i++)
+   printf("Local time (at start):%s",strstart);
-       for(j=i+1;j<=NDIM;j++)
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-         matcov[i][j]=matcov[j][i];
+   fflush(ficlog);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     printf("\nCovariance matrix\n ");
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
-     for(i=1; i <=NDIM; i++) {
-       for(j=1;j<=NDIM;j++){
+   /* */
-         printf("%f ",matcov[i][j]);
+   strcpy(fileres,"r");
-       }
+   strcat(fileres, optionfilefiname);
-       printf("\n ");
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     }
+   /*---------arguments file --------*/
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-     for (i=1;i<=NDIM;i++)
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
+     fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
-     lsurv=vector(1,AGESUP);
+     fflush(ficlog);
-     lpop=vector(1,AGESUP);
+     /* goto end; */
-     tpop=vector(1,AGESUP);
+     exit(70);
-     lsurv[agegomp]=100000;
+   }
-     for (k=agegomp;k<=AGESUP;k++) {
-       agemortsup=k;
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+   strcpy(filereso,"o");
-     }
+   strcat(filereso,fileres);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-     for (k=agegomp;k<agemortsup;k++)
+     printf("Problem with Output resultfile: %s\n", filereso);
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
-     for (k=agegomp;k<agemortsup;k++){
+     goto end;
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   }
-       sumlpop=sumlpop+lpop[k];
-     }
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
-     tpop[agegomp]=sumlpop;
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     for (k=agegomp;k<(agemortsup-3);k++){
+     ungetc(c,ficpar);
-       /*  tpop[k+1]=2;*/
+     fgets(line, MAXLINE, ficpar);
-       tpop[k+1]=tpop[k]-lpop[k];
+     numlinepar++;
-     }
+     fputs(line,stdout);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   }
-     for (k=agegomp;k<(agemortsup-2);k++)
+   ungetc(c,ficpar);
-       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]);
+   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);
+   numlinepar++;
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   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);
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   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);
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+   fflush(ficlog);
-                      stepm, weightopt,\
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                      model,imx,p,matcov,agemortsup);
+     ungetc(c,ficpar);
+     fgets(line, MAXLINE, ficpar);
-     free_vector(lsurv,1,AGESUP);
+     numlinepar++;
-     free_vector(lpop,1,AGESUP);
+     fputs(line, stdout);
-     free_vector(tpop,1,AGESUP);
+     //puts(line);
-   } /* Endof if mle==-3 */
+     fputs(line,ficparo);
+     fputs(line,ficlog);
-   else{ /* For mle >=1 */
+   }
+   ungetc(c,ficpar);
-     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++)
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-       printf(" %d %8.5f",k,p[k]);
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-     printf("\n");
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-     globpr=1; /* to print the contributions */
+      v1+v2*age+v2*v3 makes cptcovn = 3
-     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);
+   if (strlen(model)>1)
-     for (k=1; k<=npar;k++)
+     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(" %d %8.5f",k,p[k]);
+   else
-     printf("\n");
+     ncovmodel=2;
-     if(mle>=1){ /* Could be 1 or 2 */
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-     }
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-     /*--------- results files --------------*/
+     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(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(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fflush(stdout);
+     fclose (ficlog);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     goto end;
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   }
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1,jk=1; i <=nlstate; i++){
+   delti=delti3[1][1];
-       for(k=1; k <=(nlstate+ndeath); k++){
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-         if (k != i) {
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-           printf("%d%d ",i,k);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-           fprintf(ficlog,"%d%d ",i,k);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-           fprintf(ficres,"%1d%1d ",i,k);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-           for(j=1; j <=ncovmodel; j++){
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-             printf("%lf ",p[jk]);
+     fclose (ficparo);
-             fprintf(ficlog,"%lf ",p[jk]);
+     fclose (ficlog);
-             fprintf(ficres,"%lf ",p[jk]);
+     goto end;
-             jk++;
+     exit(0);
-           }
+   }
-           printf("\n");
+   else if(mle==-3) {
-           fprintf(ficlog,"\n");
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-           fprintf(ficres,"\n");
+     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);
-       }
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     }
+     matcov=matrix(1,npar,1,npar);
-     if(mle!=0){
+   }
-       /* Computing hessian and covariance matrix */
+   else{
-       ftolhess=ftol; /* Usually correct */
+     /* Read guessed parameters */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+     /* Reads comments: lines beginning with '#' */
-     }
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+       ungetc(c,ficpar);
-     printf("# Scales (for hessian or gradient estimation)\n");
+       fgets(line, MAXLINE, ficpar);
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+       numlinepar++;
-     for(i=1,jk=1; i <=nlstate; i++){
+       fputs(line,stdout);
-       for(j=1; j <=nlstate+ndeath; j++){
+       fputs(line,ficparo);
-         if (j!=i) {
+       fputs(line,ficlog);
-           fprintf(ficres,"%1d%1d",i,j);
+     }
-           printf("%1d%1d",i,j);
+     ungetc(c,ficpar);
-           fprintf(ficlog,"%1d%1d",i,j);
-           for(k=1; k<=ncovmodel;k++){
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-             printf(" %.5e",delti[jk]);
+     for(i=1; i <=nlstate; i++){
-             fprintf(ficlog," %.5e",delti[jk]);
+       j=0;
-             fprintf(ficres," %.5e",delti[jk]);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-             jk++;
+         if(jj==i) continue;
-           }
+         j++;
-           printf("\n");
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-           fprintf(ficlog,"\n");
+         if ((i1 != i) && (j1 != j)){
-           fprintf(ficres,"\n");
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-         }
+ It might be a problem of design; if ncovcol and the model are correct\n \
-       }
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-     }
+           exit(1);
+         }
-     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     if(mle>=1)
+         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");
+           printf("%1d%1d",i,j);
-     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,"%1d%1d",i,j);
-     /* # 121 Var(a12)\n\ */
+         for(k=1; k<=ncovmodel;k++){
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           fscanf(ficpar," %lf",&param[i][j][k]);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+           if(mle==1){
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+             printf(" %lf",param[i][j][k]);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+             fprintf(ficlog," %lf",param[i][j][k]);
-     /* # 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
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
-     /* Just to have a covariance matrix which will be more understandable
+         fscanf(ficpar,"\n");
-        even is we still don't want to manage dictionary of variables
+         numlinepar++;
-     */
+         if(mle==1)
-     for(itimes=1;itimes<=2;itimes++){
+           printf("\n");
-       jj=0;
+         fprintf(ficlog,"\n");
-       for(i=1; i <=nlstate; i++){
+         fprintf(ficparo,"\n");
-         for(j=1; j <=nlstate+ndeath; j++){
+       }
-           if(j==i) continue;
+     }
-           for(k=1; k<=ncovmodel;k++){
+     fflush(ficlog);
-             jj++;
-             ca[0]= k+'a'-1;ca[1]='\0';
+     /* Reads scales values */
-             if(itimes==1){
+     p=param[1][1];
-               if(mle>=1)
-                 printf("#%1d%1d%d",i,j,k);
+     /* Reads comments: lines beginning with '#' */
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+       ungetc(c,ficpar);
-             }else{
+       fgets(line, MAXLINE, ficpar);
-               if(mle>=1)
+       numlinepar++;
-                 printf("%1d%1d%d",i,j,k);
+       fputs(line,stdout);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+       fputs(line,ficparo);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+       fputs(line,ficlog);
-             }
+     }
-             ll=0;
+     ungetc(c,ficpar);
-             for(li=1;li <=nlstate; li++){
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+     for(i=1; i <=nlstate; i++){
-                 if(lj==li) continue;
+       for(j=1; j <=nlstate+ndeath-1; j++){
-                 for(lk=1;lk<=ncovmodel;lk++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-                   ll++;
+         if ((i1-i)*(j1-j)!=0){
-                   if(ll<=jj){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+           exit(1);
-                     if(ll<jj){
+         }
-                       if(itimes==1){
+         printf("%1d%1d",i,j);
-                         if(mle>=1)
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         for(k=1; k<=ncovmodel;k++){
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-                       }else{
+           printf(" %le",delti3[i][j][k]);
-                         if(mle>=1)
+           fprintf(ficparo," %le",delti3[i][j][k]);
-                           printf(" %.5e",matcov[jj][ll]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+         }
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+         fscanf(ficpar,"\n");
-                       }
+         numlinepar++;
-                     }else{
+         printf("\n");
-                       if(itimes==1){
+         fprintf(ficparo,"\n");
-                         if(mle>=1)
+         fprintf(ficlog,"\n");
-                           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);
+     fflush(ficlog);
-                       }else{
-                         if(mle>=1)
+     /* Reads covariance matrix */
-                           printf(" %.5e",matcov[jj][ll]);
+     delti=delti3[1][1];
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-                     }
-                   }
+     /* Reads comments: lines beginning with '#' */
-                 } /* end lk */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-               } /* end lj */
+       ungetc(c,ficpar);
-             } /* end li */
+       fgets(line, MAXLINE, ficpar);
-             if(mle>=1)
+       numlinepar++;
-               printf("\n");
+       fputs(line,stdout);
-             fprintf(ficlog,"\n");
+       fputs(line,ficparo);
-             fprintf(ficres,"\n");
+       fputs(line,ficlog);
-             numlinepar++;
+     }
-           } /* end k*/
+     ungetc(c,ficpar);
-         } /*end j */
-       } /* end i */
+     matcov=matrix(1,npar,1,npar);
-     } /* end itimes */
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-     fflush(ficlog);
-     fflush(ficres);
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",str);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       if(mle==1)
-       ungetc(c,ficpar);
+         printf("%s",str);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"%s",str);
-       puts(line);
+       fprintf(ficparo,"%s",str);
-       fputs(line,ficparo);
+       for(j=1; j <=i; j++){
-     }
+         fscanf(ficpar," %le",&matcov[i][j]);
-     ungetc(c,ficpar);
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
-     estepm=0;
+         }
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+         fprintf(ficparo," %.5le",matcov[i][j]);
-     if (fage <= 2) {
+       }
-       bage = ageminpar;
+       fscanf(ficpar,"\n");
-       fage = agemaxpar;
+       numlinepar++;
-     }
+       if(mle==1)
+         printf("\n");
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+       fprintf(ficlog,"\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       fprintf(ficparo,"\n");
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     }
+     for(i=1; i <=npar; i++)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       for(j=i+1;j<=npar;j++)
-       ungetc(c,ficpar);
+         matcov[i][j]=matcov[j][i];
-       fgets(line, MAXLINE, ficpar);
-       puts(line);
+     if(mle==1)
-       fputs(line,ficparo);
+       printf("\n");
-     }
+     fprintf(ficlog,"\n");
-     ungetc(c,ficpar);
+     fflush(ficlog);
-     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);
+     /*-------- Rewriting parameter file ----------*/
-     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);
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     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);
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-       ungetc(c,ficpar);
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-       puts(line);
+     }
-       fputs(line,ficparo);
+     fprintf(ficres,"#%s\n",version);
-     }
+   }    /* End of mle != -3 */
-     ungetc(c,ficpar);
+   n= lastobs;
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+   num=lvector(1,n);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+   moisnais=vector(1,n);
+   annais=vector(1,n);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+   moisdc=vector(1,n);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+   andc=vector(1,n);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+   agedc=vector(1,n);
+   cod=ivector(1,n);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   weight=vector(1,n);
-       ungetc(c,ficpar);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-       fgets(line, MAXLINE, ficpar);
+   mint=matrix(1,maxwav,1,n);
-       puts(line);
+   anint=matrix(1,maxwav,1,n);
-       fputs(line,ficparo);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-     }
+   tab=ivector(1,NCOVMAX);
-     ungetc(c,ficpar);
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-     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);
+   /* Reads data from file datafile */
-     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);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     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);
+     goto end;
-     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);
+   /* Calculation of the number of parameters from char model */
-     /* day and month of proj2 are not used but only year anproj2.*/
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+         k=1 Tvar[1]=2 (from V2)
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+       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.
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+   */
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+   /* For model-covariate k tells which data-covariate to use but
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     because this model-covariate is a construction we invent a new column
+     ncovcol + k1
-    /*------------ free_vector  -------------*/
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-    /*  chdir(path); */
+     Tvar[3=V1*V4]=4+1 etc */
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-     free_ivector(wav,1,imx);
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+   */
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-     free_lvector(num,1,n);
+   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
-     free_vector(agedc,1,n);
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-     fclose(ficparo);
+covariates (3 plus signs)
-     fclose(ficres);
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
-     strcpy(filerespl,"pl");
-     strcat(filerespl,fileres);
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     nbwarn++;
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-     }
+   }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     /*  if(mle==1){*/
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     pstamp(ficrespl);
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+   }
-     fprintf(ficrespl,"#Age ");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     /*-calculation of age at interview from date of interview and age at death -*/
-     fprintf(ficrespl,"\n");
+   agev=matrix(1,maxwav,1,imx);
-     prlim=matrix(1,nlstate,1,nlstate);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+     goto end;
-     agebase=ageminpar;
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
+   agegomp=(int)agemin;
-     i1=cptcoveff;
+   free_vector(moisnais,1,n);
-     if (cptcovn < 1){i1=1;}
+   free_vector(annais,1,n);
+   /* free_matrix(mint,1,maxwav,1,n);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+      free_matrix(anint,1,maxwav,1,n);*/
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   free_vector(moisdc,1,n);
-         k=k+1;
+   free_vector(andc,1,n);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+   /* */
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+   wav=ivector(1,imx);
-         fprintf(ficlog,"\n#******");
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-         for(j=1;j<=cptcoveff;j++) {
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-           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]]);
+   /* Concatenates waves */
-         }
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-         fprintf(ficrespl,"******\n");
+   /* */
-         printf("******\n");
-         fprintf(ficlog,"******\n");
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-         for (age=agebase; age<=agelim; age++){
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+   ncodemax[1]=1;
-           fprintf(ficrespl,"%.0f ",age );
+   Ndum =ivector(-1,NCOVMAX);
-           for(j=1;j<=cptcoveff;j++)
+   if (ncovmodel > 2)
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-           fprintf(ficrespl,"\n");
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-         }
+   h=0;
-       }
-     }
-     fclose(ficrespl);
+   /*if (cptcovn > 0) */
-     /*------------- h Pij x at various ages ------------*/
+   m=pow(2,cptcoveff);
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-     }
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-     printf("Computing pij: result on file '%s' \n", filerespij);
+           h++;
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+           if (h>m)
+             h=1;
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-     /*if (stepm<=24) stepsize=2;*/
+            *     h     1     2     3     4
+            *______________________________
-     agelim=AGESUP;
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-     hstepm=stepsize*YEARM; /* Every year of age */
+            *     2     2     1     1     1
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
-     /* hstepm=1;   aff par mois*/
+            *     5 i=3 1 i=2 1     2     1
-     pstamp(ficrespij);
+            *     6     2     1     2     1
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+            *     7 i=4 1     2     2     1
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+            *     8     2     2     2     1
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+            *     9 i=5 1 i=3 1 i=2 1     1
-         k=k+1;
+            *    10     2     1     1     1
-         fprintf(ficrespij,"\n#****** ");
+            *    11 i=6 1     2     1     1
-         for(j=1;j<=cptcoveff;j++)
+            *    12     2     2     1     1
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+            *    13 i=7 1 i=4 1     2     1
-         fprintf(ficrespij,"******\n");
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+            *    16     2     2     2     1
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+            */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           codtab[h][k]=j;
+           /*codtab[h][Tvar[k]]=j;*/
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+           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]]);
+         }
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-           oldm=oldms;savm=savms;
+     }
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   }
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-           for(i=1; i<=nlstate;i++)
+      codtab[1][2]=1;codtab[2][2]=2; */
-             for(j=1; j<=nlstate+ndeath;j++)
+   /* for(i=1; i <=m ;i++){
-               fprintf(ficrespij," %1d-%1d",i,j);
+      for(k=1; k <=cptcovn; k++){
-           fprintf(ficrespij,"\n");
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-           for (h=0; h<=nhstepm; h++){
+      }
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+      printf("\n");
-             for(i=1; i<=nlstate;i++)
+      }
-               for(j=1; j<=nlstate+ndeath;j++)
+      scanf("%d",i);*/
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
+  free_ivector(Ndum,-1,NCOVMAX);
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
-         }
+   /*------------ gnuplot -------------*/
-       }
+   strcpy(optionfilegnuplot,optionfilefiname);
-     }
+   if(mle==-3)
+     strcat(optionfilegnuplot,"-mort");
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   strcat(optionfilegnuplot,".gp");
-     fclose(ficrespij);
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     printf("Problem with file %s",optionfilegnuplot);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }
-     for(i=1;i<=AGESUP;i++)
+   else{
-       for(j=1;j<=NCOVMAX;j++)
+     fprintf(ficgp,"\n# %s\n", version);
-         for(k=1;k<=NCOVMAX;k++)
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-           probs[i][j][k]=0.;
+     //fprintf(ficgp,"set missing 'NaNq'\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-     /*---------- Forecasting ------------------*/
+   }
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+   /*  fclose(ficgp);*/
-     if(prevfcast==1){
+   /*--------- index.htm --------*/
-       /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+   if(mle==-3)
-       /*      }  */
+     strcat(optionfilehtm,"-mort");
-       /*      else{ */
+   strcat(optionfilehtm,".htm");
-       /*        erreur=108; */
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     printf("Problem with %s \n",optionfilehtm);
-       /*        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); */
+     exit(0);
-       /*      } */
+   }
-     }
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+   strcat(optionfilehtmcov,"-cov.htm");
-     /*---------- Health expectancies and variances ------------*/
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-     strcpy(filerest,"t");
+   }
-     strcat(filerest,fileres);
+   else{
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+ 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);
-     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);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     strcpy(filerese,"e");
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     strcat(filerese,fileres);
+ \n\
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+  <ul><li><h4>Parameter files</h4>\n\
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+  - 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\
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+  - Date and time at start: %s</ul>\n",\
-     strcpy(fileresstde,"stde");
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     strcat(fileresstde,fileres);
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+           fileres,fileres,\
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+   fflush(fichtm);
-     }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   strcpy(pathr,path);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     strcpy(filerescve,"cve");
-     strcat(filerescve,fileres);
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+      and prints on file fileres'p'. */
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
-     }
+   fprintf(fichtm,"\n");
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ 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",\
-     strcpy(fileresv,"v");
+           imx,agemin,agemax,jmin,jmax,jmean);
-     strcat(fileresv,fileres);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     }
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     */
+   if (mle==-3){
-     if (mobilav!=0) {
+     ximort=matrix(1,NDIM,1,NDIM);
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     cens=ivector(1,n);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     ageexmed=vector(1,n);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     agecens=vector(1,n);
-       }
+     dcwave=ivector(1,n);
-     }
+     for (i=1; i<=imx; i++){
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       dcwave[i]=-1;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for (m=firstpass; m<=lastpass; m++)
-         k=k+1;
+         if (s[m][i]>nlstate) {
-         fprintf(ficrest,"\n#****** ");
+           dcwave[i]=m;
-         for(j=1;j<=cptcoveff;j++)
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           break;
-         fprintf(ficrest,"******\n");
+         }
+     }
-         fprintf(ficreseij,"\n#****** ");
-         fprintf(ficresstdeij,"\n#****** ");
+     for (i=1; i<=imx; i++) {
-         fprintf(ficrescveij,"\n#****** ");
+       if (wav[i]>0){
-         for(j=1;j<=cptcoveff;j++) {
+         ageexmed[i]=agev[mw[1][i]][i];
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         j=wav[i];
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         agecens[i]=1.;
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
+         if (ageexmed[i]> 1 && wav[i] > 0){
-         fprintf(ficreseij,"******\n");
+           agecens[i]=agev[mw[j][i]][i];
-         fprintf(ficresstdeij,"******\n");
+           cens[i]= 1;
-         fprintf(ficrescveij,"******\n");
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
-         fprintf(ficresvij,"\n#****** ");
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-         for(j=1;j<=cptcoveff;j++)
+           cens[i]=0 ;
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-         fprintf(ficresvij,"******\n");
+       else cens[i]=-1;
+     }
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+     for (i=1;i<=NDIM;i++) {
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       for (j=1;j<=NDIM;j++)
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
+     }
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+     /*printf("%lf %lf", p[1], p[2]);*/
-         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);
-         }
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-         pstamp(ficrest);
+ #elsedef
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+ #endif
-         fprintf(ficrest,"\n");
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
-         epj=vector(1,nlstate+1);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-         for(age=bage; age <=fage ;age++){
+       printf("Problem with resultfile: %s\n", filerespow);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-           if (popbased==1) {
+     }
-             if(mobilav ==0){
+ #ifdef GSL
-               for(i=1; i<=nlstate;i++)
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-                 prlim[i][i]=probs[(int)age][i][k];
+ #elsedef
-             }else{ /* mobilav */
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-               for(i=1; i<=nlstate;i++)
+ #endif
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     /*  for (i=1;i<=nlstate;i++)
-             }
+         for(j=1;j<=nlstate+ndeath;j++)
-           }
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+     */
-           fprintf(ficrest," %4.0f",age);
+     fprintf(ficrespow,"\n");
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+ #ifdef GSL
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     /* gsl starts here */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     T = gsl_multimin_fminimizer_nmsimplex;
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     gsl_multimin_fminimizer *sfm = NULL;
-             }
+     gsl_vector *ss, *x;
-             epj[nlstate+1] +=epj[j];
+     gsl_multimin_function minex_func;
-           }
+     /* Initial vertex size vector */
-           for(i=1, vepp=0.;i <=nlstate;i++)
+     ss = gsl_vector_alloc (NDIM);
-             for(j=1;j <=nlstate;j++)
-               vepp += vareij[i][j][(int)age];
+     if (ss == NULL){
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-           for(j=1;j <=nlstate;j++){
+     }
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     /* Set all step sizes to 1 */
-           }
+     gsl_vector_set_all (ss, 0.001);
-           fprintf(ficrest,"\n");
-         }
+     /* Starting point */
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     x = gsl_vector_alloc (NDIM);
-         free_vector(epj,1,nlstate+1);
-       }
+     if (x == NULL){
-     }
+       gsl_vector_free(ss);
-     free_vector(weight,1,n);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-     free_imatrix(Tvard,1,15,1,2);
+     }
-     free_imatrix(s,1,maxwav+1,1,n);
-     free_matrix(anint,1,maxwav,1,n);
+     /* Initialize method and iterate */
-     free_matrix(mint,1,maxwav,1,n);
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-     free_ivector(cod,1,n);
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     free_ivector(tab,1,NCOVMAX);
+ /*     gsl_vector_set(x, 1, 0.083); */
-     fclose(ficreseij);
+     gsl_vector_set(x, 0, p[1]);
-     fclose(ficresstdeij);
+     gsl_vector_set(x, 1, p[2]);
-     fclose(ficrescveij);
-     fclose(ficresvij);
+     minex_func.f = &gompertz_f;
-     fclose(ficrest);
+     minex_func.n = NDIM;
-     fclose(ficpar);
+     minex_func.params = (void *)&p; /* ??? */
-     /*------- Variance of period (stable) prevalence------*/
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
+     printf("Iterations beginning .....\n\n");
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
+     iteri=0;
-     }
+     while (rval == GSL_CONTINUE){
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       if (status) printf("error: %s\n", gsl_strerror (status));
-         k=k+1;
+       fflush(0);
-         fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+       if (status)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         break;
-         fprintf(ficresvpl,"******\n");
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       ssval = gsl_multimin_fminimizer_size (sfm);
-         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+       if (rval == GSL_SUCCESS)
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+         printf ("converged to a local maximum at\n");
-       }
-     }
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
-     fclose(ficresvpl);
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
-     /*---------- End : free ----------------*/
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     }
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-   }  /* mle==-3 arrives here for freeing */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     gsl_vector_free(x); /* initial values */
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     gsl_vector_free(ss); /* inital step size */
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     for (it=0; it<NDIM; it++){
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       p[it+1]=gsl_vector_get(sfm->x,it);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       fprintf(ficrespow," %.12lf", p[it]);
-     free_matrix(covar,0,NCOVMAX,1,n);
+     }
-     free_matrix(matcov,1,npar,1,npar);
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
-     /*free_vector(delti,1,npar);*/
+ #endif
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ #ifdef POWELL
-     free_matrix(agev,1,maxwav,1,imx);
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ #endif
+     fclose(ficrespow);
-     free_ivector(ncodemax,1,8);
-     free_ivector(Tvar,1,15);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     free_ivector(Tprod,1,15);
-     free_ivector(Tvaraff,1,15);
+     for(i=1; i <=NDIM; i++)
-     free_ivector(Tage,1,15);
+       for(j=i+1;j<=NDIM;j++)
-     free_ivector(Tcode,1,100);
+         matcov[i][j]=matcov[j][i];
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     printf("\nCovariance matrix\n ");
-     free_imatrix(codtab,1,100,1,10);
+     for(i=1; i <=NDIM; i++) {
-   fflush(fichtm);
+       for(j=1;j<=NDIM;j++){
-   fflush(ficgp);
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
-   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);
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-   }else{
+     for (i=1;i<=NDIM;i++)
-     printf("End of Imach\n");
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-     fprintf(ficlog,"End of Imach\n");
-   }
+     lsurv=vector(1,AGESUP);
-   printf("See log file on %s\n",filelog);
+     lpop=vector(1,AGESUP);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     tpop=vector(1,AGESUP);
-   (void) gettimeofday(&end_time,&tzp);
+     lsurv[agegomp]=100000;
-   tm = *localtime(&end_time.tv_sec);
-   tmg = *gmtime(&end_time.tv_sec);
+     for (k=agegomp;k<=AGESUP;k++) {
-   strcpy(strtend,asctime(&tm));
+       agemortsup=k;
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-   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));
+     for (k=agegomp;k<agemortsup;k++)
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     for (k=agegomp;k<agemortsup;k++){
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+       sumlpop=sumlpop+lpop[k];
-   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);
+     tpop[agegomp]=sumlpop;
-   fclose(fichtmcov);
+     for (k=agegomp;k<(agemortsup-3);k++){
-   fclose(ficgp);
+       /*  tpop[k+1]=2;*/
-   fclose(ficlog);
+       tpop[k+1]=tpop[k]-lpop[k];
-   /*------ End -----------*/
+     }
-    printf("Before Current directory %s!\n",pathcd);
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-    if(chdir(pathcd) != 0)
+     for (k=agegomp;k<(agemortsup-2);k++)
-     printf("Can't move to directory %s!\n",path);
+       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]);
-   if(getcwd(pathcd,MAXLINE) > 0)
-     printf("Current directory %s!\n",pathcd);
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-   sprintf(plotcmd,"gnuplot");
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
- #ifndef UNIX
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
- #endif
+                      stepm, weightopt,\
-   if(!stat(plotcmd,&info)){
+                      model,imx,p,matcov,agemortsup);
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     free_vector(lsurv,1,AGESUP);
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     free_vector(lpop,1,AGESUP);
-     }else
+     free_vector(tpop,1,AGESUP);
-       strcpy(pplotcmd,plotcmd);
+ #ifdef GSL
- #ifdef UNIX
+     free_ivector(cens,1,n);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     free_vector(agecens,1,n);
-     if(!stat(plotcmd,&info)){
+     free_ivector(dcwave,1,n);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     free_matrix(ximort,1,NDIM,1,NDIM);
-     }else
+ #endif
-       strcpy(pplotcmd,plotcmd);
+   } /* Endof if mle==-3 */
- #endif
-   }else
+   else{ /* For mle >=1 */
-     strcpy(pplotcmd,plotcmd);
+     globpr=0;/* debug */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
-   if((outcmd=system(plotcmd)) != 0){
+     printf("\n");
-     printf("\n Problem with gnuplot\n");
+     globpr=1; /* to print the contributions */
-   }
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-   printf(" Wait...");
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-   while (z[0] != 'q') {
+     for (k=1; k<=npar;k++)
-     /* chdir(path); */
+       printf(" %d %8.5f",k,p[k]);
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     printf("\n");
-     scanf("%s",z);
+     if(mle>=1){ /* Could be 1 or 2 */
- /*     if (z[0] == 'c') system("./imach"); */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     if (z[0] == 'e') {
+     }
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
-       system(optionfilehtm);
+     /*--------- results files --------------*/
-     }
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-     else if (z[0] == 'g') system(plotcmd);
-     else if (z[0] == 'q') exit(0);
-   }
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   end:
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   while (z[0] != 'q') {
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("\nType  q for exiting: ");
+     for(i=1,jk=1; i <=nlstate; i++){
-     scanf("%s",z);
+       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 */
+           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
+           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(" Successul, 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.1.157