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Diff for /imach/src/imach.c between versions 1.125 and 1.152

-version 1.125, 2006/04/04 15:20:31
+version 1.152, 2014/06/18 17:54:09
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
+ #ifdef GSL
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+ #include <gsl/gsl_errno.h>
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #include <gsl/gsl_multimin.h>
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #endif
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ /* #include <libintl.h> */
- #define AGESUP 130
+ /* #define _(String) gettext (String) */
- #define AGEBASE 40
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- #ifdef UNIX
- #define DIRSEPARATOR '/'
+ #define GNUPLOTPROGRAM "gnuplot"
- #define CHARSEPARATOR "/"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define ODIRSEPARATOR '\\'
+ #define FILENAMELENGTH 132
- #else
- #define DIRSEPARATOR '\\'
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define CHARSEPARATOR "\\"
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define ODIRSEPARATOR '/'
- #endif
+ #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
+ #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
- /* $Id$ */
- /* $State$ */
+ #define NINTERVMAX 8
+ #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- char fullversion[]="$Revision$ $Date$";
+ #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
- char strstart[80];
+ #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #define MAXN 20000
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
+ #define YEARM 12. /**< Number of months per year */
- int nvar;
+ #define AGESUP 130
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ #define AGEBASE 40
- int npar=NPARMAX;
+ #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
- int nlstate=2; /* Number of live states */
+ #ifdef UNIX
- int ndeath=1; /* Number of dead states */
+ #define DIRSEPARATOR '/'
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ #define CHARSEPARATOR "/"
- int popbased=0;
+ #define ODIRSEPARATOR '\\'
+ #else
- int *wav; /* Number of waves for this individuual 0 is possible */
+ #define DIRSEPARATOR '\\'
- int maxwav; /* Maxim number of waves */
+ #define CHARSEPARATOR "\\"
- int jmin, jmax; /* min, max spacing between 2 waves */
+ #define ODIRSEPARATOR '/'
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ #endif
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ /* $Id$ */
- int mle, weightopt;
+ /* $State$ */
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ char fullversion[]="$Revision$ $Date$";
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ char strstart[80];
- double jmean; /* Mean space between 2 waves */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
- FILE *ficlog, *ficrespow;
+ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
- int globpr; /* Global variable for printing or not */
+ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- double fretone; /* Only one call to likelihood */
+ int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
- long ipmx; /* Number of contributions */
+ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
- double sw; /* Sum of weights */
+ int cptcovprodnoage=0; /**< Number of covariate products without age */
- char filerespow[FILENAMELENGTH];
+ int cptcoveff=0; /* Total number of covariates to vary for printing results */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ int cptcov=0; /* Working variable */
- FILE *ficresilk;
+ int npar=NPARMAX;
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ int nlstate=2; /* Number of live states */
- FILE *ficresprobmorprev;
+ int ndeath=1; /* Number of dead states */
- FILE *fichtm, *fichtmcov; /* Html File */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- FILE *ficreseij;
+ int popbased=0;
- char filerese[FILENAMELENGTH];
- FILE *ficresstdeij;
+ int *wav; /* Number of waves for this individuual 0 is possible */
- char fileresstde[FILENAMELENGTH];
+ int maxwav=0; /* Maxim number of waves */
- FILE *ficrescveij;
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- char filerescve[FILENAMELENGTH];
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- FILE  *ficresvij;
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- char fileresv[FILENAMELENGTH];
+                    to the likelihood and the sum of weights (done by funcone)*/
- FILE  *ficresvpl;
+ int mle=1, weightopt=0;
- char fileresvpl[FILENAMELENGTH];
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- char title[MAXLINE];
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ double jmean=1; /* Mean space between 2 waves */
- char command[FILENAMELENGTH];
+ double **matprod2(); /* test */
- int  outcmd=0;
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ /*FILE *fic ; */ /* Used in readdata only */
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- char filelog[FILENAMELENGTH]; /* Log file */
+ FILE *ficlog, *ficrespow;
- char filerest[FILENAMELENGTH];
+ int globpr=0; /* Global variable for printing or not */
- char fileregp[FILENAMELENGTH];
+ double fretone; /* Only one call to likelihood */
- char popfile[FILENAMELENGTH];
+ long ipmx=0; /* Number of contributions */
+ double sw; /* Sum of weights */
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ char filerespow[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ FILE *ficresilk;
- struct timezone tzp;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- extern int gettimeofday();
+ FILE *ficresprobmorprev;
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ FILE *fichtm, *fichtmcov; /* Html File */
- long time_value;
+ FILE *ficreseij;
- extern long time();
+ char filerese[FILENAMELENGTH];
- char strcurr[80], strfor[80];
+ FILE *ficresstdeij;
+ char fileresstde[FILENAMELENGTH];
- char *endptr;
+ FILE *ficrescveij;
- long lval;
+ char filerescve[FILENAMELENGTH];
- double dval;
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- #define NR_END 1
+ FILE  *ficresvpl;
- #define FREE_ARG char*
+ char fileresvpl[FILENAMELENGTH];
- #define FTOL 1.0e-10
+ char title[MAXLINE];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- #define NRANSI
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- #define ITMAX 200
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- #define TOL 2.0e-4
+ int  outcmd=0;
- #define CGOLD 0.3819660
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- #define ZEPS 1.0e-10
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ char filelog[FILENAMELENGTH]; /* Log file */
+ char filerest[FILENAMELENGTH];
- #define GOLD 1.618034
+ char fileregp[FILENAMELENGTH];
- #define GLIMIT 100.0
+ char popfile[FILENAMELENGTH];
- #define TINY 1.0e-20
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- static double maxarg1,maxarg2;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ struct timezone tzp;
+ extern int gettimeofday();
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
- #define rint(a) floor(a+0.5)
+ long time_value;
+ extern long time();
- static double sqrarg;
+ char strcurr[80], strfor[80];
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ char *endptr;
- int agegomp= AGEGOMP;
+ long lval;
+ double dval;
- int imx;
- int stepm=1;
+ #define NR_END 1
- /* Stepm, step in month: minimum step interpolation*/
+ #define FREE_ARG char*
+ #define FTOL 1.0e-10
- int estepm;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ #define NRANSI
+ #define ITMAX 200
- int m,nb;
- long *num;
+ #define TOL 2.0e-4
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ #define CGOLD 0.3819660
- double **pmmij, ***probs;
+ #define ZEPS 1.0e-10
- double *ageexmed,*agecens;
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- double dateintmean=0;
+ #define GOLD 1.618034
- double *weight;
+ #define GLIMIT 100.0
- int **s; /* Status */
+ #define TINY 1.0e-20
- double *agedc, **covar, idx;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ static double maxarg1,maxarg2;
- double *lsurv, *lpop, *tpop;
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ #define rint(a) floor(a+0.5)
- /**************** split *************************/
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ static double sqrarg;
- {
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ int agegomp= AGEGOMP;
-   */
-   char  *ss;                            /* pointer */
+ int imx;
-   int   l1, l2;                         /* length counters */
+ int stepm=1;
+ /* Stepm, step in month: minimum step interpolation*/
-   l1 = strlen(path );                   /* length of path */
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ int estepm;
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ int m,nb;
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ long *num;
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-     /* get current working directory */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ double **pmmij, ***probs;
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ double *ageexmed,*agecens;
-       return( GLOCK_ERROR_GETCWD );
+ double dateintmean=0;
-     }
-     /* got dirc from getcwd*/
+ double *weight;
-     printf(" DIRC = %s \n",dirc);
+ int **s; /* Status */
-   } else {                              /* strip direcotry from path */
+ double *agedc;
-     ss++;                               /* after this, the filename */
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
-     l2 = strlen( ss );                  /* length of filename */
+                   * covar=matrix(0,NCOVMAX,1,n);
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-     strcpy( name, ss );         /* save file name */
+ double  idx;
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
-     dirc[l1-l2] = 0;                    /* add zero */
+ int *Ndum; /** Freq of modality (tricode */
-     printf(" DIRC2 = %s \n",dirc);
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   }
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   /* We add a separator at the end of dirc if not exists */
+ double *lsurv, *lpop, *tpop;
-   l1 = strlen( dirc );                  /* length of directory */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-     dirc[l1] =  DIRSEPARATOR;
+ double ftolhess; /**< Tolerance for computing hessian */
-     dirc[l1+1] = 0;
-     printf(" DIRC3 = %s \n",dirc);
+ /**************** split *************************/
-   }
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-   ss = strrchr( name, '.' );            /* find last / */
+ {
-   if (ss >0){
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-     ss++;
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-     strcpy(ext,ss);                     /* save extension */
+   */
-     l1= strlen( name);
+   char  *ss;                            /* pointer */
-     l2= strlen(ss)+1;
+   int   l1, l2;                         /* length counters */
-     strncpy( finame, name, l1-l2);
-     finame[l1-l2]= 0;
+   l1 = strlen(path );                   /* length of path */
-   }
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   return( 0 );                          /* we're done */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
- }
+     strcpy( name, path );               /* we got the fullname name because no directory */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- /******************************************/
+     /* get current working directory */
+     /*    extern  char* getcwd ( char *buf , int len);*/
- void replace_back_to_slash(char *s, char*t)
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
- {
+       return( GLOCK_ERROR_GETCWD );
-   int i;
+     }
-   int lg=0;
+     /* got dirc from getcwd*/
-   i=0;
+     printf(" DIRC = %s \n",dirc);
-   lg=strlen(t);
+   } else {                              /* strip direcotry from path */
-   for(i=0; i<= lg; i++) {
+     ss++;                               /* after this, the filename */
-     (s[i] = t[i]);
+     l2 = strlen( ss );                  /* length of filename */
-     if (t[i]== '\\') s[i]='/';
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   }
+     strcpy( name, ss );         /* save file name */
- }
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     dirc[l1-l2] = 0;                    /* add zero */
- int nbocc(char *s, char occ)
+     printf(" DIRC2 = %s \n",dirc);
- {
+   }
-   int i,j=0;
+   /* We add a separator at the end of dirc if not exists */
-   int lg=20;
+   l1 = strlen( dirc );                  /* length of directory */
-   i=0;
+   if( dirc[l1-1] != DIRSEPARATOR ){
-   lg=strlen(s);
+     dirc[l1] =  DIRSEPARATOR;
-   for(i=0; i<= lg; i++) {
+     dirc[l1+1] = 0;
-   if  (s[i] == occ ) j++;
+     printf(" DIRC3 = %s \n",dirc);
    }
-   return j;
+   ss = strrchr( name, '.' );            /* find last / */
- }
+   if (ss >0){
+     ss++;
- void cutv(char *u,char *v, char*t, char occ)
+     strcpy(ext,ss);                     /* save extension */
- {
+     l1= strlen( name);
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     l2= strlen(ss)+1;
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+     strncpy( finame, name, l1-l2);
-      gives u="abcedf" and v="ghi2j" */
+     finame[l1-l2]= 0;
-   int i,lg,j,p=0;
+   }
-   i=0;
-   for(j=0; j<=strlen(t)-1; j++) {
+   return( 0 );                          /* we're done */
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ }
-   }
-   lg=strlen(t);
+ /******************************************/
-   for(j=0; j<p; j++) {
-     (u[j] = t[j]);
+ void replace_back_to_slash(char *s, char*t)
-   }
+ {
-      u[p]='\0';
+   int i;
+   int lg=0;
-    for(j=0; j<= lg; j++) {
+   i=0;
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+   lg=strlen(t);
-   }
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- /********************** nrerror ********************/
+   }
+ }
- void nrerror(char error_text[])
- {
+ char *trimbb(char *out, char *in)
-   fprintf(stderr,"ERREUR ...\n");
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   fprintf(stderr,"%s\n",error_text);
+   char *s;
-   exit(EXIT_FAILURE);
+   s=out;
- }
+   while (*in != '\0'){
- /*********************** vector *******************/
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- double *vector(int nl, int nh)
+       in++;
- {
+     }
-   double *v;
+     *out++ = *in++;
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   }
-   if (!v) nrerror("allocation failure in vector");
+   *out='\0';
-   return v-nl+NR_END;
+   return s;
  }
- /************************ free vector ******************/
+ char *cutl(char *blocc, char *alocc, char *in, char occ)
- void free_vector(double*v, int nl, int nh)
+ {
- {
+   /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
-   free((FREE_ARG)(v+nl-NR_END));
+      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- }
+      gives blocc="abcdef2ghi" and alocc="j".
+      If occ is not found blocc is null and alocc is equal to in. Returns blocc
- /************************ivector *******************************/
+   */
- int *ivector(long nl,long nh)
+   char *s, *t, *bl;
- {
+   t=in;s=in;
-   int *v;
+   while ((*in != occ) && (*in != '\0')){
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+     *alocc++ = *in++;
-   if (!v) nrerror("allocation failure in ivector");
+   }
-   return v-nl+NR_END;
+   if( *in == occ){
- }
+     *(alocc)='\0';
+     s=++in;
- /******************free ivector **************************/
+   }
- void free_ivector(int *v, long nl, long nh)
- {
+   if (s == t) {/* occ not found */
-   free((FREE_ARG)(v+nl-NR_END));
+     *(alocc-(in-s))='\0';
- }
+     in=s;
+   }
- /************************lvector *******************************/
+   while ( *in != '\0'){
- long *lvector(long nl,long nh)
+     *blocc++ = *in++;
- {
+   }
-   long *v;
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+   *blocc='\0';
-   if (!v) nrerror("allocation failure in ivector");
+   return t;
-   return v-nl+NR_END;
+ }
- }
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
+ {
- /******************free lvector **************************/
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
- void free_lvector(long *v, long nl, long nh)
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
- {
+      gives blocc="abcdef2ghi" and alocc="j".
-   free((FREE_ARG)(v+nl-NR_END));
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
- }
+   */
+   char *s, *t;
- /******************* imatrix *******************************/
+   t=in;s=in;
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   while (*in != '\0'){
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+     while( *in == occ){
- {
+       *blocc++ = *in++;
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+       s=in;
-   int **m;
+     }
+     *blocc++ = *in++;
-   /* allocate pointers to rows */
+   }
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   if (s == t) /* occ not found */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+     *(blocc-(in-s))='\0';
-   m += NR_END;
+   else
-   m -= nrl;
+     *(blocc-(in-s)-1)='\0';
+   in=s;
+   while ( *in != '\0'){
-   /* allocate rows and set pointers to them */
+     *alocc++ = *in++;
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+   }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+   *alocc='\0';
-   m[nrl] -= ncl;
+   return s;
+ }
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ int nbocc(char *s, char occ)
-   /* return pointer to array of pointers to rows */
+ {
-   return m;
+   int i,j=0;
- }
+   int lg=20;
+   i=0;
- /****************** free_imatrix *************************/
+   lg=strlen(s);
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   for(i=0; i<= lg; i++) {
-       int **m;
+   if  (s[i] == occ ) j++;
-       long nch,ncl,nrh,nrl;
+   }
-      /* free an int matrix allocated by imatrix() */
+   return j;
- {
+ }
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-   free((FREE_ARG) (m+nrl-NR_END));
+ /* void cutv(char *u,char *v, char*t, char occ) */
- }
+ /* { */
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- /******************* matrix *******************************/
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
- double **matrix(long nrl, long nrh, long ncl, long nch)
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
- {
+ /*   int i,lg,j,p=0; */
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ /*   i=0; */
-   double **m;
+ /*   lg=strlen(t); */
+ /*   for(j=0; j<=lg-1; j++) { */
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /*   } */
-   m += NR_END;
-   m -= nrl;
+ /*   for(j=0; j<p; j++) { */
+ /*     (u[j] = t[j]); */
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ /*   } */
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ /*      u[p]='\0'; */
-   m[nrl] += NR_END;
-   m[nrl] -= ncl;
+ /*    for(j=0; j<= lg; j++) { */
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /*   } */
-   return m;
+ /* } */
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
-    */
+ /********************** nrerror ********************/
- }
+ void nrerror(char error_text[])
- /*************************free matrix ************************/
+ {
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   fprintf(stderr,"ERREUR ...\n");
- {
+   fprintf(stderr,"%s\n",error_text);
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   exit(EXIT_FAILURE);
-   free((FREE_ARG)(m+nrl-NR_END));
+ }
- }
+ /*********************** vector *******************/
+ double *vector(int nl, int nh)
- /******************* ma3x *******************************/
+ {
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   double *v;
- {
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   if (!v) nrerror("allocation failure in vector");
-   double ***m;
+   return v-nl+NR_END;
+ }
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /************************ free vector ******************/
-   m += NR_END;
+ void free_vector(double*v, int nl, int nh)
-   m -= nrl;
+ {
+   free((FREE_ARG)(v+nl-NR_END));
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+ /************************ivector *******************************/
-   m[nrl] -= ncl;
+ int *ivector(long nl,long nh)
+ {
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   int *v;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+   if (!v) nrerror("allocation failure in ivector");
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   return v-nl+NR_END;
-   m[nrl][ncl] += NR_END;
+ }
-   m[nrl][ncl] -= nll;
-   for (j=ncl+1; j<=nch; j++)
+ /******************free ivector **************************/
-     m[nrl][j]=m[nrl][j-1]+nlay;
+ void free_ivector(int *v, long nl, long nh)
+ {
-   for (i=nrl+1; i<=nrh; i++) {
+   free((FREE_ARG)(v+nl-NR_END));
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ }
-     for (j=ncl+1; j<=nch; j++)
-       m[i][j]=m[i][j-1]+nlay;
+ /************************lvector *******************************/
-   }
+ long *lvector(long nl,long nh)
-   return m;
+ {
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   long *v;
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   */
+   if (!v) nrerror("allocation failure in ivector");
- }
+   return v-nl+NR_END;
+ }
- /*************************free ma3x ************************/
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ /******************free lvector **************************/
- {
+ void free_lvector(long *v, long nl, long nh)
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ {
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   free((FREE_ARG)(v+nl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+ }
- }
+ /******************* imatrix *******************************/
- /*************** function subdirf ***********/
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
- char *subdirf(char fileres[])
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
  {
-   /* Caution optionfilefiname is hidden */
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   strcpy(tmpout,optionfilefiname);
+   int **m;
-   strcat(tmpout,"/"); /* Add to the right */
-   strcat(tmpout,fileres);
+   /* allocate pointers to rows */
-   return tmpout;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- }
+   if (!m) nrerror("allocation failure 1 in matrix()");
+   m += NR_END;
- /*************** function subdirf2 ***********/
+   m -= nrl;
- char *subdirf2(char fileres[], char *preop)
- {
+   /* allocate rows and set pointers to them */
-   /* Caution optionfilefiname is hidden */
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   strcpy(tmpout,optionfilefiname);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   strcat(tmpout,"/");
+   m[nrl] += NR_END;
-   strcat(tmpout,preop);
+   m[nrl] -= ncl;
-   strcat(tmpout,fileres);
-   return tmpout;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
- }
+   /* return pointer to array of pointers to rows */
- /*************** function subdirf3 ***********/
+   return m;
- char *subdirf3(char fileres[], char *preop, char *preop2)
+ }
- {
+ /****************** free_imatrix *************************/
-   /* Caution optionfilefiname is hidden */
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   strcpy(tmpout,optionfilefiname);
+       int **m;
-   strcat(tmpout,"/");
+       long nch,ncl,nrh,nrl;
-   strcat(tmpout,preop);
+      /* free an int matrix allocated by imatrix() */
-   strcat(tmpout,preop2);
+ {
-   strcat(tmpout,fileres);
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-   return tmpout;
+   free((FREE_ARG) (m+nrl-NR_END));
  }
- /***************** f1dim *************************/
+ /******************* matrix *******************************/
- extern int ncom;
+ double **matrix(long nrl, long nrh, long ncl, long nch)
- extern double *pcom,*xicom;
+ {
- extern double (*nrfunc)(double []);
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   double **m;
- double f1dim(double x)
- {
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   int j;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   double f;
+   m += NR_END;
-   double *xt;
+   m -= nrl;
-   xt=vector(1,ncom);
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   f=(*nrfunc)(xt);
+   m[nrl] += NR_END;
-   free_vector(xt,1,ncom);
+   m[nrl] -= ncl;
-   return f;
- }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   return m;
- /*****************brent *************************/
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+ 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.
-   int iter;
+    */
-   double a,b,d,etemp;
+ }
-   double fu,fv,fw,fx;
-   double ftemp;
+ /*************************free matrix ************************/
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-   double e=0.0;
+ {
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   a=(ax < cx ? ax : cx);
+   free((FREE_ARG)(m+nrl-NR_END));
-   b=(ax > cx ? ax : cx);
+ }
-   x=w=v=bx;
-   fw=fv=fx=(*f)(x);
+ /******************* ma3x *******************************/
-   for (iter=1;iter<=ITMAX;iter++) {
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-     xm=0.5*(a+b);
+ {
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   double ***m;
-     printf(".");fflush(stdout);
-     fprintf(ficlog,".");fflush(ficlog);
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- #ifdef DEBUG
+   if (!m) nrerror("allocation failure 1 in matrix()");
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   m += NR_END;
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   m -= nrl;
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
- #endif
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-       *xmin=x;
+   m[nrl] += NR_END;
-       return fx;
+   m[nrl] -= ncl;
-     }
-     ftemp=fu;
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-       q=(x-v)*(fx-fw);
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-       p=(x-v)*q-(x-w)*r;
+   m[nrl][ncl] += NR_END;
-       q=2.0*(q-r);
+   m[nrl][ncl] -= nll;
-       if (q > 0.0) p = -p;
+   for (j=ncl+1; j<=nch; j++)
-       q=fabs(q);
+     m[nrl][j]=m[nrl][j-1]+nlay;
-       etemp=e;
-       e=d;
+   for (i=nrl+1; i<=nrh; i++) {
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+     for (j=ncl+1; j<=nch; j++)
-       else {
+       m[i][j]=m[i][j-1]+nlay;
-         d=p/q;
+   }
-         u=x+d;
+   return m;
-         if (u-a < tol2 || b-u < tol2)
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-           d=SIGN(tol1,xm-x);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-       }
+   */
-     } else {
+ }
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+ /*************************free ma3x ************************/
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-     fu=(*f)(u);
+ {
-     if (fu <= fx) {
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-       if (u >= x) a=x; else b=x;
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-       SHFT(v,w,x,u)
+   free((FREE_ARG)(m+nrl-NR_END));
-         SHFT(fv,fw,fx,fu)
+ }
-         } else {
-           if (u < x) a=u; else b=u;
+ /*************** function subdirf ***********/
-           if (fu <= fw || w == x) {
+ char *subdirf(char fileres[])
-             v=w;
+ {
-             w=u;
+   /* Caution optionfilefiname is hidden */
-             fv=fw;
+   strcpy(tmpout,optionfilefiname);
-             fw=fu;
+   strcat(tmpout,"/"); /* Add to the right */
-           } else if (fu <= fv || v == x || v == w) {
+   strcat(tmpout,fileres);
-             v=u;
+   return tmpout;
-             fv=fu;
+ }
-           }
-         }
+ /*************** function subdirf2 ***********/
-   }
+ char *subdirf2(char fileres[], char *preop)
-   nrerror("Too many iterations in brent");
+ {
-   *xmin=x;
-   return fx;
+   /* Caution optionfilefiname is hidden */
- }
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
- /****************** mnbrak ***********************/
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+   return tmpout;
-             double (*func)(double))
+ }
- {
-   double ulim,u,r,q, dum;
+ /*************** function subdirf3 ***********/
-   double fu;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
+ {
-   *fa=(*func)(*ax);
-   *fb=(*func)(*bx);
+   /* Caution optionfilefiname is hidden */
-   if (*fb > *fa) {
+   strcpy(tmpout,optionfilefiname);
-     SHFT(dum,*ax,*bx,dum)
+   strcat(tmpout,"/");
-       SHFT(dum,*fb,*fa,dum)
+   strcat(tmpout,preop);
-       }
+   strcat(tmpout,preop2);
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   strcat(tmpout,fileres);
-   *fc=(*func)(*cx);
+   return tmpout;
-   while (*fb > *fc) {
+ }
-     r=(*bx-*ax)*(*fb-*fc);
-     q=(*bx-*cx)*(*fb-*fa);
+ /***************** f1dim *************************/
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+ extern int ncom;
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+ extern double *pcom,*xicom;
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+ extern double (*nrfunc)(double []);
-     if ((*bx-u)*(u-*cx) > 0.0) {
-       fu=(*func)(u);
+ double f1dim(double x)
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ {
-       fu=(*func)(u);
+   int j;
-       if (fu < *fc) {
+   double f;
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+   double *xt;
-           SHFT(*fb,*fc,fu,(*func)(u))
-           }
+   xt=vector(1,ncom);
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-       u=ulim;
+   f=(*nrfunc)(xt);
-       fu=(*func)(u);
+   free_vector(xt,1,ncom);
-     } else {
+   return f;
-       u=(*cx)+GOLD*(*cx-*bx);
+ }
-       fu=(*func)(u);
-     }
+ /*****************brent *************************/
-     SHFT(*ax,*bx,*cx,u)
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-       SHFT(*fa,*fb,*fc,fu)
+ {
-       }
+   int iter;
- }
+   double a,b,d,etemp;
+   double fu,fv,fw,fx;
- /*************** linmin ************************/
+   double ftemp;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
- int ncom;
+   double e=0.0;
- double *pcom,*xicom;
- double (*nrfunc)(double []);
+   a=(ax < cx ? ax : cx);
+   b=(ax > cx ? ax : cx);
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+   x=w=v=bx;
- {
+   fw=fv=fx=(*f)(x);
-   double brent(double ax, double bx, double cx,
+   for (iter=1;iter<=ITMAX;iter++) {
-                double (*f)(double), double tol, double *xmin);
+     xm=0.5*(a+b);
-   double f1dim(double x);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-               double *fc, double (*func)(double));
+     printf(".");fflush(stdout);
-   int j;
+     fprintf(ficlog,".");fflush(ficlog);
-   double xx,xmin,bx,ax;
+ #ifdef DEBUG
-   double fx,fb,fa;
+     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);
+     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);
-   ncom=n;
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-   pcom=vector(1,n);
+ #endif
-   xicom=vector(1,n);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-   nrfunc=func;
+       *xmin=x;
-   for (j=1;j<=n;j++) {
+       return fx;
-     pcom[j]=p[j];
+     }
-     xicom[j]=xi[j];
+     ftemp=fu;
-   }
+     if (fabs(e) > tol1) {
-   ax=0.0;
+       r=(x-w)*(fx-fv);
-   xx=1.0;
+       q=(x-v)*(fx-fw);
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+       p=(x-v)*q-(x-w)*r;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+       q=2.0*(q-r);
- #ifdef DEBUG
+       if (q > 0.0) p = -p;
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+       q=fabs(q);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+       etemp=e;
- #endif
+       e=d;
-   for (j=1;j<=n;j++) {
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-     xi[j] *= xmin;
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     p[j] += xi[j];
+       else {
-   }
+         d=p/q;
-   free_vector(xicom,1,n);
+         u=x+d;
-   free_vector(pcom,1,n);
+         if (u-a < tol2 || b-u < tol2)
- }
+           d=SIGN(tol1,xm-x);
+       }
- char *asc_diff_time(long time_sec, char ascdiff[])
+     } else {
- {
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-   long sec_left, days, hours, minutes;
+     }
-   days = (time_sec) / (60*60*24);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-   sec_left = (time_sec) % (60*60*24);
+     fu=(*f)(u);
-   hours = (sec_left) / (60*60) ;
+     if (fu <= fx) {
-   sec_left = (sec_left) %(60*60);
+       if (u >= x) a=x; else b=x;
-   minutes = (sec_left) /60;
+       SHFT(v,w,x,u)
-   sec_left = (sec_left) % (60);
+         SHFT(fv,fw,fx,fu)
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+         } else {
-   return ascdiff;
+           if (u < x) a=u; else b=u;
- }
+           if (fu <= fw || w == x) {
+             v=w;
- /*************** powell ************************/
+             w=u;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+             fv=fw;
-             double (*func)(double []))
+             fw=fu;
- {
+           } else if (fu <= fv || v == x || v == w) {
-   void linmin(double p[], double xi[], int n, double *fret,
+             v=u;
-               double (*func)(double []));
+             fv=fu;
-   int i,ibig,j;
+           }
-   double del,t,*pt,*ptt,*xit;
+         }
-   double fp,fptt;
+   }
-   double *xits;
+   nrerror("Too many iterations in brent");
-   int niterf, itmp;
+   *xmin=x;
+   return fx;
-   pt=vector(1,n);
+ }
-   ptt=vector(1,n);
-   xit=vector(1,n);
+ /****************** mnbrak ***********************/
-   xits=vector(1,n);
-   *fret=(*func)(p);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-   for (j=1;j<=n;j++) pt[j]=p[j];
+             double (*func)(double))
-   for (*iter=1;;++(*iter)) {
+ {
-     fp=(*fret);
+   double ulim,u,r,q, dum;
-     ibig=0;
+   double fu;
-     del=0.0;
-     last_time=curr_time;
+   *fa=(*func)(*ax);
-     (void) gettimeofday(&curr_time,&tzp);
+   *fb=(*func)(*bx);
-     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);
+   if (*fb > *fa) {
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+     SHFT(dum,*ax,*bx,dum)
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+       SHFT(dum,*fb,*fa,dum)
-    for (i=1;i<=n;i++) {
+       }
-       printf(" %d %.12f",i, p[i]);
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   *fc=(*func)(*cx);
-       fprintf(ficrespow," %.12lf", p[i]);
+   while (*fb > *fc) {
-     }
+     r=(*bx-*ax)*(*fb-*fc);
-     printf("\n");
+     q=(*bx-*cx)*(*fb-*fa);
-     fprintf(ficlog,"\n");
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-     if(*iter <=3){
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
-       tm = *localtime(&curr_time.tv_sec);
+     if ((*bx-u)*(u-*cx) > 0.0) {
-       strcpy(strcurr,asctime(&tm));
+       fu=(*func)(u);
- /*       asctime_r(&tm,strcurr); */
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
-       forecast_time=curr_time;
+       fu=(*func)(u);
-       itmp = strlen(strcurr);
+       if (fu < *fc) {
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         strcurr[itmp-1]='\0';
+           SHFT(*fb,*fc,fu,(*func)(u))
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+           }
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-       for(niterf=10;niterf<=30;niterf+=10){
+       u=ulim;
-         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);
+     } else {
- /*      asctime_r(&tmf,strfor); */
+       u=(*cx)+GOLD*(*cx-*bx);
-         strcpy(strfor,asctime(&tmf));
+       fu=(*func)(u);
-         itmp = strlen(strfor);
+     }
-         if(strfor[itmp-1]=='\n')
+     SHFT(*ax,*bx,*cx,u)
-         strfor[itmp-1]='\0';
+       SHFT(*fa,*fb,*fc,fu)
-         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);
+       }
-         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);
+ }
-       }
-     }
+ /*************** linmin ************************/
-     for (i=1;i<=n;i++) {
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+ int ncom;
-       fptt=(*fret);
+ double *pcom,*xicom;
- #ifdef DEBUG
+ double (*nrfunc)(double []);
-       printf("fret=%lf \n",*fret);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
- #endif
+ {
-       printf("%d",i);fflush(stdout);
+   double brent(double ax, double bx, double cx,
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+                double (*f)(double), double tol, double *xmin);
-       linmin(p,xit,n,fret,func);
+   double f1dim(double x);
-       if (fabs(fptt-(*fret)) > del) {
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-         del=fabs(fptt-(*fret));
+               double *fc, double (*func)(double));
-         ibig=i;
+   int j;
-       }
+   double xx,xmin,bx,ax;
- #ifdef DEBUG
+   double fx,fb,fa;
-       printf("%d %.12e",i,(*fret));
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   ncom=n;
-       for (j=1;j<=n;j++) {
+   pcom=vector(1,n);
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   xicom=vector(1,n);
-         printf(" x(%d)=%.12e",j,xit[j]);
+   nrfunc=func;
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+   for (j=1;j<=n;j++) {
-       }
+     pcom[j]=p[j];
-       for(j=1;j<=n;j++) {
+     xicom[j]=xi[j];
-         printf(" p=%.12e",p[j]);
+   }
-         fprintf(ficlog," p=%.12e",p[j]);
+   ax=0.0;
-       }
+   xx=1.0;
-       printf("\n");
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-       fprintf(ficlog,"\n");
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
- #endif
+ #ifdef DEBUG
-     }
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- #ifdef DEBUG
+ #endif
-       int k[2],l;
+   for (j=1;j<=n;j++) {
-       k[0]=1;
+     xi[j] *= xmin;
-       k[1]=-1;
+     p[j] += xi[j];
-       printf("Max: %.12e",(*func)(p));
+   }
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+   free_vector(xicom,1,n);
-       for (j=1;j<=n;j++) {
+   free_vector(pcom,1,n);
-         printf(" %.12e",p[j]);
+ }
-         fprintf(ficlog," %.12e",p[j]);
-       }
+ char *asc_diff_time(long time_sec, char ascdiff[])
-       printf("\n");
+ {
-       fprintf(ficlog,"\n");
+   long sec_left, days, hours, minutes;
-       for(l=0;l<=1;l++) {
+   days = (time_sec) / (60*60*24);
-         for (j=1;j<=n;j++) {
+   sec_left = (time_sec) % (60*60*24);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+   hours = (sec_left) / (60*60) ;
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   sec_left = (sec_left) %(60*60);
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+   minutes = (sec_left) /60;
-         }
+   sec_left = (sec_left) % (60);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+   return ascdiff;
-       }
+ }
- #endif
+ /*************** powell ************************/
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-       free_vector(xit,1,n);
+             double (*func)(double []))
-       free_vector(xits,1,n);
+ {
-       free_vector(ptt,1,n);
+   void linmin(double p[], double xi[], int n, double *fret,
-       free_vector(pt,1,n);
+               double (*func)(double []));
-       return;
+   int i,ibig,j;
-     }
+   double del,t,*pt,*ptt,*xit;
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+   double fp,fptt;
-     for (j=1;j<=n;j++) {
+   double *xits;
-       ptt[j]=2.0*p[j]-pt[j];
+   int niterf, itmp;
-       xit[j]=p[j]-pt[j];
-       pt[j]=p[j];
+   pt=vector(1,n);
-     }
+   ptt=vector(1,n);
-     fptt=(*func)(ptt);
+   xit=vector(1,n);
-     if (fptt < fp) {
+   xits=vector(1,n);
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+   *fret=(*func)(p);
-       if (t < 0.0) {
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         linmin(p,xit,n,fret,func);
+   for (*iter=1;;++(*iter)) {
-         for (j=1;j<=n;j++) {
+     fp=(*fret);
-           xi[j][ibig]=xi[j][n];
+     ibig=0;
-           xi[j][n]=xit[j];
+     del=0.0;
-         }
+     last_time=curr_time;
- #ifdef DEBUG
+     (void) gettimeofday(&curr_time,&tzp);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     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);
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     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);
-         for(j=1;j<=n;j++){
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-           printf(" %.12e",xit[j]);
+    for (i=1;i<=n;i++) {
-           fprintf(ficlog," %.12e",xit[j]);
+       printf(" %d %.12f",i, p[i]);
-         }
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-         printf("\n");
+       fprintf(ficrespow," %.12lf", p[i]);
-         fprintf(ficlog,"\n");
+     }
- #endif
+     printf("\n");
-       }
+     fprintf(ficlog,"\n");
-     }
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-   }
+     if(*iter <=3){
- }
+       tm = *localtime(&curr_time.tv_sec);
+       strcpy(strcurr,asctime(&tm));
- /**** Prevalence limit (stable or period prevalence)  ****************/
+ /*       asctime_r(&tm,strcurr); */
+       forecast_time=curr_time;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+       itmp = strlen(strcurr);
- {
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+         strcurr[itmp-1]='\0';
-      matrix by transitions matrix until convergence is reached */
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-   int i, ii,j,k;
+       for(niterf=10;niterf<=30;niterf+=10){
-   double min, max, maxmin, maxmax,sumnew=0.;
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
-   double **matprod2();
+         tmf = *localtime(&forecast_time.tv_sec);
-   double **out, cov[NCOVMAX], **pmij();
+ /*      asctime_r(&tmf,strfor); */
-   double **newm;
+         strcpy(strfor,asctime(&tmf));
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+         itmp = strlen(strfor);
+         if(strfor[itmp-1]=='\n')
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+         strfor[itmp-1]='\0';
-     for (j=1;j<=nlstate+ndeath;j++){
+         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);
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         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);
-     }
+       }
+     }
-    cov[1]=1.;
+     for (i=1;i<=n;i++) {
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       fptt=(*fret);
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ #ifdef DEBUG
-     newm=savm;
+       printf("fret=%lf \n",*fret);
-     /* Covariates have to be included here again */
+       fprintf(ficlog,"fret=%lf \n",*fret);
-      cov[2]=agefin;
+ #endif
+       printf("%d",i);fflush(stdout);
-       for (k=1; k<=cptcovn;k++) {
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       linmin(p,xit,n,fret,func);
-         /*      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]]);*/
+       if (fabs(fptt-(*fret)) > del) {
-       }
+         del=fabs(fptt-(*fret));
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         ibig=i;
-       for (k=1; k<=cptcovprod;k++)
+       }
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ #ifdef DEBUG
+       printf("%d %.12e",i,(*fret));
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       for (j=1;j<=n;j++) {
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+         printf(" x(%d)=%.12e",j,xit[j]);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-     savm=oldm;
+       }
-     oldm=newm;
+       for(j=1;j<=n;j++) {
-     maxmax=0.;
+         printf(" p=%.12e",p[j]);
-     for(j=1;j<=nlstate;j++){
+         fprintf(ficlog," p=%.12e",p[j]);
-       min=1.;
+       }
-       max=0.;
+       printf("\n");
-       for(i=1; i<=nlstate; i++) {
+       fprintf(ficlog,"\n");
-         sumnew=0;
+ #endif
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+     }
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-         max=FMAX(max,prlim[i][j]);
+ #ifdef DEBUG
-         min=FMIN(min,prlim[i][j]);
+       int k[2],l;
-       }
+       k[0]=1;
-       maxmin=max-min;
+       k[1]=-1;
-       maxmax=FMAX(maxmax,maxmin);
+       printf("Max: %.12e",(*func)(p));
-     }
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-     if(maxmax < ftolpl){
+       for (j=1;j<=n;j++) {
-       return prlim;
+         printf(" %.12e",p[j]);
-     }
+         fprintf(ficlog," %.12e",p[j]);
-   }
+       }
- }
+       printf("\n");
+       fprintf(ficlog,"\n");
- /*************** transition probabilities ***************/
+       for(l=0;l<=1;l++) {
+         for (j=1;j<=n;j++) {
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+           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]);
-   double s1, s2;
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-   /*double t34;*/
+         }
-   int i,j,j1, nc, ii, jj;
+         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(i=1; i<= nlstate; i++){
+       }
-       for(j=1; j<i;j++){
+ #endif
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-           /*s2 += param[i][j][nc]*cov[nc];*/
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       free_vector(xit,1,n);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+       free_vector(xits,1,n);
-         }
+       free_vector(ptt,1,n);
-         ps[i][j]=s2;
+       free_vector(pt,1,n);
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       return;
-       }
+     }
-       for(j=i+1; j<=nlstate+ndeath;j++){
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     for (j=1;j<=n;j++) {
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       ptt[j]=2.0*p[j]-pt[j];
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+       xit[j]=p[j]-pt[j];
-         }
+       pt[j]=p[j];
-         ps[i][j]=s2;
+     }
-       }
+     fptt=(*func)(ptt);
-     }
+     if (fptt < fp) {
-     /*ps[3][2]=1;*/
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+       if (t < 0.0) {
-     for(i=1; i<= nlstate; i++){
+         linmin(p,xit,n,fret,func);
-       s1=0;
+         for (j=1;j<=n;j++) {
-       for(j=1; j<i; j++)
+           xi[j][ibig]=xi[j][n];
-         s1+=exp(ps[i][j]);
+           xi[j][n]=xit[j];
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         }
-         s1+=exp(ps[i][j]);
+ #ifdef DEBUG
-       ps[i][i]=1./(s1+1.);
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       for(j=1; j<i; j++)
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         for(j=1;j<=n;j++){
-       for(j=i+1; j<=nlstate+ndeath; j++)
+           printf(" %.12e",xit[j]);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+           fprintf(ficlog," %.12e",xit[j]);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         }
-     } /* end i */
+         printf("\n");
+         fprintf(ficlog,"\n");
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ #endif
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+       }
-         ps[ii][jj]=0;
+     }
-         ps[ii][ii]=1;
+   }
-       }
+ }
-     }
+ /**** Prevalence limit (stable or period prevalence)  ****************/
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ {
- /*         printf("ddd %lf ",ps[ii][jj]); */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
- /*       } */
+      matrix by transitions matrix until convergence is reached */
- /*       printf("\n "); */
- /*        } */
+   int i, ii,j,k;
- /*        printf("\n ");printf("%lf ",cov[2]); */
+   double min, max, maxmin, maxmax,sumnew=0.;
-        /*
+   /* double **matprod2(); */ /* test */
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+   double **out, cov[NCOVMAX+1], **pmij();
-       goto end;*/
+   double **newm;
-     return ps;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
- }
+   for (ii=1;ii<=nlstate+ndeath;ii++)
- /**************** Product of 2 matrices ******************/
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+     }
- {
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+    cov[1]=1.;
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-   /* in, b, out are matrice of pointers which should have been initialized
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-      before: only the contents of out is modified. The function returns
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-      a pointer to pointers identical to out */
+     newm=savm;
-   long i, j, k;
+     /* Covariates have to be included here again */
-   for(i=nrl; i<= nrh; i++)
+     cov[2]=agefin;
-     for(k=ncolol; k<=ncoloh; k++)
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+     for (k=1; k<=cptcovn;k++) {
-         out[i][k] +=in[i][j]*b[j][k];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-   return out;
+     }
- }
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
- /************* Higher Matrix Product ***************/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+     /*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]);*/
-   /* Computes the transition matrix starting at age 'age' over
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-      'nhstepm*hstepm*stepm' months (i.e. until
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-      nhstepm*hstepm matrices.
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     savm=oldm;
-      (typically every 2 years instead of every month which is too big
+     oldm=newm;
-      for the memory).
+     maxmax=0.;
-      Model is determined by parameters x and covariates have to be
+     for(j=1;j<=nlstate;j++){
-      included manually here.
+       min=1.;
+       max=0.;
-      */
+       for(i=1; i<=nlstate; i++) {
+         sumnew=0;
-   int i, j, d, h, k;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-   double **out, cov[NCOVMAX];
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-   double **newm;
+         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
+         max=FMAX(max,prlim[i][j]);
-   /* Hstepm could be zero and should return the unit matrix */
+         min=FMIN(min,prlim[i][j]);
-   for (i=1;i<=nlstate+ndeath;i++)
+       }
-     for (j=1;j<=nlstate+ndeath;j++){
+       maxmin=max-min;
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       maxmax=FMAX(maxmax,maxmin);
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     }
-     }
+     if(maxmax < ftolpl){
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       return prlim;
-   for(h=1; h <=nhstepm; h++){
+     }
-     for(d=1; d <=hstepm; d++){
+   }
-       newm=savm;
+ }
-       /* Covariates have to be included here again */
-       cov[1]=1.;
+ /*************** transition probabilities ***************/
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-       for (k=1; k<=cptcovage;k++)
+ {
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   /* According to parameters values stored in x and the covariate's values stored in cov,
-       for (k=1; k<=cptcovprod;k++)
+      computes the probability to be observed in state j being in state i by appying the
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+      ncth covariate in the global vector x is given by the formula:
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-       savm=oldm;
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-       oldm=newm;
+      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]
-     for(i=1; i<=nlstate+ndeath; i++)
+   */
-       for(j=1;j<=nlstate+ndeath;j++) {
+   double s1, lnpijopii;
-         po[i][j][h]=newm[i][j];
+   /*double t34;*/
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   int i,j,j1, nc, ii, jj;
-          */
-       }
+     for(i=1; i<= nlstate; i++){
-   } /* end h */
+       for(j=1; j<i;j++){
-   return po;
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- }
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
- /*************** log-likelihood *************/
+         }
- double func( double *x)
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- {
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-   int i, ii, j, k, mi, d, kk;
+       }
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+       for(j=i+1; j<=nlstate+ndeath;j++){
-   double **out;
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   double sw; /* Sum of weights */
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-   double lli; /* Individual log likelihood */
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-   int s1, s2;
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-   double bbh, survp;
+         }
-   long ipmx;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   /*extern weight */
+       }
-   /* We are differentiating ll according to initial status */
+     }
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   /*for(i=1;i<imx;i++)
+     for(i=1; i<= nlstate; i++){
-     printf(" %d\n",s[4][i]);
+       s1=0;
-   */
+       for(j=1; j<i; j++){
-   cov[1]=1.;
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
-   if(mle==1){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       }
-       for(mi=1; mi<= wav[i]-1; mi++){
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       ps[i][i]=1./(s1+1.);
-           for (j=1;j<=nlstate+ndeath;j++){
+       /* Computing other pijs */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       for(j=1; j<i; j++)
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-           }
+       for(j=i+1; j<=nlstate+ndeath; j++)
-         for(d=0; d<dh[mi][i]; d++){
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-           newm=savm;
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     } /* end i */
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-           }
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         ps[ii][jj]=0;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         ps[ii][ii]=1;
-           savm=oldm;
+       }
-           oldm=newm;
+     }
-         } /* end mult */
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-          * (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
+     /*   printf("\n "); */
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     /* } */
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+     /* printf("\n ");printf("%lf ",cov[2]);*/
-          * 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
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-          * -stepm/2 to stepm/2 .
+       goto end;*/
-          * For stepm=1 the results are the same as for previous versions of Imach.
+     return ps;
-          * For stepm > 1 the results are less biased than in previous versions.
+ }
-          */
-         s1=s[mw[mi][i]][i];
+ /**************** Product of 2 matrices ******************/
-         s2=s[mw[mi+1][i]][i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
-         /* bias bh is positive if real duration
+ {
-          * is higher than the multiple of stepm and negative otherwise.
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-          */
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+   /* in, b, out are matrice of pointers which should have been initialized
-         if( s2 > nlstate){
+      before: only the contents of out is modified. The function returns
-           /* i.e. if s2 is a death state and if the date of death is known
+      a pointer to pointers identical to out */
-              then the contribution to the likelihood is the probability to
+   int i, j, k;
-              die between last step unit time and current  step unit time,
+   for(i=nrl; i<= nrh; i++)
-              which is also equal to probability to die before dh
+     for(k=ncolol; k<=ncoloh; k++){
-              minus probability to die before dh-stepm .
+       out[i][k]=0.;
-              In version up to 0.92 likelihood was computed
+       for(j=ncl; j<=nch; j++)
-         as if date of death was unknown. Death was treated as any other
+         out[i][k] +=in[i][j]*b[j][k];
-         health state: the date of the interview describes the actual state
+     }
-         and not the date of a change in health state. The former idea was
+   return out;
-         to consider that at each interview the state was recorded
+ }
-         (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
+ /************* Higher Matrix Product ***************/
-         contribution is smaller and very dependent of the step unit
-         stepm. It is no more the probability to die between last interview
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-         and month of death but the probability to survive from last
+ {
-         interview up to one month before death multiplied by the
+   /* Computes the transition matrix starting at age 'age' over
-         probability to die within a month. Thanks to Chris
+      'nhstepm*hstepm*stepm' months (i.e. until
-         Jackson for correcting this bug.  Former versions increased
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-         mortality artificially. The bad side is that we add another loop
+      nhstepm*hstepm matrices.
-         which slows down the processing. The difference can be up to 10%
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-         lower mortality.
+      (typically every 2 years instead of every month which is too big
-           */
+      for the memory).
-           lli=log(out[s1][s2] - savm[s1][s2]);
+      Model is determined by parameters x and covariates have to be
+      included manually here.
-         } else if  (s2==-2) {
+      */
-           for (j=1,survp=0. ; j<=nlstate; j++)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   int i, j, d, h, k;
-           /*survp += out[s1][j]; */
+   double **out, cov[NCOVMAX+1];
-           lli= log(survp);
+   double **newm;
-         }
+   /* Hstepm could be zero and should return the unit matrix */
-         else if  (s2==-4) {
+   for (i=1;i<=nlstate+ndeath;i++)
-           for (j=3,survp=0. ; j<=nlstate; j++)
+     for (j=1;j<=nlstate+ndeath;j++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-           lli= log(survp);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         }
+     }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-         else if  (s2==-5) {
+   for(h=1; h <=nhstepm; h++){
-           for (j=1,survp=0. ; j<=2; j++)
+     for(d=1; d <=hstepm; d++){
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       newm=savm;
-           lli= log(survp);
+       /* Covariates have to be included here again */
-         }
+       cov[1]=1.;
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-         else{
+       for (k=1; k<=cptcovn;k++)
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
+       for (k=1; k<=cptcovage;k++)
-         }
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-         /*if(lli ==000.0)*/
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-         ipmx +=1;
-         sw += weight[i];
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-       } /* end of wave */
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-     } /* end of individual */
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-   }  else if(mle==2){
+       savm=oldm;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       oldm=newm;
-       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+ndeath; i++)
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+       for(j=1;j<=nlstate+ndeath;j++) {
-           for (j=1;j<=nlstate+ndeath;j++){
+         po[i][j][h]=newm[i][j];
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+       }
-           }
+     /*printf("h=%d ",h);*/
-         for(d=0; d<=dh[mi][i]; d++){
+   } /* end h */
-           newm=savm;
+ /*     printf("\n H=%d \n",h); */
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   return po;
-           for (kk=1; kk<=cptcovage;kk++) {
+ }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ /*************** log-likelihood *************/
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ double func( double *x)
-           savm=oldm;
+ {
-           oldm=newm;
+   int i, ii, j, k, mi, d, kk;
-         } /* end mult */
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
+   double **out;
-         s1=s[mw[mi][i]][i];
+   double sw; /* Sum of weights */
-         s2=s[mw[mi+1][i]][i];
+   double lli; /* Individual log likelihood */
-         bbh=(double)bh[mi][i]/(double)stepm;
+   int s1, s2;
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+   double bbh, survp;
-         ipmx +=1;
+   long ipmx;
-         sw += weight[i];
+   /*extern weight */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+   /* We are differentiating ll according to initial status */
-       } /* end of wave */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-     } /* end of individual */
+   /*for(i=1;i<imx;i++)
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+     printf(" %d\n",s[4][i]);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   cov[1]=1.;
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   if(mle==1){
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           }
+       /* Computes the values of the ncovmodel covariates of the model
-         for(d=0; d<dh[mi][i]; d++){
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-           newm=savm;
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+          to be observed in j being in i according to the model.
-           for (kk=1; kk<=cptcovage;kk++) {
+        */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-           }
+         cov[2+k]=covar[Tvar[k]][i];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       }
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-           savm=oldm;
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-           oldm=newm;
+          has been calculated etc */
-         } /* end mult */
+       for(mi=1; mi<= wav[i]-1; mi++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         s1=s[mw[mi][i]][i];
+           for (j=1;j<=nlstate+ndeath;j++){
-         s2=s[mw[mi+1][i]][i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         bbh=(double)bh[mi][i]/(double)stepm;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+           }
-         ipmx +=1;
+         for(d=0; d<dh[mi][i]; d++){
-         sw += weight[i];
+           newm=savm;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       } /* end of wave */
+           for (kk=1; kk<=cptcovage;kk++) {
-     } /* end of individual */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+           }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       for(mi=1; mi<= wav[i]-1; mi++){
+           savm=oldm;
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+           oldm=newm;
-           for (j=1;j<=nlstate+ndeath;j++){
+         } /* end mult */
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-           }
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-         for(d=0; d<dh[mi][i]; d++){
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-           newm=savm;
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-           for (kk=1; kk<=cptcovage;kk++) {
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+          * (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
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+          * -stepm/2 to stepm/2 .
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+          * For stepm=1 the results are the same as for previous versions of Imach.
-           savm=oldm;
+          * For stepm > 1 the results are less biased than in previous versions.
-           oldm=newm;
+          */
-         } /* end mult */
+         s1=s[mw[mi][i]][i];
+         s2=s[mw[mi+1][i]][i];
-         s1=s[mw[mi][i]][i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-         s2=s[mw[mi+1][i]][i];
+         /* bias bh is positive if real duration
-         if( s2 > nlstate){
+          * is higher than the multiple of stepm and negative otherwise.
-           lli=log(out[s1][s2] - savm[s1][s2]);
+          */
-         }else{
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         if( s2 > nlstate){
-         }
+           /* i.e. if s2 is a death state and if the date of death is known
-         ipmx +=1;
+              then the contribution to the likelihood is the probability to
-         sw += weight[i];
+              die between last step unit time and current  step unit time,
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+              which is also equal to probability to die before dh
- /*      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]); */
+              minus probability to die before dh-stepm .
-       } /* end of wave */
+              In version up to 0.92 likelihood was computed
-     } /* end of individual */
+         as if date of death was unknown. Death was treated as any other
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+         health state: the date of the interview describes the actual state
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         and not the date of a change in health state. The former idea was
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         to consider that at each interview the state was recorded
-       for(mi=1; mi<= wav[i]-1; mi++){
+         (healthy, disable or death) and IMaCh was corrected; but when we
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         introduced the exact date of death then we should have modified
-           for (j=1;j<=nlstate+ndeath;j++){
+         the contribution of an exact death to the likelihood. This new
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         contribution is smaller and very dependent of the step unit
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         stepm. It is no more the probability to die between last interview
-           }
+         and month of death but the probability to survive from last
-         for(d=0; d<dh[mi][i]; d++){
+         interview up to one month before death multiplied by the
-           newm=savm;
+         probability to die within a month. Thanks to Chris
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         Jackson for correcting this bug.  Former versions increased
-           for (kk=1; kk<=cptcovage;kk++) {
+         mortality artificially. The bad side is that we add another loop
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         which slows down the processing. The difference can be up to 10%
-           }
+         lower mortality.
+           */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           lli=log(out[s1][s2] - savm[s1][s2]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
-           oldm=newm;
+         } else if  (s2==-2) {
-         } /* end mult */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         s1=s[mw[mi][i]][i];
+           /*survp += out[s1][j]; */
-         s2=s[mw[mi+1][i]][i];
+           lli= log(survp);
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         }
-         ipmx +=1;
-         sw += weight[i];
+         else if  (s2==-4) {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           for (j=3,survp=0. ; j<=nlstate; j++)
-         /*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]);*/
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       } /* end of wave */
+           lli= log(survp);
-     } /* end of individual */
+         }
-   } /* End of if */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         else if  (s2==-5) {
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           for (j=1,survp=0. ; j<=2; j++)
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-   return -l;
+           lli= log(survp);
- }
+         }
- /*************** log-likelihood *************/
+         else{
- double funcone( double *x)
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- {
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-   /* Same as likeli but slower because of a lot of printf and if */
+         }
-   int i, ii, j, k, mi, d, kk;
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+         /*if(lli ==000.0)*/
-   double **out;
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-   double lli; /* Individual log likelihood */
+         ipmx +=1;
-   double llt;
+         sw += weight[i];
-   int s1, s2;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   double bbh, survp;
+       } /* end of wave */
-   /*extern weight */
+     } /* end of individual */
-   /* We are differentiating ll according to initial status */
+   }  else if(mle==2){
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   /*for(i=1;i<imx;i++)
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     printf(" %d\n",s[4][i]);
+       for(mi=1; mi<= wav[i]-1; mi++){
-   */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   cov[1]=1.;
+           for (j=1;j<=nlstate+ndeath;j++){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         for(d=0; d<=dh[mi][i]; d++){
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+           newm=savm;
-     for(mi=1; mi<= wav[i]-1; mi++){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+           for (kk=1; kk<=cptcovage;kk++) {
-         for (j=1;j<=nlstate+ndeath;j++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       for(d=0; d<dh[mi][i]; d++){
+           savm=oldm;
-         newm=savm;
+           oldm=newm;
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         } /* end mult */
-         for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         s1=s[mw[mi][i]][i];
-         }
+         s2=s[mw[mi+1][i]][i];
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         bbh=(double)bh[mi][i]/(double)stepm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         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 */
-         savm=oldm;
+         ipmx +=1;
-         oldm=newm;
+         sw += weight[i];
-       } /* end mult */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+       } /* end of wave */
-       s1=s[mw[mi][i]][i];
+     } /* end of individual */
-       s2=s[mw[mi+1][i]][i];
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-       bbh=(double)bh[mi][i]/(double)stepm;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       /* bias is positive if real duration
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-        * is higher than the multiple of stepm and negative otherwise.
+       for(mi=1; mi<= wav[i]-1; mi++){
-        */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+           for (j=1;j<=nlstate+ndeath;j++){
-         lli=log(out[s1][s2] - savm[s1][s2]);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } else if  (s2==-2) {
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for (j=1,survp=0. ; j<=nlstate; j++)
+           }
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         for(d=0; d<dh[mi][i]; d++){
-         lli= log(survp);
+           newm=savm;
-       }else if (mle==1){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           for (kk=1; kk<=cptcovage;kk++) {
-       } else if(mle==2){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+           }
-       } else if(mle==3){  /* exponential inter-extrapolation */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         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 */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+           savm=oldm;
-         lli=log(out[s1][s2]); /* Original formula */
+           oldm=newm;
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         } /* end mult */
-         lli=log(out[s1][s2]); /* Original formula */
-       } /* End of if */
+         s1=s[mw[mi][i]][i];
-       ipmx +=1;
+         s2=s[mw[mi+1][i]][i];
-       sw += weight[i];
+         bbh=(double)bh[mi][i]/(double)stepm;
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
- /*       printf("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]); */
+         ipmx +=1;
-       if(globpr){
+         sw += weight[i];
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-  %11.6f %11.6f %11.6f ", \
+       } /* end of wave */
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+     } /* end of individual */
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           llt +=ll[k]*gipmx/gsw;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+       for(mi=1; mi<= wav[i]-1; mi++){
-         }
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         fprintf(ficresilk," %10.6f\n", -llt);
+           for (j=1;j<=nlstate+ndeath;j++){
-       }
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     } /* end of wave */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   } /* end of individual */
+           }
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         for(d=0; d<dh[mi][i]; d++){
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           newm=savm;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   if(globpr==0){ /* First time we count the contributions and weights */
+           for (kk=1; kk<=cptcovage;kk++) {
-     gipmx=ipmx;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     gsw=sw;
+           }
-   }
-   return -l;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
- /*************** function likelione ***********/
+         } /* end mult */
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
- {
+         s1=s[mw[mi][i]][i];
-   /* This routine should help understanding what is done with
+         s2=s[mw[mi+1][i]][i];
-      the selection of individuals/waves and
+         if( s2 > nlstate){
-      to check the exact contribution to the likelihood.
+           lli=log(out[s1][s2] - savm[s1][s2]);
-      Plotting could be done.
+         }else{
-    */
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   int k;
+         }
+         ipmx +=1;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+         sw += weight[i];
-     strcpy(fileresilk,"ilk");
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-     strcat(fileresilk,fileres);
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       } /* end of wave */
-       printf("Problem with resultfile: %s\n", fileresilk);
+     } /* end of individual */
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-     }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     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");
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+       for(mi=1; mi<= wav[i]-1; mi++){
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for(k=1; k<=nlstate; k++)
+           for (j=1;j<=nlstate+ndeath;j++){
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   }
+           }
+         for(d=0; d<dh[mi][i]; d++){
-   *fretone=(*funcone)(p);
+           newm=savm;
-   if(*globpri !=0){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     fclose(ficresilk);
+           for (kk=1; kk<=cptcovage;kk++) {
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     fflush(fichtm);
+           }
-   }
-   return;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           savm=oldm;
+           oldm=newm;
- /*********** Maximum Likelihood Estimation ***************/
+         } /* end mult */
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+         s1=s[mw[mi][i]][i];
- {
+         s2=s[mw[mi+1][i]][i];
-   int i,j, iter;
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   double **xi;
+         ipmx +=1;
-   double fret;
+         sw += weight[i];
-   double fretone; /* Only one call to likelihood */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   /*  char filerespow[FILENAMELENGTH];*/
+         /*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]);*/
-   xi=matrix(1,npar,1,npar);
+       } /* end of wave */
-   for (i=1;i<=npar;i++)
+     } /* end of individual */
-     for (j=1;j<=npar;j++)
+   } /* End of if */
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   strcpy(filerespow,"pow");
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   strcat(filerespow,fileres);
+   return -l;
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ }
-     printf("Problem with resultfile: %s\n", filerespow);
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ /*************** log-likelihood *************/
-   }
+ double funcone( double *x)
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ {
-   for (i=1;i<=nlstate;i++)
+   /* Same as likeli but slower because of a lot of printf and if */
-     for(j=1;j<=nlstate+ndeath;j++)
+   int i, ii, j, k, mi, d, kk;
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   fprintf(ficrespow,"\n");
+   double **out;
+   double lli; /* Individual log likelihood */
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+   double llt;
+   int s1, s2;
-   free_matrix(xi,1,npar,1,npar);
+   double bbh, survp;
-   fclose(ficrespow);
+   /*extern weight */
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   /* We are differentiating ll according to initial status */
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
- }
+   */
+   cov[1]=1.;
- /**** Computes Hessian and covariance matrix ***/
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
- {
-   double  **a,**y,*x,pd;
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double **hess;
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   int i, j,jk;
+     for(mi=1; mi<= wav[i]-1; mi++){
-   int *indx;
+       for (ii=1;ii<=nlstate+ndeath;ii++)
+         for (j=1;j<=nlstate+ndeath;j++){
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+         }
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+       for(d=0; d<dh[mi][i]; d++){
-   double gompertz(double p[]);
+         newm=savm;
-   hess=matrix(1,npar,1,npar);
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         for (kk=1; kk<=cptcovage;kk++) {
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+         }
-   for (i=1;i<=npar;i++){
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-     printf("%d",i);fflush(stdout);
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         savm=oldm;
-     /*  printf(" %f ",p[i]);
+         oldm=newm;
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+       } /* end mult */
-   }
+       s1=s[mw[mi][i]][i];
-   for (i=1;i<=npar;i++) {
+       s2=s[mw[mi+1][i]][i];
-     for (j=1;j<=npar;j++)  {
+       bbh=(double)bh[mi][i]/(double)stepm;
-       if (j>i) {
+       /* bias is positive if real duration
-         printf(".%d%d",i,j);fflush(stdout);
+        * is higher than the multiple of stepm and negative otherwise.
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+        */
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
-         hess[j][i]=hess[i][j];
+       } else if  (s2==-2) {
-         /*printf(" %lf ",hess[i][j]);*/
+         for (j=1,survp=0. ; j<=nlstate; j++)
-       }
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     }
+         lli= log(survp);
-   }
+       }else if (mle==1){
-   printf("\n");
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   fprintf(ficlog,"\n");
+       } else if(mle==2){
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-   a=matrix(1,npar,1,npar);
+         lli=log(out[s1][s2]); /* Original formula */
-   y=matrix(1,npar,1,npar);
+       } else{  /* mle=0 back to 1 */
-   x=vector(1,npar);
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   indx=ivector(1,npar);
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   for (i=1;i<=npar;i++)
+       } /* End of if */
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+       ipmx +=1;
-   ludcmp(a,npar,indx,&pd);
+       sw += weight[i];
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   for (j=1;j<=npar;j++) {
+       /*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++) x[i]=0;
+       if(globpr){
-     x[j]=1;
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     lubksb(a,npar,indx,x);
+  %11.6f %11.6f %11.6f ", \
-     for (i=1;i<=npar;i++){
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-       matcov[i][j]=x[i];
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-     }
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   }
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   printf("\n#Hessian matrix#\n");
+         }
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+         fprintf(ficresilk," %10.6f\n", -llt);
-   for (i=1;i<=npar;i++) {
+       }
-     for (j=1;j<=npar;j++) {
+     } /* end of wave */
-       printf("%.3e ",hess[i][j]);
+   } /* end of individual */
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     }
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     printf("\n");
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     fprintf(ficlog,"\n");
+   if(globpr==0){ /* First time we count the contributions and weights */
-   }
+     gipmx=ipmx;
+     gsw=sw;
-   /* Recompute Inverse */
+   }
-   for (i=1;i<=npar;i++)
+   return -l;
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+ }
-   ludcmp(a,npar,indx,&pd);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+ /*************** function likelione ***********/
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-   for (j=1;j<=npar;j++) {
+ {
-     for (i=1;i<=npar;i++) x[i]=0;
+   /* This routine should help understanding what is done with
-     x[j]=1;
+      the selection of individuals/waves and
-     lubksb(a,npar,indx,x);
+      to check the exact contribution to the likelihood.
-     for (i=1;i<=npar;i++){
+      Plotting could be done.
-       y[i][j]=x[i];
+    */
-       printf("%.3e ",y[i][j]);
+   int k;
-       fprintf(ficlog,"%.3e ",y[i][j]);
-     }
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     printf("\n");
+     strcpy(fileresilk,"ilk");
-     fprintf(ficlog,"\n");
+     strcat(fileresilk,fileres);
-   }
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-   */
+       printf("Problem with resultfile: %s\n", fileresilk);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   free_matrix(a,1,npar,1,npar);
+     }
-   free_matrix(y,1,npar,1,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");
-   free_vector(x,1,npar);
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-   free_ivector(indx,1,npar);
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-   free_matrix(hess,1,npar,1,npar);
+     for(k=1; k<=nlstate; k++)
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
- }
+   }
- /*************** hessian matrix ****************/
+   *fretone=(*funcone)(p);
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   if(*globpri !=0){
- {
+     fclose(ficresilk);
-   int i;
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   int l=1, lmax=20;
+     fflush(fichtm);
-   double k1,k2;
+   }
-   double p2[NPARMAX+1];
+   return;
-   double res;
+ }
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
-   int k=0,kmax=10;
+ /*********** Maximum Likelihood Estimation ***************/
-   double l1;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   fx=func(x);
+ {
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+   int i,j, iter;
-   for(l=0 ; l <=lmax; l++){
+   double **xi;
-     l1=pow(10,l);
+   double fret;
-     delts=delt;
+   double fretone; /* Only one call to likelihood */
-     for(k=1 ; k <kmax; k=k+1){
+   /*  char filerespow[FILENAMELENGTH];*/
-       delt = delta*(l1*k);
+   xi=matrix(1,npar,1,npar);
-       p2[theta]=x[theta] +delt;
+   for (i=1;i<=npar;i++)
-       k1=func(p2)-fx;
+     for (j=1;j<=npar;j++)
-       p2[theta]=x[theta]-delt;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-       k2=func(p2)-fx;
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   strcpy(filerespow,"pow");
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
- #ifdef DEBUG
+     printf("Problem with resultfile: %s\n", filerespow);
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-       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
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   for (i=1;i<=nlstate;i++)
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+     for(j=1;j<=nlstate+ndeath;j++)
-         k=kmax;
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-       }
+   fprintf(ficrespow,"\n");
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-         k=kmax; l=lmax*10.;
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-       }
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   free_matrix(xi,1,npar,1,npar);
-         delts=delt;
+   fclose(ficrespow);
-       }
+   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));
-   }
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-   delti[theta]=delts;
-   return res;
+ }
- }
+ /**** Computes Hessian and covariance matrix ***/
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ {
- {
+   double  **a,**y,*x,pd;
-   int i;
+   double **hess;
-   int l=1, l1, lmax=20;
+   int i, j,jk;
-   double k1,k2,k3,k4,res,fx;
+   int *indx;
-   double p2[NPARMAX+1];
-   int k;
+   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);
-   fx=func(x);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   for (k=1; k<=2; k++) {
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+   double gompertz(double p[]);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   hess=matrix(1,npar,1,npar);
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-     k1=func(p2)-fx;
+   printf("\nCalculation of the hessian matrix. Wait...\n");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   for (i=1;i<=npar;i++){
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     printf("%d",i);fflush(stdout);
-     k2=func(p2)-fx;
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-     k3=func(p2)-fx;
+     /*  printf(" %f ",p[i]);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   }
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     k4=func(p2)-fx;
+   for (i=1;i<=npar;i++) {
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     for (j=1;j<=npar;j++)  {
- #ifdef DEBUG
+       if (j>i) {
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+         printf(".%d%d",i,j);fflush(stdout);
-     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(ficlog,".%d%d",i,j);fflush(ficlog);
- #endif
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   }
-   return res;
+         hess[j][i]=hess[i][j];
- }
+         /*printf(" %lf ",hess[i][j]);*/
+       }
- /************** Inverse of matrix **************/
+     }
- void ludcmp(double **a, int n, int *indx, double *d)
+   }
- {
+   printf("\n");
-   int i,imax,j,k;
+   fprintf(ficlog,"\n");
-   double big,dum,sum,temp;
-   double *vv;
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-   vv=vector(1,n);
-   *d=1.0;
+   a=matrix(1,npar,1,npar);
-   for (i=1;i<=n;i++) {
+   y=matrix(1,npar,1,npar);
-     big=0.0;
+   x=vector(1,npar);
-     for (j=1;j<=n;j++)
+   indx=ivector(1,npar);
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+   for (i=1;i<=npar;i++)
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-     vv[i]=1.0/big;
+   ludcmp(a,npar,indx,&pd);
-   }
-   for (j=1;j<=n;j++) {
+   for (j=1;j<=npar;j++) {
-     for (i=1;i<j;i++) {
+     for (i=1;i<=npar;i++) x[i]=0;
-       sum=a[i][j];
+     x[j]=1;
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+     lubksb(a,npar,indx,x);
-       a[i][j]=sum;
+     for (i=1;i<=npar;i++){
-     }
+       matcov[i][j]=x[i];
-     big=0.0;
+     }
-     for (i=j;i<=n;i++) {
+   }
-       sum=a[i][j];
-       for (k=1;k<j;k++)
+   printf("\n#Hessian matrix#\n");
-         sum -= a[i][k]*a[k][j];
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-       a[i][j]=sum;
+   for (i=1;i<=npar;i++) {
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+     for (j=1;j<=npar;j++) {
-         big=dum;
+       printf("%.3e ",hess[i][j]);
-         imax=i;
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-       }
+     }
-     }
+     printf("\n");
-     if (j != imax) {
+     fprintf(ficlog,"\n");
-       for (k=1;k<=n;k++) {
+   }
-         dum=a[imax][k];
-         a[imax][k]=a[j][k];
+   /* Recompute Inverse */
-         a[j][k]=dum;
+   for (i=1;i<=npar;i++)
-       }
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-       *d = -(*d);
+   ludcmp(a,npar,indx,&pd);
-       vv[imax]=vv[j];
-     }
+   /*  printf("\n#Hessian matrix recomputed#\n");
-     indx[j]=imax;
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   for (j=1;j<=npar;j++) {
-     if (j != n) {
+     for (i=1;i<=npar;i++) x[i]=0;
-       dum=1.0/(a[j][j]);
+     x[j]=1;
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+     lubksb(a,npar,indx,x);
-     }
+     for (i=1;i<=npar;i++){
-   }
+       y[i][j]=x[i];
-   free_vector(vv,1,n);  /* Doesn't work */
+       printf("%.3e ",y[i][j]);
- ;
+       fprintf(ficlog,"%.3e ",y[i][j]);
- }
+     }
+     printf("\n");
- void lubksb(double **a, int n, int *indx, double b[])
+     fprintf(ficlog,"\n");
- {
+   }
-   int i,ii=0,ip,j;
+   */
-   double sum;
+   free_matrix(a,1,npar,1,npar);
-   for (i=1;i<=n;i++) {
+   free_matrix(y,1,npar,1,npar);
-     ip=indx[i];
+   free_vector(x,1,npar);
-     sum=b[ip];
+   free_ivector(indx,1,npar);
-     b[ip]=b[i];
+   free_matrix(hess,1,npar,1,npar);
-     if (ii)
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-     else if (sum) ii=i;
+ }
-     b[i]=sum;
-   }
+ /*************** hessian matrix ****************/
-   for (i=n;i>=1;i--) {
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-     sum=b[i];
+ {
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+   int i;
-     b[i]=sum/a[i][i];
+   int l=1, lmax=20;
-   }
+   double k1,k2;
- }
+   double p2[MAXPARM+1]; /* identical to x */
+   double res;
- void pstamp(FILE *fichier)
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
- {
+   double fx;
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   int k=0,kmax=10;
- }
+   double l1;
- /************ Frequencies ********************/
+   fx=func(x);
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
+   for (i=1;i<=npar;i++) p2[i]=x[i];
- {  /* Some frequencies */
+   for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
+     l1=pow(10,l);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+     delts=delt;
-   int first;
+     for(k=1 ; k <kmax; k=k+1){
-   double ***freq; /* Frequencies */
+       delt = delta*(l1*k);
-   double *pp, **prop;
+       p2[theta]=x[theta] +delt;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+       k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
-   char fileresp[FILENAMELENGTH];
+       p2[theta]=x[theta]-delt;
+       k2=func(p2)-fx;
-   pp=vector(1,nlstate);
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   strcpy(fileresp,"p");
-   strcat(fileresp,fileres);
+ #ifdef DEBUGHESS
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+       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);
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+       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);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+ #endif
-     exit(0);
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-   }
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+         k=kmax;
-   j1=0;
+       }
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-   j=cptcoveff;
+         k=kmax; l=lmax*10.;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+       }
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-   first=1;
+         delts=delt;
+       }
-   for(k1=1; k1<=j;k1++){
+     }
-     for(i1=1; i1<=ncodemax[k1];i1++){
+   }
-       j1++;
+   delti[theta]=delts;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   return res;
-         scanf("%d", i);*/
-       for (i=-5; i<=nlstate+ndeath; i++)
+ }
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
-           for(m=iagemin; m <= iagemax+3; m++)
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-             freq[i][jk][m]=0;
+ {
+   int i;
-     for (i=1; i<=nlstate; i++)
+   int l=1, l1, lmax=20;
-       for(m=iagemin; m <= iagemax+3; m++)
+   double k1,k2,k3,k4,res,fx;
-         prop[i][m]=0;
+   double p2[MAXPARM+1];
+   int k;
-       dateintsum=0;
-       k2cpt=0;
+   fx=func(x);
-       for (i=1; i<=imx; i++) {
+   for (k=1; k<=2; k++) {
-         bool=1;
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-         if  (cptcovn>0) {
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-           for (z1=1; z1<=cptcoveff; z1++)
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+     k1=func(p2)-fx;
-               bool=0;
-         }
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-         if (bool==1){
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-           for(m=firstpass; m<=lastpass; m++){
+     k2=func(p2)-fx;
-             k2=anint[m][i]+(mint[m][i]/12.);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     k3=func(p2)-fx;
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               if (m<lastpass) {
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+     k4=func(p2)-fx;
-               }
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+ #ifdef DEBUG
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+     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);
-                 dateintsum=dateintsum+k2;
+     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);
-                 k2cpt++;
+ #endif
-               }
+   }
-               /*}*/
+   return res;
-           }
+ }
-         }
-       }
+ /************** Inverse of matrix **************/
+ void ludcmp(double **a, int n, int *indx, double *d)
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ {
-       pstamp(ficresp);
+   int i,imax,j,k;
-       if  (cptcovn>0) {
+   double big,dum,sum,temp;
-         fprintf(ficresp, "\n#********** Variable ");
+   double *vv;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresp, "**********\n#");
+   vv=vector(1,n);
-       }
+   *d=1.0;
-       for(i=1; i<=nlstate;i++)
+   for (i=1;i<=n;i++) {
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+     big=0.0;
-       fprintf(ficresp, "\n");
+     for (j=1;j<=n;j++)
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-       for(i=iagemin; i <= iagemax+3; i++){
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-         if(i==iagemax+3){
+     vv[i]=1.0/big;
-           fprintf(ficlog,"Total");
+   }
-         }else{
+   for (j=1;j<=n;j++) {
-           if(first==1){
+     for (i=1;i<j;i++) {
-             first=0;
+       sum=a[i][j];
-             printf("See log file for details...\n");
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-           }
+       a[i][j]=sum;
-           fprintf(ficlog,"Age %d", i);
+     }
-         }
+     big=0.0;
-         for(jk=1; jk <=nlstate ; jk++){
+     for (i=j;i<=n;i++) {
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       sum=a[i][j];
-             pp[jk] += freq[jk][m][i];
+       for (k=1;k<j;k++)
-         }
+         sum -= a[i][k]*a[k][j];
-         for(jk=1; jk <=nlstate ; jk++){
+       a[i][j]=sum;
-           for(m=-1, pos=0; m <=0 ; m++)
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-             pos += freq[jk][m][i];
+         big=dum;
-           if(pp[jk]>=1.e-10){
+         imax=i;
-             if(first==1){
+       }
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     }
-             }
+     if (j != imax) {
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+       for (k=1;k<=n;k++) {
-           }else{
+         dum=a[imax][k];
-             if(first==1)
+         a[imax][k]=a[j][k];
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         a[j][k]=dum;
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       }
-           }
+       *d = -(*d);
-         }
+       vv[imax]=vv[j];
+     }
-         for(jk=1; jk <=nlstate ; jk++){
+     indx[j]=imax;
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-             pp[jk] += freq[jk][m][i];
+     if (j != n) {
-         }
+       dum=1.0/(a[j][j]);
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-           pos += pp[jk];
+     }
-           posprop += prop[jk][i];
+   }
-         }
+   free_vector(vv,1,n);  /* Doesn't work */
-         for(jk=1; jk <=nlstate ; jk++){
+ ;
-           if(pos>=1.e-5){
+ }
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ void lubksb(double **a, int n, int *indx, double b[])
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ {
-           }else{
+   int i,ii=0,ip,j;
-             if(first==1)
+   double sum;
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+   for (i=1;i<=n;i++) {
-           }
+     ip=indx[i];
-           if( i <= iagemax){
+     sum=b[ip];
-             if(pos>=1.e-5){
+     b[ip]=b[i];
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+     if (ii)
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+     else if (sum) ii=i;
-             }
+     b[i]=sum;
-             else
+   }
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+   for (i=n;i>=1;i--) {
-           }
+     sum=b[i];
-         }
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     b[i]=sum/a[i][i];
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+   }
-           for(m=-1; m <=nlstate+ndeath; m++)
+ }
-             if(freq[jk][m][i] !=0 ) {
-             if(first==1)
+ void pstamp(FILE *fichier)
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+ {
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-             }
+ }
-         if(i <= iagemax)
-           fprintf(ficresp,"\n");
+ /************ Frequencies ********************/
-         if(first==1)
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-           printf("Others in log...\n");
+ {  /* Some frequencies */
-         fprintf(ficlog,"\n");
-       }
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-     }
+   int first;
-   }
+   double ***freq; /* Frequencies */
-   dateintmean=dateintsum/k2cpt;
+   double *pp, **prop;
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   fclose(ficresp);
+   char fileresp[FILENAMELENGTH];
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   free_vector(pp,1,nlstate);
+   pp=vector(1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   /* End of Freq */
+   strcpy(fileresp,"p");
- }
+   strcat(fileresp,fileres);
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
- /************ Prevalence ********************/
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
- {
+     exit(0);
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   }
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-      We still use firstpass and lastpass as another selection.
+   j1=0;
-   */
+   j=cptcoveff;
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   double ***freq; /* Frequencies */
-   double *pp, **prop;
+   first=1;
-   double pos,posprop;
-   double  y2; /* in fractional years */
+   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
-   int iagemin, iagemax;
+   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+   /*    j1++;
-   iagemin= (int) agemin;
+ */
-   iagemax= (int) agemax;
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
-   /*pp=vector(1,nlstate);*/
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         scanf("%d", i);*/
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+       for (i=-5; i<=nlstate+ndeath; i++)
-   j1=0;
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
+           for(m=iagemin; m <= iagemax+3; m++)
-   j=cptcoveff;
+             freq[i][jk][m]=0;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+       for (i=1; i<=nlstate; i++)
-   for(k1=1; k1<=j;k1++){
+         for(m=iagemin; m <= iagemax+3; m++)
-     for(i1=1; i1<=ncodemax[k1];i1++){
+           prop[i][m]=0;
-       j1++;
+       dateintsum=0;
-       for (i=1; i<=nlstate; i++)
+       k2cpt=0;
-         for(m=iagemin; m <= iagemax+3; m++)
+       for (i=1; i<=imx; i++) {
-           prop[i][m]=0.0;
+         bool=1;
+         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-       for (i=1; i<=imx; i++) { /* Each individual */
+           for (z1=1; z1<=cptcoveff; z1++)
-         bool=1;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
-         if  (cptcovn>0) {
+                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-           for (z1=1; z1<=cptcoveff; z1++)
+               bool=0;
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-               bool=0;
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-         }
+                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-         if (bool==1) {
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+             }
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+         }
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+         if (bool==1){
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+           for(m=firstpass; m<=lastpass; m++){
-               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);
+             k2=anint[m][i]+(mint[m][i]/12.);
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-                 /*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]]);*/
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-                 prop[s[m][i]][iagemax+3] += weight[i];
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               }
+               if (m<lastpass) {
-             }
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-           } /* end selection of waves */
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-         }
+               }
-       }
-       for(i=iagemin; i <= iagemax+3; i++){
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+                 dateintsum=dateintsum+k2;
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+                 k2cpt++;
-           posprop += prop[jk][i];
+               }
-         }
+               /*}*/
+           }
-         for(jk=1; jk <=nlstate ; jk++){
+         }
-           if( i <=  iagemax){
+       } /* end i */
-             if(posprop>=1.e-5){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-             }
+       pstamp(ficresp);
-           }
+       if  (cptcovn>0) {
-         }/* end jk */
+         fprintf(ficresp, "\n#********** Variable ");
-       }/* end i */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-     } /* end i1 */
+         fprintf(ficresp, "**********\n#");
-   } /* end k1 */
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+         fprintf(ficlog, "**********\n#");
-   /*free_vector(pp,1,nlstate);*/
+       }
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+       for(i=1; i<=nlstate;i++)
- }  /* End of prevalence */
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, "\n");
- /************* Waves Concatenation ***************/
+       for(i=iagemin; i <= iagemax+3; i++){
- void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+         if(i==iagemax+3){
- {
+           fprintf(ficlog,"Total");
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+         }else{
-      Death is a valid wave (if date is known).
+           if(first==1){
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+             first=0;
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+             printf("See log file for details...\n");
-      and mw[mi+1][i]. dh depends on stepm.
+           }
-      */
+           fprintf(ficlog,"Age %d", i);
+         }
-   int i, mi, m;
+         for(jk=1; jk <=nlstate ; jk++){
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-      double sum=0., jmean=0.;*/
+             pp[jk] += freq[jk][m][i];
-   int first;
+         }
-   int j, k=0,jk, ju, jl;
+         for(jk=1; jk <=nlstate ; jk++){
-   double sum=0.;
+           for(m=-1, pos=0; m <=0 ; m++)
-   first=0;
+             pos += freq[jk][m][i];
-   jmin=1e+5;
+           if(pp[jk]>=1.e-10){
-   jmax=-1;
+             if(first==1){
-   jmean=0.;
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   for(i=1; i<=imx; i++){
+             }
-     mi=0;
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-     m=firstpass;
+           }else{
-     while(s[m][i] <= nlstate){
+             if(first==1)
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+               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);
-       if(m >=lastpass)
+           }
-         break;
+         }
-       else
-         m++;
+         for(jk=1; jk <=nlstate ; jk++){
-     }/* end while */
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-     if (s[m][i] > nlstate){
+             pp[jk] += freq[jk][m][i];
-       mi++;     /* Death is another wave */
+         }
-       /* if(mi==0)  never been interviewed correctly before death */
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-          /* Only death is a correct wave */
+           pos += pp[jk];
-       mw[mi][i]=m;
+           posprop += prop[jk][i];
-     }
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-     wav[i]=mi;
+           if(pos>=1.e-5){
-     if(mi==0){
+             if(first==1)
-       nbwarn++;
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-       if(first==0){
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+           }else{
-         first=1;
+             if(first==1)
-       }
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-       if(first==1){
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+           }
-       }
+           if( i <= iagemax){
-     } /* end mi==0 */
+             if(pos>=1.e-5){
-   } /* End individuals */
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   for(i=1; i<=imx; i++){
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-     for(mi=1; mi<wav[i];mi++){
+             }
-       if (stepm <=0)
+             else
-         dh[mi][i]=1;
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-       else{
+           }
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         }
-           if (agedc[i] < 2*AGESUP) {
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-             if(j==0) j=1;  /* Survives at least one month after exam */
+           for(m=-1; m <=nlstate+ndeath; m++)
-             else if(j<0){
+             if(freq[jk][m][i] !=0 ) {
-               nberr++;
+             if(first==1)
-               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]);
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-               j=1; /* Temporary Dangerous patch */
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-               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(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         if(i <= iagemax)
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+           fprintf(ficresp,"\n");
-             }
+         if(first==1)
-             k=k+1;
+           printf("Others in log...\n");
-             if (j >= jmax){
+         fprintf(ficlog,"\n");
-               jmax=j;
+       }
-               ijmax=i;
+       /*}*/
-             }
+   }
-             if (j <= jmin){
+   dateintmean=dateintsum/k2cpt;
-               jmin=j;
-               ijmin=i;
+   fclose(ficresp);
-             }
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-             sum=sum+j;
+   free_vector(pp,1,nlstate);
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+   /* End of Freq */
-           }
+ }
-         }
-         else{
+ /************ Prevalence ********************/
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ 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<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]); */
+ {
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-           k=k+1;
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-           if (j >= jmax) {
+      We still use firstpass and lastpass as another selection.
-             jmax=j;
+   */
-             ijmax=i;
-           }
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-           else if (j <= jmin){
+   double ***freq; /* Frequencies */
-             jmin=j;
+   double *pp, **prop;
-             ijmin=i;
+   double pos,posprop;
-           }
+   double  y2; /* in fractional years */
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   int iagemin, iagemax;
-           /*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]);*/
+   int first; /** to stop verbosity which is redirected to log file */
-           if(j<0){
-             nberr++;
+   iagemin= (int) agemin;
-             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]);
+   iagemax= (int) agemax;
-             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]);
+   /*pp=vector(1,nlstate);*/
-           }
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-           sum=sum+j;
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-         }
+   j1=0;
-         jk= j/stepm;
-         jl= j -jk*stepm;
+   /*j=cptcoveff;*/
-         ju= j -(jk+1)*stepm;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-           if(jl==0){
+   first=1;
-             dh[mi][i]=jk;
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-             bh[mi][i]=0;
+     /*for(i1=1; i1<=ncodemax[k1];i1++){
-           }else{ /* We want a negative bias in order to only have interpolation ie
+       j1++;*/
-                   * at the price of an extra matrix product in likelihood */
-             dh[mi][i]=jk+1;
+       for (i=1; i<=nlstate; i++)
-             bh[mi][i]=ju;
+         for(m=iagemin; m <= iagemax+3; m++)
-           }
+           prop[i][m]=0.0;
-         }else{
-           if(jl <= -ju){
+       for (i=1; i<=imx; i++) { /* Each individual */
-             dh[mi][i]=jk;
+         bool=1;
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         if  (cptcovn>0) {
-                                  * is higher than the multiple of stepm and negative otherwise.
+           for (z1=1; z1<=cptcoveff; z1++)
-                                  */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-           }
+               bool=0;
-           else{
+         }
-             dh[mi][i]=jk+1;
+         if (bool==1) {
-             bh[mi][i]=ju;
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-           }
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-           if(dh[mi][i]==0){
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-             dh[mi][i]=1; /* At least one step */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-             bh[mi][i]=ju; /* At least one step */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-           }
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-         } /* end if mle */
+                 /*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];
-     } /* end wave */
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   }
+               }
-   jmean=sum/k;
+             }
-   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+           } /* end selection of waves */
-   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);
+         }
-  }
+       }
+       for(i=iagemin; i <= iagemax+3; i++){
- /*********** Tricode ****************************/
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
- void tricode(int *Tvar, int **nbcode, int imx)
+           posprop += prop[jk][i];
- {
+         }
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+         for(jk=1; jk <=nlstate ; jk++){
-   int cptcode=0;
+           if( i <=  iagemax){
-   cptcoveff=0;
+             if(posprop>=1.e-5){
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+             } else{
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+               if(first==1){
+                 first=0;
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
-     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*/
+           }
-       Ndum[ij]++; /*store the modality */
+         }/* end jk */
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       }/* end i */
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+     /*} *//* end i1 */
-                                        Tvar[j]. If V=sex and male is 0 and
+   } /* end j1 */
-                                        female is 1, then  cptcode=1.*/
-     }
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*free_vector(pp,1,nlstate);*/
-     for (i=0; i<=cptcode; i++) {
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-       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 of prevalence */
-     }
+ /************* Waves Concatenation ***************/
-     ij=1;
-     for (i=1; i<=ncodemax[j]; i++) {
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
-       for (k=0; k<= maxncov; k++) {
+ {
-         if (Ndum[k] != 0) {
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-           nbcode[Tvar[j]][ij]=k;
+      Death is a valid wave (if date is known).
-           /* 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; */
+      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]
-           ij++;
+      and mw[mi+1][i]. dh depends on stepm.
-         }
+      */
-         if (ij > ncodemax[j]) break;
-       }
+   int i, mi, m;
-     }
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-   }
+      double sum=0., jmean=0.;*/
+   int first;
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   int j, k=0,jk, ju, jl;
+   double sum=0.;
-  for (i=1; i<=ncovmodel-2; i++) {
+   first=0;
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+   jmin=1e+5;
-    ij=Tvar[i];
+   jmax=-1;
-    Ndum[ij]++;
+   jmean=0.;
-  }
+   for(i=1; i<=imx; i++){
+     mi=0;
-  ij=1;
+     m=firstpass;
-  for (i=1; i<= maxncov; i++) {
+     while(s[m][i] <= nlstate){
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-      Tvaraff[ij]=i; /*For printing */
+         mw[++mi][i]=m;
-      ij++;
+       if(m >=lastpass)
-    }
+         break;
-  }
+       else
+         m++;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+     }/* end while */
- }
+     if (s[m][i] > nlstate){
+       mi++;     /* Death is another wave */
- /*********** Health Expectancies ****************/
+       /* if(mi==0)  never been interviewed correctly before death */
+          /* Only death is a correct wave */
- 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;
+     }
- {
-   /* Health expectancies, no variances */
+     wav[i]=mi;
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+     if(mi==0){
-   double age, agelim, hf;
+       nbwarn++;
-   double ***p3mat;
+       if(first==0){
-   double eip;
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         first=1;
-   pstamp(ficreseij);
+       }
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+       if(first==1){
-   fprintf(ficreseij,"# Age");
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-   for(i=1; i<=nlstate;i++){
+       }
-     for(j=1; j<=nlstate;j++){
+     } /* end mi==0 */
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   } /* End individuals */
-     }
-     fprintf(ficreseij," e%1d. ",i);
+   for(i=1; i<=imx; i++){
-   }
+     for(mi=1; mi<wav[i];mi++){
-   fprintf(ficreseij,"\n");
+       if (stepm <=0)
+         dh[mi][i]=1;
+       else{
-   if(estepm < stepm){
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+           if (agedc[i] < 2*AGESUP) {
-   }
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-   else  hstepm=estepm;
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+             else if(j<0){
-    * This is mainly to measure the difference between two models: for example
+               nberr++;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+               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]);
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+               j=1; /* Temporary Dangerous patch */
-    * progression in between and thus overestimating or underestimating according
+               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);
-    * to the curvature of the survival function. If, for the same date, we
+               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]);
-    * estimate the model with stepm=1 month, we can keep estepm to 24 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);
-    * to compare the new estimate of Life expectancy with the same linear
+             }
-    * hypothesis. A more precise result, taking into account a more precise
+             k=k+1;
-    * curvature will be obtained if estepm is as small as stepm. */
+             if (j >= jmax){
+               jmax=j;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+               ijmax=i;
-   /* 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
+             if (j <= jmin){
-      nstepm is the number of stepm from age to agelin.
+               jmin=j;
-      Look at hpijx to understand the reason of that which relies in memory size
+               ijmin=i;
-      and note for a fixed period like estepm months */
+             }
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+             sum=sum+j;
-      survival function given by stepm (the optimization length). Unfortunately it
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-      means that if the survival funtion is printed only each two years of age and if
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+           }
-      results. So we changed our mind and took the option of the best precision.
+         }
-   */
+         else{
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-   agelim=AGESUP;
-   /* If stepm=6 months */
+           k=k+1;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+           if (j >= jmax) {
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+             jmax=j;
+             ijmax=i;
- /* nhstepm age range expressed in number of stepm */
+           }
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+           else if (j <= jmin){
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+             jmin=j;
-   /* if (stepm >= YEARM) hstepm=1;*/
+             ijmin=i;
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+           }
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /*        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]);*/
-   for (age=bage; age<=fage; age ++){
+           if(j<0){
+             nberr++;
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+           }
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           sum=sum+j;
+         }
-     printf("%d|",(int)age);fflush(stdout);
+         jk= j/stepm;
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+         jl= j -jk*stepm;
+         ju= j -(jk+1)*stepm;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-     /* Computing expectancies */
+           if(jl==0){
-     for(i=1; i<=nlstate;i++)
+             dh[mi][i]=jk;
-       for(j=1; j<=nlstate;j++)
+             bh[mi][i]=0;
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           }else{ /* We want a negative bias in order to only have interpolation ie
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+                   * to avoid the price of an extra matrix product in likelihood */
+             dh[mi][i]=jk+1;
-           /*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]);*/
+             bh[mi][i]=ju;
+           }
-         }
+         }else{
+           if(jl <= -ju){
-     fprintf(ficreseij,"%3.0f",age );
+             dh[mi][i]=jk;
-     for(i=1; i<=nlstate;i++){
+             bh[mi][i]=jl;       /* bias is positive if real duration
-       eip=0;
+                                  * is higher than the multiple of stepm and negative otherwise.
-       for(j=1; j<=nlstate;j++){
+                                  */
-         eip +=eij[i][j][(int)age];
+           }
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+           else{
-       }
+             dh[mi][i]=jk+1;
-       fprintf(ficreseij,"%9.4f", eip );
+             bh[mi][i]=ju;
-     }
+           }
-     fprintf(ficreseij,"\n");
+           if(dh[mi][i]==0){
+             dh[mi][i]=1; /* At least one step */
-   }
+             bh[mi][i]=ju; /* At least one step */
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             /*  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);*/
-   printf("\n");
+           }
-   fprintf(ficlog,"\n");
+         } /* end if mle */
+       }
- }
+     } /* end wave */
+   }
- 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[] )
+   jmean=sum/k;
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
- {
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-   /* Covariances of health expectancies eij and of total life expectancies according
+  }
-    to initial status i, ei. .
-   */
+ /*********** Tricode ****************************/
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+ void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
-   double age, agelim, hf;
+ {
-   double ***p3matp, ***p3matm, ***varhe;
+   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   double **dnewm,**doldm;
+   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   double *xp, *xm;
+   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
-   double **gp, **gm;
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-   double ***gradg, ***trgradg;
+   /* nbcode[Tvar[j]][1]=
-   int theta;
+   */
-   double eip, vip;
+   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   int modmaxcovj=0; /* Modality max of covariates j */
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+   int cptcode=0; /* Modality max of covariates j */
-   xp=vector(1,npar);
+   int modmincovj=0; /* Modality min of covariates j */
-   xm=vector(1,npar);
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   cptcoveff=0;
-   pstamp(ficresstdeij);
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   fprintf(ficresstdeij,"# 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 */
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-     fprintf(ficresstdeij," e%1d. ",i);
+                                modality of this covariate Vj*/
-   }
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-   fprintf(ficresstdeij,"\n");
+                                     * If product of Vn*Vm, still boolean *:
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-   pstamp(ficrescveij);
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   fprintf(ficrescveij,"# Age");
+                                       modality of the nth covariate of individual i. */
-   for(i=1; i<=nlstate;i++)
+       if (ij > modmaxcovj)
-     for(j=1; j<=nlstate;j++){
+         modmaxcovj=ij;
-       cptj= (j-1)*nlstate+i;
+       else if (ij < modmincovj)
-       for(i2=1; i2<=nlstate;i2++)
+         modmincovj=ij;
-         for(j2=1; j2<=nlstate;j2++){
+       if ((ij < -1) && (ij > NCOVMAX)){
-           cptj2= (j2-1)*nlstate+i2;
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-           if(cptj2 <= cptj)
+         exit(1);
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+       }else
-         }
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-     }
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-   fprintf(ficrescveij,"\n");
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+       /* getting the maximum value of the modality of the covariate
-   if(estepm < stepm){
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+          female is 1, then modmaxcovj=1.*/
-   }
+     }
-   else  hstepm=estepm;
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     cptcode=modmaxcovj;
-    * This is mainly to measure the difference between two models: for example
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+    /*for (i=0; i<=cptcode; i++) {*/
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-    * progression in between and thus overestimating or underestimating according
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-    * to the curvature of the survival function. If, for the same date, we
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-    * to compare the new estimate of Life expectancy with the same linear
+       }
-    * hypothesis. A more precise result, taking into account a more precise
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-    * curvature will be obtained if estepm is as small as stepm. */
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
-   /* 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.
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-      nhstepm is the number of hstepm from age to agelim
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
-      nstepm is the number of stepm from age to agelin.
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
-      Look at hpijx to understand the reason of that which relies in memory size
+        modmincovj=3; modmaxcovj = 7;
-      and note for a fixed period like estepm months */
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
-      survival function given by stepm (the optimization length). Unfortunately it
+        variables V1_1 and V1_2.
-      means that if the survival funtion is printed only each two years of age and if
+        nbcode[Tvar[j]][ij]=k;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+        nbcode[Tvar[j]][1]=0;
-      results. So we changed our mind and took the option of the best precision.
+        nbcode[Tvar[j]][2]=1;
-   */
+        nbcode[Tvar[j]][3]=2;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     */
+     ij=1; /* ij is similar to i but can jumps over null modalities */
-   /* If stepm=6 months */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
-   /* nhstepm age range expressed in number of stepm */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
-   agelim=AGESUP;
+         /*recode from 0 */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   /* if (stepm >= YEARM) hstepm=1;*/
+                                      k is a modality. If we have model=V1+V1*sex
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+           ij++;
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if (ij > ncodemax[j]) break;
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+       }  /* end of loop on */
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+     } /* end of loop on modality */
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+  for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   for (age=bage; age<=fage; age ++){
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
+    Ndum[ij]++;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+  }
-     /* Computing  Variances of health expectancies */
+  ij=1;
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-        decrease memory allocation */
+    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     for(theta=1; theta <=npar; theta++){
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-       for(i=1; i<=npar; i++){
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+      Tvaraff[ij]=i; /*For printing (unclear) */
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+      ij++;
-       }
+    }else
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+        Tvaraff[ij]=0;
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+  }
+  ij--;
-       for(j=1; j<= nlstate; j++){
+  cptcoveff=ij; /*Number of total covariates*/
-         for(i=1; i<=nlstate; i++){
-           for(h=0; h<=nhstepm-1; h++){
+ }
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-           }
+ /*********** Health Expectancies ****************/
-         }
-       }
+ 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(ij=1; ij<= nlstate*nlstate; ij++)
+ {
-         for(h=0; h<=nhstepm-1; h++){
+   /* Health expectancies, no variances */
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-         }
+   int nhstepma, nstepma; /* Decreasing with age */
-     }/* End theta */
+   double age, agelim, hf;
+   double ***p3mat;
+   double eip;
-     for(h=0; h<=nhstepm-1; h++)
-       for(j=1; j<=nlstate*nlstate;j++)
+   pstamp(ficreseij);
-         for(theta=1; theta <=npar; theta++)
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   fprintf(ficreseij,"# Age");
+   for(i=1; i<=nlstate;i++){
+     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] =0.;
+     fprintf(ficreseij," e%1d. ",i);
+   }
-      printf("%d|",(int)age);fflush(stdout);
+   fprintf(ficreseij,"\n");
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
-       for(k=0;k<=nhstepm-1;k++){
+   if(estepm < stepm){
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+   }
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+   else  hstepm=estepm;
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+    * This is mainly to measure the difference between two models: for example
-       }
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     }
+    * we are calculating an estimate of the Life Expectancy assuming a linear
+    * progression in between and thus overestimating or underestimating according
-     /* Computing expectancies */
+    * to the curvature of the survival function. If, for the same date, we
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+    * 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
-       for(j=1; j<=nlstate;j++)
+    * hypothesis. A more precise result, taking into account a more precise
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+    * curvature will be obtained if estepm is as small as stepm. */
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-           /* 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]);*/
+   /* 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
-     fprintf(ficresstdeij,"%3.0f",age );
+      and note for a fixed period like estepm months */
-     for(i=1; i<=nlstate;i++){
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       eip=0.;
+      survival function given by stepm (the optimization length). Unfortunately it
-       vip=0.;
+      means that if the survival funtion is printed only each two years of age and if
-       for(j=1; j<=nlstate;j++){
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         eip += eij[i][j][(int)age];
+      results. So we changed our mind and took the option of the best precision.
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+   */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-       }
+   agelim=AGESUP;
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+   /* If stepm=6 months */
-     }
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-     fprintf(ficresstdeij,"\n");
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     fprintf(ficrescveij,"%3.0f",age );
+ /* nhstepm age range expressed in number of stepm */
-     for(i=1; i<=nlstate;i++)
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       for(j=1; j<=nlstate;j++){
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         cptj= (j-1)*nlstate+i;
+   /* if (stepm >= YEARM) hstepm=1;*/
-         for(i2=1; i2<=nlstate;i2++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           for(j2=1; j2<=nlstate;j2++){
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             cptj2= (j2-1)*nlstate+i2;
-             if(cptj2 <= cptj)
+   for (age=bage; age<=fage; age ++){
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-           }
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       }
+     /* if (stepm >= YEARM) hstepm=1;*/
-     fprintf(ficrescveij,"\n");
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   }
+     /* If stepm=6 months */
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   printf("\n");
-   fprintf(ficlog,"\n");
+     printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   free_vector(xm,1,npar);
-   free_vector(xp,1,npar);
+     /* Computing expectancies */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+     for(i=1; i<=nlstate;i++)
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+       for(j=1; j<=nlstate;j++)
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+         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;
- /************ Variance ******************/
+           /* 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]);*/
- 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[])
- {
+         }
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     fprintf(ficreseij,"%3.0f",age );
-   /* double **newm;*/
+     for(i=1; i<=nlstate;i++){
-   double **dnewm,**doldm;
+       eip=0;
-   double **dnewmp,**doldmp;
+       for(j=1; j<=nlstate;j++){
-   int i, j, nhstepm, hstepm, h, nstepm ;
+         eip +=eij[i][j][(int)age];
-   int k, cptcode;
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-   double *xp;
+       }
-   double **gp, **gm;  /* for var eij */
+       fprintf(ficreseij,"%9.4f", eip );
-   double ***gradg, ***trgradg; /*for var eij */
+     }
-   double **gradgp, **trgradgp; /* for var p point j */
+     fprintf(ficreseij,"\n");
-   double *gpp, *gmp; /* for var p point j */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   }
-   double ***p3mat;
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   double age,agelim, hf;
+   printf("\n");
-   double ***mobaverage;
+   fprintf(ficlog,"\n");
-   int theta;
-   char digit[4];
+ }
-   char digitp[25];
+ 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[] )
-   char fileresprobmorprev[FILENAMELENGTH];
+ {
-   if(popbased==1){
+   /* Covariances of health expectancies eij and of total life expectancies according
-     if(mobilav!=0)
+    to initial status i, ei. .
-       strcpy(digitp,"-populbased-mobilav-");
+   */
-     else strcpy(digitp,"-populbased-nomobil-");
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   }
+   int nhstepma, nstepma; /* Decreasing with age */
-   else
+   double age, agelim, hf;
-     strcpy(digitp,"-stablbased-");
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
-   if (mobilav!=0) {
+   double *xp, *xm;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double **gp, **gm;
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   double ***gradg, ***trgradg;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   int theta;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
+   double eip, vip;
-   }
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   strcpy(fileresprobmorprev,"prmorprev");
+   xp=vector(1,npar);
-   sprintf(digit,"%-d",ij);
+   xm=vector(1,npar);
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+   pstamp(ficresstdeij);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+   fprintf(ficresstdeij,"# Age");
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+   for(i=1; i<=nlstate;i++){
-   }
+     for(j=1; j<=nlstate;j++)
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+     fprintf(ficresstdeij," e%1d. ",i);
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   }
-   pstamp(ficresprobmorprev);
+   fprintf(ficresstdeij,"\n");
-   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   pstamp(ficrescveij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   fprintf(ficrescveij,"# 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++){
-   }
+       cptj= (j-1)*nlstate+i;
-   fprintf(ficresprobmorprev,"\n");
+       for(i2=1; i2<=nlstate;i2++)
-   fprintf(ficgp,"\n# Routine varevsij");
+         for(j2=1; j2<=nlstate;j2++){
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+           cptj2= (j2-1)*nlstate+i2;
-   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");
+           if(cptj2 <= cptj)
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
- /*   } */
+         }
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     }
-   pstamp(ficresvij);
+   fprintf(ficrescveij,"\n");
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   if(popbased==1)
+   if(estepm < stepm){
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   else
+   }
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   else  hstepm=estepm;
-   fprintf(ficresvij,"# Age");
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   for(i=1; i<=nlstate;i++)
+    * This is mainly to measure the difference between two models: for example
-     for(j=1; j<=nlstate;j++)
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   fprintf(ficresvij,"\n");
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-   xp=vector(1,npar);
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   dnewm=matrix(1,nlstate,1,npar);
+    * to compare the new estimate of Life expectancy with the same linear
-   doldm=matrix(1,nlstate,1,nlstate);
+    * hypothesis. A more precise result, taking into account a more precise
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    * curvature will be obtained if estepm is as small as stepm. */
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   gpp=vector(nlstate+1,nlstate+ndeath);
+      nhstepm is the number of hstepm from age to agelim
-   gmp=vector(nlstate+1,nlstate+ndeath);
+      nstepm is the number of stepm from age to agelin.
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+      Look at hpijx to understand the reason of that which relies in memory size
+      and note for a fixed period like estepm months */
-   if(estepm < stepm){
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+      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
-   else  hstepm=estepm;
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   /* For example we decided to compute the life expectancy with the smallest unit */
+      results. So we changed our mind and took the option of the best precision.
-   /* 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
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-      nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+   /* If stepm=6 months */
-      and note for a fixed period like k years */
+   /* nhstepm age range expressed in number of stepm */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   agelim=AGESUP;
-      survival function given by stepm (the optimization length). Unfortunately it
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-      means that if the survival funtion is printed every two years of age and if
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   /* if (stepm >= YEARM) hstepm=1;*/
-      results. So we changed our mind and took the option of the best precision.
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   agelim = AGESUP;
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
+   for (age=bage; age<=fage; age ++){
-     gm=matrix(0,nhstepm,1,nlstate);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     /* if (stepm >= YEARM) hstepm=1;*/
-     for(theta=1; theta <=npar; theta++){
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     /* If stepm=6 months */
-       }
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-       if (popbased==1) {
-         if(mobilav ==0){
+     /* Computing  Variances of health expectancies */
-           for(i=1; i<=nlstate;i++)
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-             prlim[i][i]=probs[(int)age][i][ij];
+        decrease memory allocation */
-         }else{ /* mobilav */
+     for(theta=1; theta <=npar; theta++){
-           for(i=1; i<=nlstate;i++)
+       for(i=1; i<=npar; i++){
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         }
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-       for(j=1; j<= nlstate; j++){
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-         for(h=0; h<=nhstepm; h++){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+       for(j=1; j<= nlstate; j++){
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+         for(i=1; i<=nlstate; i++){
-         }
+           for(h=0; h<=nhstepm-1; h++){
-       }
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-       /* This for computing probability of death (h=1 means
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-          computed over hstepm matrices product = hstepm*stepm months)
+           }
-          as a weighted average of prlim.
+         }
-       */
+       }
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+         for(h=0; h<=nhstepm-1; h++){
-       }
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-       /* end probability of death */
+         }
+     }/* End theta */
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+     for(h=0; h<=nhstepm-1; h++)
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       for(j=1; j<=nlstate*nlstate;j++)
+         for(theta=1; theta <=npar; theta++)
-       if (popbased==1) {
+           trgradg[h][j][theta]=gradg[h][theta][j];
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-         }else{ /* mobilav */
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-           for(i=1; i<=nlstate;i++)
+         varhe[ij][ji][(int)age] =0.;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
+      printf("%d|",(int)age);fflush(stdout);
-       }
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+      for(h=0;h<=nhstepm-1;h++){
-       for(j=1; j<= nlstate; j++){
+       for(k=0;k<=nhstepm-1;k++){
-         for(h=0; h<=nhstepm; h++){
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-             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] += doldm[ij][ji]*hf*hf;
-       /* This for computing probability of death (h=1 means
+       }
-          computed over hstepm matrices product = hstepm*stepm months)
+     }
-          as a weighted average of prlim.
-       */
+     /* Computing expectancies */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+     for(i=1; i<=nlstate;i++)
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       for(j=1; j<=nlstate;j++)
-       }
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-       /* end probability of death */
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-       for(j=1; j<= nlstate; j++) /* vareij */
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-         for(h=0; h<=nhstepm; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+         }
-         }
+     fprintf(ficresstdeij,"%3.0f",age );
-       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];
+       eip=0.;
-       }
+       vip=0.;
+       for(j=1; j<=nlstate;j++){
-     } /* End theta */
+         eip += eij[i][j][(int)age];
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-     for(h=0; h<=nhstepm; h++) /* veij */
+       }
-       for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-         for(theta=1; theta <=npar; theta++)
+     }
-           trgradg[h][j][theta]=gradg[h][theta][j];
+     fprintf(ficresstdeij,"\n");
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+     fprintf(ficrescveij,"%3.0f",age );
-       for(theta=1; theta <=npar; theta++)
+     for(i=1; i<=nlstate;i++)
-         trgradgp[j][theta]=gradgp[theta][j];
+       for(j=1; j<=nlstate;j++){
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+           for(j2=1; j2<=nlstate;j2++){
-     for(i=1;i<=nlstate;i++)
+             cptj2= (j2-1)*nlstate+i2;
-       for(j=1;j<=nlstate;j++)
+             if(cptj2 <= cptj)
-         vareij[i][j][(int)age] =0.;
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+           }
-     for(h=0;h<=nhstepm;h++){
+       }
-       for(k=0;k<=nhstepm;k++){
+     fprintf(ficrescveij,"\n");
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+   }
-         for(i=1;i<=nlstate;i++)
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-           for(j=1;j<=nlstate;j++)
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-       }
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     }
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* pptj */
+   printf("\n");
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   fprintf(ficlog,"\n");
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+   free_vector(xm,1,npar);
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+   free_vector(xp,1,npar);
-         varppt[j][i]=doldmp[j][i];
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-     /* end ppptj */
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-     /*  x centered again */
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+ }
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+ /************ Variance ******************/
-     if (popbased==1) {
+ 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[])
-       if(mobilav ==0){
+ {
-         for(i=1; i<=nlstate;i++)
+   /* Variance of health expectancies */
-           prlim[i][i]=probs[(int)age][i][ij];
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-       }else{ /* mobilav */
+   /* double **newm;*/
-         for(i=1; i<=nlstate;i++)
+   double **dnewm,**doldm;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+   double **dnewmp,**doldmp;
-       }
+   int i, j, nhstepm, hstepm, h, nstepm ;
-     }
+   int k, cptcode;
+   double *xp;
-     /* This for computing probability of death (h=1 means
+   double **gp, **gm;  /* for var eij */
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+   double ***gradg, ***trgradg; /*for var eij */
-        as a weighted average of prlim.
+   double **gradgp, **trgradgp; /* for var p point j */
-     */
+   double *gpp, *gmp; /* for var p point j */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+   double ***p3mat;
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   double age,agelim, hf;
-     }
+   double ***mobaverage;
-     /* end probability of death */
+   int theta;
+   char digit[4];
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+   char digitp[25];
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+   char fileresprobmorprev[FILENAMELENGTH];
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+   if(popbased==1){
-       }
+     if(mobilav!=0)
-     }
+       strcpy(digitp,"-populbased-mobilav-");
-     fprintf(ficresprobmorprev,"\n");
+     else strcpy(digitp,"-populbased-nomobil-");
+   }
-     fprintf(ficresvij,"%.0f ",age );
+   else
-     for(i=1; i<=nlstate;i++)
+     strcpy(digitp,"-stablbased-");
-       for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+   if (mobilav!=0) {
-       }
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     fprintf(ficresvij,"\n");
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-     free_matrix(gp,0,nhstepm,1,nlstate);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     }
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+   }
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   } /* End age */
+   strcpy(fileresprobmorprev,"prmorprev");
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+   sprintf(digit,"%-d",ij);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+   strcat(fileresprobmorprev,fileres);
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
- /*   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); */
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+   pstamp(ficresprobmorprev);
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   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(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(ficresprobmorprev,"# Age cov=%-d",ij);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- */
+     fprintf(ficresprobmorprev," p.%-d SE",j);
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+     for(i=1; i<=nlstate;i++)
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   }
-   free_vector(xp,1,npar);
+   fprintf(ficresprobmorprev,"\n");
-   free_matrix(doldm,1,nlstate,1,nlstate);
+   fprintf(ficgp,"\n# Routine varevsij");
-   free_matrix(dnewm,1,nlstate,1,npar);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   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");
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ /*   } */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   fclose(ficresprobmorprev);
+   pstamp(ficresvij);
-   fflush(ficgp);
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   fflush(fichtm);
+   if(popbased==1)
- }  /* end varevsij */
+     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);
+   else
- /************ Variance of prevlim ******************/
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
- 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(ficresvij,"# Age");
- {
+   for(i=1; i<=nlstate;i++)
-   /* Variance of prevalence limit */
+     for(j=1; j<=nlstate;j++)
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   double **newm;
+   fprintf(ficresvij,"\n");
-   double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm;
+   xp=vector(1,npar);
-   int k, cptcode;
+   dnewm=matrix(1,nlstate,1,npar);
-   double *xp;
+   doldm=matrix(1,nlstate,1,nlstate);
-   double *gp, *gm;
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   double **gradg, **trgradg;
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   double age,agelim;
-   int theta;
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   gpp=vector(nlstate+1,nlstate+ndeath);
-   pstamp(ficresvpl);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   fprintf(ficresvpl,"# Age");
-   for(i=1; i<=nlstate;i++)
+   if(estepm < stepm){
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   fprintf(ficresvpl,"\n");
+   }
+   else  hstepm=estepm;
-   xp=vector(1,npar);
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   dnewm=matrix(1,nlstate,1,npar);
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-   doldm=matrix(1,nlstate,1,nlstate);
+      nhstepm is the number of hstepm from age to agelim
+      nstepm is the number of stepm from age to agelin.
-   hstepm=1*YEARM; /* Every year of age */
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-   agelim = AGESUP;
+      survival function given by stepm (the optimization length). Unfortunately it
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+      means that if the survival funtion is printed every two years of age and if
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     if (stepm >= YEARM) hstepm=1;
+      results. So we changed our mind and took the option of the best precision.
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   */
-     gradg=matrix(1,npar,1,nlstate);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     gp=vector(1,nlstate);
+   agelim = AGESUP;
-     gm=vector(1,nlstate);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     for(theta=1; theta <=npar; theta++){
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-       }
+     gp=matrix(0,nhstepm,1,nlstate);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     gm=matrix(0,nhstepm,1,nlstate);
-       for(i=1;i<=nlstate;i++)
-         gp[i] = prlim[i][i];
+     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++) /* Computes gradient */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       for(i=1;i<=nlstate;i++)
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         gm[i] = prlim[i][i];
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       for(i=1;i<=nlstate;i++)
+       if (popbased==1) {
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+         if(mobilav ==0){
-     } /* End theta */
+           for(i=1; i<=nlstate;i++)
+             prlim[i][i]=probs[(int)age][i][ij];
-     trgradg =matrix(1,nlstate,1,npar);
+         }else{ /* mobilav */
+           for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++)
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-       for(theta=1; theta <=npar; theta++)
+         }
-         trgradg[j][theta]=gradg[theta][j];
+       }
-     for(i=1;i<=nlstate;i++)
+       for(j=1; j<= nlstate; j++){
-       varpl[i][(int)age] =0.;
+         for(h=0; h<=nhstepm; h++){
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-     for(i=1;i<=nlstate;i++)
+         }
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+       }
+       /* This for computing probability of death (h=1 means
-     fprintf(ficresvpl,"%.0f ",age );
+          computed over hstepm matrices product = hstepm*stepm months)
-     for(i=1; i<=nlstate;i++)
+          as a weighted average of prlim.
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       */
-     fprintf(ficresvpl,"\n");
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     free_vector(gp,1,nlstate);
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-     free_vector(gm,1,nlstate);
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-     free_matrix(gradg,1,npar,1,nlstate);
+       }
-     free_matrix(trgradg,1,nlstate,1,npar);
+       /* end probability of death */
-   } /* End age */
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-   free_vector(xp,1,npar);
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   free_matrix(doldm,1,nlstate,1,npar);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- }
+       if (popbased==1) {
+         if(mobilav ==0){
- /************ Variance of one-step probabilities  ******************/
+           for(i=1; i<=nlstate;i++)
- 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[])
+             prlim[i][i]=probs[(int)age][i][ij];
- {
+         }else{ /* mobilav */
-   int i, j=0,  i1, k1, l1, t, tj;
+           for(i=1; i<=nlstate;i++)
-   int k2, l2, j1,  z1;
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-   int k=0,l, cptcode;
+         }
-   int first=1, first1;
+       }
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-   double *xp;
+         for(h=0; h<=nhstepm; h++){
-   double *gp, *gm;
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-   double **gradg, **trgradg;
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   double **mu;
+         }
-   double age,agelim, cov[NCOVMAX];
+       }
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+       /* This for computing probability of death (h=1 means
-   int theta;
+          computed over hstepm matrices product = hstepm*stepm months)
-   char fileresprob[FILENAMELENGTH];
+          as a weighted average of prlim.
-   char fileresprobcov[FILENAMELENGTH];
+       */
-   char fileresprobcor[FILENAMELENGTH];
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-   double ***varpij;
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+       }
-   strcpy(fileresprob,"prob");
+       /* end probability of death */
-   strcat(fileresprob,fileres);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+       for(j=1; j<= nlstate; j++) /* vareij */
-     printf("Problem with resultfile: %s\n", fileresprob);
+         for(h=0; h<=nhstepm; h++){
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   }
+         }
-   strcpy(fileresprobcov,"probcov");
-   strcat(fileresprobcov,fileres);
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+       }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   }
+     } /* End theta */
-   strcpy(fileresprobcor,"probcor");
-   strcat(fileresprobcor,fileres);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+     for(h=0; h<=nhstepm; h++) /* veij */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+       for(j=1; j<=nlstate;j++)
-   }
+         for(theta=1; theta <=npar; theta++)
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   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);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+       for(theta=1; theta <=npar; theta++)
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+         trgradgp[j][theta]=gradgp[theta][j];
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   fprintf(ficresprob,"# Age");
+     for(i=1;i<=nlstate;i++)
-   pstamp(ficresprobcov);
+       for(j=1;j<=nlstate;j++)
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+         vareij[i][j][(int)age] =0.;
-   fprintf(ficresprobcov,"# Age");
-   pstamp(ficresprobcor);
+     for(h=0;h<=nhstepm;h++){
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+       for(k=0;k<=nhstepm;k++){
-   fprintf(ficresprobcor,"# Age");
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+         for(i=1;i<=nlstate;i++)
-   for(i=1; i<=nlstate;i++)
+           for(j=1;j<=nlstate;j++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       }
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     }
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+     /* pptj */
-  /* fprintf(ficresprob,"\n");
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-   fprintf(ficresprobcov,"\n");
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-   fprintf(ficresprobcor,"\n");
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-  */
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-  xp=vector(1,npar);
+         varppt[j][i]=doldmp[j][i];
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+     /* end ppptj */
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+     /*  x centered again */
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-   first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+     if (popbased==1) {
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+       if(mobilav ==0){
-   fprintf(fichtm,"\n");
+         for(i=1; i<=nlstate;i++)
+           prlim[i][i]=probs[(int)age][i][ij];
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+       }else{ /* mobilav */
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+         for(i=1; i<=nlstate;i++)
-   file %s<br>\n",optionfilehtmcov);
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+       }
- and drawn. It helps understanding how is the covariance between two incidences.\
+     }
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   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. \
+     /* This for computing probability of death (h=1 means
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+        as a weighted average of prlim.
- standard deviations wide on each axis. <br>\
+     */
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+       for(i=1,gmp[j]=0.;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");
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     }
-   cov[1]=1;
+     /* end probability of death */
-   tj=cptcoveff;
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-   j1=0;
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   for(t=1; t<=tj;t++){
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-     for(i1=1; i1<=ncodemax[t];i1++){
+       for(i=1; i<=nlstate;i++){
-       j1++;
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       if  (cptcovn>0) {
+       }
-         fprintf(ficresprob, "\n#********** Variable ");
+     }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     fprintf(ficresprobmorprev,"\n");
-         fprintf(ficresprob, "**********\n#\n");
-         fprintf(ficresprobcov, "\n#********** Variable ");
+     fprintf(ficresvij,"%.0f ",age );
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     for(i=1; i<=nlstate;i++)
-         fprintf(ficresprobcov, "**********\n#\n");
+       for(j=1; j<=nlstate;j++){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-         fprintf(ficgp, "\n#********** Variable ");
+       }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     fprintf(ficresvij,"\n");
-         fprintf(ficgp, "**********\n#\n");
+     free_matrix(gp,0,nhstepm,1,nlstate);
+     free_matrix(gm,0,nhstepm,1,nlstate);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   } /* End age */
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-         fprintf(ficresprobcor, "**********\n#");
+   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");
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-       for (age=bage; age<=fage; age ++){
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-         cov[2]=age;
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-         for (k=1; k<=cptcovn;k++) {
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-         }
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-         for (k=1; k<=cptcovprod;k++)
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   /*  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);
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ */
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-         for(theta=1; theta <=npar; theta++){
+   free_vector(xp,1,npar);
-           for(i=1; i<=npar; i++)
+   free_matrix(doldm,1,nlstate,1,nlstate);
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   free_matrix(dnewm,1,nlstate,1,npar);
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-           k=0;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-           for(i=1; i<= (nlstate); i++){
+   fclose(ficresprobmorprev);
-             for(j=1; j<=(nlstate+ndeath);j++){
+   fflush(ficgp);
-               k=k+1;
+   fflush(fichtm);
-               gp[k]=pmmij[i][j];
+ }  /* end varevsij */
-             }
-           }
+ /************ 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[])
-           for(i=1; i<=npar; i++)
+ {
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   /* Variance of prevalence limit */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   double **newm;
-           k=0;
+   double **dnewm,**doldm;
-           for(i=1; i<=(nlstate); i++){
+   int i, j, nhstepm, hstepm;
-             for(j=1; j<=(nlstate+ndeath);j++){
+   int k, cptcode;
-               k=k+1;
+   double *xp;
-               gm[k]=pmmij[i][j];
+   double *gp, *gm;
-             }
+   double **gradg, **trgradg;
-           }
+   double age,agelim;
+   int theta;
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+   pstamp(ficresvpl);
-         }
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficresvpl,"# Age");
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+   for(i=1; i<=nlstate;i++)
-           for(theta=1; theta <=npar; theta++)
+       fprintf(ficresvpl," %1d-%1d",i,i);
-             trgradg[j][theta]=gradg[theta][j];
+   fprintf(ficresvpl,"\n");
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+   xp=vector(1,npar);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+   dnewm=matrix(1,nlstate,1,npar);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   doldm=matrix(1,nlstate,1,nlstate);
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   hstepm=1*YEARM; /* Every year of age */
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGESUP;
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         k=0;
+     if (stepm >= YEARM) hstepm=1;
-         for(i=1; i<=(nlstate); i++){
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           for(j=1; j<=(nlstate+ndeath);j++){
+     gradg=matrix(1,npar,1,nlstate);
-             k=k+1;
+     gp=vector(1,nlstate);
-             mu[k][(int) age]=pmmij[i][j];
+     gm=vector(1,nlstate);
-           }
-         }
+     for(theta=1; theta <=npar; theta++){
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-             varpij[i][j][(int)age] = doldm[i][j];
+       }
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         /*printf("\n%d ",(int)age);
+       for(i=1;i<=nlstate;i++)
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         gp[i] = prlim[i][i];
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+       for(i=1; i<=npar; i++) /* Computes gradient */
-           }*/
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         fprintf(ficresprob,"\n%d ",(int)age);
+       for(i=1;i<=nlstate;i++)
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+         gm[i] = prlim[i][i];
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+       for(i=1;i<=nlstate;i++)
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+     } /* End theta */
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+     trgradg =matrix(1,nlstate,1,npar);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
+     for(j=1; j<=nlstate;j++)
-         i=0;
+       for(theta=1; theta <=npar; theta++)
-         for (k=1; k<=(nlstate);k++){
+         trgradg[j][theta]=gradg[theta][j];
-           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);
+       varpl[i][(int)age] =0.;
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-             for (j=1; j<=i;j++){
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+     for(i=1;i<=nlstate;i++)
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-             }
-           }
+     fprintf(ficresvpl,"%.0f ",age );
-         }/* end of loop for state */
+     for(i=1; i<=nlstate;i++)
-       } /* end of loop for age */
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+     fprintf(ficresvpl,"\n");
-       /* Confidence intervalle of pij  */
+     free_vector(gp,1,nlstate);
-       /*
+     free_vector(gm,1,nlstate);
-         fprintf(ficgp,"\nset noparametric;unset label");
+     free_matrix(gradg,1,npar,1,nlstate);
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+     free_matrix(trgradg,1,nlstate,1,npar);
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   } /* End age */
-         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);
+   free_vector(xp,1,npar);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+   free_matrix(doldm,1,nlstate,1,npar);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-       */
+ }
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;
+ /************ Variance of one-step probabilities  ******************/
-       for (k2=1; k2<=(nlstate);k2++){
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+ {
-           if(l2==k2) continue;
+   int i, j=0,  i1, k1, l1, t, tj;
-           j=(k2-1)*(nlstate+ndeath)+l2;
+   int k2, l2, j1,  z1;
-           for (k1=1; k1<=(nlstate);k1++){
+   int k=0,l, cptcode;
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+   int first=1, first1, first2;
-               if(l1==k1) continue;
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-               i=(k1-1)*(nlstate+ndeath)+l1;
+   double **dnewm,**doldm;
-               if(i<=j) continue;
+   double *xp;
-               for (age=bage; age<=fage; age ++){
+   double *gp, *gm;
-                 if ((int)age %5==0){
+   double **gradg, **trgradg;
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+   double **mu;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   double age,agelim, cov[NCOVMAX+1];
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+   int theta;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+   char fileresprob[FILENAMELENGTH];
-                   c12=cv12/sqrt(v1*v2);
+   char fileresprobcov[FILENAMELENGTH];
-                   /* Computing eigen value of matrix of covariance */
+   char fileresprobcor[FILENAMELENGTH];
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+   double ***varpij;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   /* Eigen vectors */
+   strcpy(fileresprob,"prob");
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+   strcat(fileresprob,fileres);
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-                   v21=(lc1-v1)/cv12*v11;
+     printf("Problem with resultfile: %s\n", fileresprob);
-                   v12=-v21;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-                   v22=v11;
+   }
-                   tnalp=v21/v11;
+   strcpy(fileresprobcov,"probcov");
-                   if(first1==1){
+   strcat(fileresprobcov,fileres);
-                     first1=0;
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-                     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);
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-                   }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-                   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*/
+   strcpy(fileresprobcor,"probcor");
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+   strcat(fileresprobcor,fileres);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-                   if(first==1){
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-                     first=0;
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-                     fprintf(ficgp,"\nset parametric;unset label");
+   }
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   pstamp(ficresprob);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+   fprintf(ficresprob,"# Age");
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+   pstamp(ficresprobcov);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+   fprintf(ficresprobcov,"# Age");
-                     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",\
+   pstamp(ficresprobcor);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+   fprintf(ficresprobcor,"# Age");
-                   }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);
+     for(j=1; j<=(nlstate+ndeath);j++){
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-                     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," p%1d-%1d ",i,j);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+     }
-                   }/* if first */
+  /* fprintf(ficresprob,"\n");
-                 } /* age mod 5 */
+   fprintf(ficresprobcov,"\n");
-               } /* end loop age */
+   fprintf(ficresprobcor,"\n");
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+  */
-               first=1;
+   xp=vector(1,npar);
-             } /*l12 */
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-           } /* k12 */
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-         } /*l1 */
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-       }/* k1 */
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-     } /* loop covariates */
+   first=1;
-   }
+   fprintf(ficgp,"\n# Routine varprob");
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   fprintf(fichtm,"\n");
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   free_vector(xp,1,npar);
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-   fclose(ficresprob);
+   file %s<br>\n",optionfilehtmcov);
-   fclose(ficresprobcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-   fclose(ficresprobcor);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-   fflush(ficgp);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   fflush(fichtmcov);
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- }
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+ standard deviations wide on each axis. <br>\
- /******************* Printing html file ***********/
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-                   int lastpass, int stepm, int weightopt, char model[],\
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int estepm ,\
+   cov[1]=1;
-                   double jprev1, double mprev1,double anprev1, \
+   /* tj=cptcoveff; */
-                   double jprev2, double mprev2,double anprev2){
+   tj = (int) pow(2,cptcoveff);
-   int jj1, k1, i1, cpt;
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   j1=0;
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+   for(j1=1; j1<=tj;j1++){
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+     /*for(i1=1; i1<=ncodemax[t];i1++){ */
- </ul>");
+     /*j1++;*/
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+       if  (cptcovn>0) {
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+         fprintf(ficresprob, "\n#********** Variable ");
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+         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");
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+         fprintf(ficresprobcov, "\n#********** Variable ");
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    fprintf(fichtm,"\
+         fprintf(ficresprobcov, "**********\n#\n");
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+         fprintf(ficgp, "\n#********** Variable ");
-    fprintf(fichtm,"\
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-  - (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): \
+         fprintf(ficgp, "**********\n#\n");
-    <a href=\"%s\">%s</a> <br>\n",
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-    fprintf(fichtm,"\
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-  - Population projections by age and states: \
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-  m=cptcoveff;
+         fprintf(ficresprobcor, "**********\n#");
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+       }
-  jj1=0;
+       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-  for(k1=1; k1<=m;k1++){
+       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+       gp=vector(1,(nlstate)*(nlstate+ndeath));
-      jj1++;
+       gm=vector(1,(nlstate)*(nlstate+ndeath));
-      if (cptcovn > 0) {
+       for (age=bage; age<=fage; age ++){
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         cov[2]=age;
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+         for (k=1; k<=cptcovn;k++) {
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+                                                          * 1  1 1 1 1
-      }
+                                                          * 2  2 1 1 1
-      /* Pij */
+                                                          * 3  1 2 1 1
-      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> \
+                                                          */
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-      /* Quasi-incidences */
+         }
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-  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> \
+         for (k=1; k<=cptcovprod;k++)
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-        /* Period (stable) prevalence in each health state */
-        for(cpt=1; cpt<nlstate;cpt++){
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+         for(theta=1; theta <=npar; theta++){
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+           for(i=1; i<=npar; i++)
-        }
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-      for(cpt=1; cpt<=nlstate;cpt++) {
-         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-      }
+           k=0;
-    } /* end i1 */
+           for(i=1; i<= (nlstate); i++){
-  }/* End k1 */
+             for(j=1; j<=(nlstate+ndeath);j++){
-  fprintf(fichtm,"</ul>");
+               k=k+1;
+               gp[k]=pmmij[i][j];
+             }
-  fprintf(fichtm,"\
+           }
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+           for(i=1; i<=npar; i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-  fprintf(fichtm,"\
+           k=0;
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+           for(i=1; i<=(nlstate); i++){
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+             for(j=1; j<=(nlstate+ndeath);j++){
+               k=k+1;
-  fprintf(fichtm,"\
+               gm[k]=pmmij[i][j];
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+             }
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+           }
-  fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-    <a href=\"%s\">%s</a> <br>\n</li>",
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+         }
-  fprintf(fichtm,"\
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-    <a href=\"%s\">%s</a> <br>\n</li>",
+           for(theta=1; theta <=npar; theta++)
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+             trgradg[j][theta]=gradg[theta][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",
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-  fprintf(fichtm,"\
-  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-  fprintf(fichtm,"\
+         k=0;
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+         for(i=1; i<=(nlstate); i++){
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+           for(j=1; j<=(nlstate+ndeath);j++){
+             k=k+1;
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+             mu[k][(int) age]=pmmij[i][j];
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+           }
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+         }
- /*      <br>",fileres,fileres,fileres,fileres); */
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
- /*  else  */
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
- /*    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); */
+             varpij[i][j][(int)age] = doldm[i][j];
-  fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+         /*printf("\n%d ",(int)age);
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-  m=cptcoveff;
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           }*/
-  jj1=0;
-  for(k1=1; k1<=m;k1++){
+         fprintf(ficresprob,"\n%d ",(int)age);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-      jj1++;
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-      if (cptcovn > 0) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-      }
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-      for(cpt=1; cpt<=nlstate;cpt++) {
+         }
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+         i=0;
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+         for (k=1; k<=(nlstate);k++){
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+           for (l=1; l<=(nlstate+ndeath);l++){
-      }
+             i++;
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
- health expectancies in states (1) and (2): %s%d.png<br>\
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+             for (j=1; j<=i;j++){
-    } /* end i1 */
+               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-  }/* End k1 */
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-  fprintf(fichtm,"</ul>");
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-  fflush(fichtm);
+             }
- }
+           }
+         }/* end of loop for state */
- /******************* Gnuplot file **************/
+       } /* end of loop for age */
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   char dirfileres[132],optfileres[132];
+       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   int ng;
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+       /* Confidence intervalle of pij  */
- /*     printf("Problem with file %s",optionfilegnuplot); */
+       /*
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+         fprintf(ficgp,"\nunset parametric;unset label");
- /*   } */
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-   /*#ifdef windows */
+         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,"cd \"%s\" \n",pathc);
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-     /*#endif */
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-   m=pow(2,cptcoveff);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+       */
-   strcpy(dirfileres,optionfilefiname);
-   strcpy(optfileres,"vpl");
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-  /* 1eme*/
+       first1=1;first2=2;
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+       for (k2=1; k2<=(nlstate);k2++){
-    for (k1=1; k1<= m ; k1 ++) {
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+           if(l2==k2) continue;
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+           j=(k2-1)*(nlstate+ndeath)+l2;
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+           for (k1=1; k1<=(nlstate);k1++){
- set ylabel \"Probability\" \n\
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
- set ter png small\n\
+               if(l1==k1) continue;
- set size 0.65,0.65\n\
+               i=(k1-1)*(nlstate+ndeath)+l1;
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+               if(i<=j) continue;
+               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\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-      for (i=1; i<= nlstate ; i ++) {
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+                   c12=cv12/sqrt(v1*v2);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   /* Computing eigen value of matrix of covariance */
-      }
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-      for (i=1; i<= nlstate ; i ++) {
+                   if ((lc2 <0) || (lc1 <0) ){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+                     if(first2==1){
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+                       first1=0;
-      }
+                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+                     }
-    }
+                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-   }
+                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-   /*2 eme*/
+                     /* lc2=fabs(lc2); */
+                   }
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+                   /* Eigen vectors */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-     for (i=1; i<= nlstate+1 ; i ++) {
+                   v21=(lc1-v1)/cv12*v11;
-       k=2*i;
+                   v12=-v21;
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                   v22=v11;
-       for (j=1; j<= nlstate+1 ; j ++) {
+                   tnalp=v21/v11;
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                   if(first1==1){
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                     first1=0;
-       }
+                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+                   }
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                   /*printf(fignu*/
-       for (j=1; j<= nlstate+1 ; j ++) {
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+                   if(first==1){
-       }
+                     first=0;
-       fprintf(ficgp,"\" t\"\" w l 0,");
+                     fprintf(ficgp,"\nset parametric;unset label");
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
-       for (j=1; j<= nlstate+1 ; j ++) {
+                     fprintf(ficgp,"\nset ter png small size 320, 240");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-       }
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-     }
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   }
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-   /*3eme*/
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-   for (k1=1; k1<= m ; k1 ++) {
+                     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",\
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-       /*       k=2+nlstate*(2*cpt-2); */
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-       k=2+(nlstate+1)*(cpt-1);
+                   }else{
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+                     first=0;
-       fprintf(ficgp,"set ter png small\n\
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
- set size 0.65,0.65\n\
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- 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 label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                   }/* if first */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                 } /* age mod 5 */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+               } /* 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 */
-         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);
+           } /* k12 */
-         /*      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);*/
+         } /*l1 */
+       }/* k1 */
-       }
+       /* } /* loop covariates */
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+   }
-     }
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   }
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   /* CV preval stable (period) */
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   for (k1=1; k1<= m ; k1 ++) {
+   free_vector(xp,1,npar);
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+   fclose(ficresprob);
-       k=3;
+   fclose(ficresprobcov);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+   fclose(ficresprobcor);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+   fflush(ficgp);
- set ter png small\nset size 0.65,0.65\n\
+   fflush(fichtmcov);
- unset log y\n\
+ }
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-       for (i=1; i< nlstate ; i ++)
+ /******************* Printing html file ***********/
-         fprintf(ficgp,"+$%d",k+i+1);
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+                   int lastpass, int stepm, int weightopt, char model[],\
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-       l=3+(nlstate+ndeath)*cpt;
+                   int popforecast, int estepm ,\
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+                   double jprev1, double mprev1,double anprev1, \
-       for (i=1; i< nlstate ; i ++) {
+                   double jprev2, double mprev2,double anprev2){
-         l=3+(nlstate+ndeath)*cpt;
+   int jj1, k1, i1, cpt;
-         fprintf(ficgp,"+$%d",l+i+1);
-       }
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\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 ",
-   /* proba elementaires */
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   for(i=1,jk=1; i <=nlstate; i++){
+    fprintf(fichtm,"\
-     for(k=1; k <=(nlstate+ndeath); k++){
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-       if (k != i) {
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-         for(j=1; j <=ncovmodel; j++){
+    fprintf(fichtm,"\
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-           jk++;
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-           fprintf(ficgp,"\n");
+    fprintf(fichtm,"\
-         }
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-       }
+    <a href=\"%s\">%s</a> <br>\n",
-     }
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-    }
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-      for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-        if (ng==2)
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+  m=pow(2,cptcoveff);
-        else
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-          fprintf(ficgp,"\nset title \"Probability\"\n");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+  jj1=0;
-        i=1;
+  for(k1=1; k1<=m;k1++){
-        for(k2=1; k2<=nlstate; k2++) {
+    for(i1=1; i1<=ncodemax[k1];i1++){
-          k3=i;
+      jj1++;
-          for(k=1; k<=(nlstate+ndeath); k++) {
+      if (cptcovn > 0) {
-            if (k != k2){
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-              if(ng==2)
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-              else
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+      }
-              ij=1;
+      /* Pij */
-              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 before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+ <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+      /* Quasi-incidences */
-                  ij++;
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-                }
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
-                else
+ <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+        /* Period (stable) prevalence in each health state */
-              }
+        for(cpt=1; cpt<nlstate;cpt++){
-              fprintf(ficgp,")/(1");
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+ <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-              for(k1=1; k1 <=nlstate; k1++){
+        }
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+      for(cpt=1; cpt<=nlstate;cpt++) {
-                ij=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> \
-                for(j=3; j <=ncovmodel; j++){
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-                  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]]]);
+    } /* end i1 */
-                    ij++;
+  }/* End k1 */
-                  }
+  fprintf(fichtm,"</ul>");
-                  else
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-                }
+  fprintf(fichtm,"\
-                fprintf(ficgp,")");
+ \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);
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-              i=i+ncovmodel;
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-            }
+  fprintf(fichtm,"\
-          } /* end k */
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-        } /* end k2 */
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-      } /* end jk */
-    } /* end ng */
+  fprintf(fichtm,"\
-    fflush(ficgp);
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- }  /* end gnuplot */
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
- /*************** Moving average **************/
+    <a href=\"%s\">%s</a> <br>\n</li>",
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+  fprintf(fichtm,"\
-   int i, cpt, cptcod;
+  - (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): \
-   int modcovmax =1;
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   int mobilavrange, mob;
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-   double age;
+  fprintf(fichtm,"\
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-                            a covariate has 2 modalities */
+  fprintf(fichtm,"\
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+  fprintf(fichtm,"\
-     if(mobilav==1) mobilavrange=5; /* default */
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-     else mobilavrange=mobilav;
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-     for (age=bage; age<=fage; age++)
-       for (i=1; i<=nlstate;i++)
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-     /* We keep the original values on the extreme ages bage, fage and for
+ /*      <br>",fileres,fileres,fileres,fileres); */
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+ /*  else  */
-        we use a 5 terms etc. until the borders are no more concerned.
+ /*    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);
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-         for (i=1; i<=nlstate;i++){
+  m=pow(2,cptcoveff);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+  jj1=0;
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+  for(k1=1; k1<=m;k1++){
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+    for(i1=1; i1<=ncodemax[k1];i1++){
-               }
+      jj1++;
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+      if (cptcovn > 0) {
-           }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-         }
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-       }/* end age */
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-     }/* end mob */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   }else return -1;
+      }
-   return 0;
+      for(cpt=1; cpt<=nlstate;cpt++) {
- }/* End movingaverage */
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+ prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
+ <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
- /************** Forecasting ******************/
+      }
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   /* proj1, year, month, day of starting projection
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-      agemin, agemax range of age
+ true period expectancies (those weighted with period prevalences are also\
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+  drawn in addition to the population based expectancies computed using\
-      anproj2 year of en of projection (same day and month as proj1).
+  observed and cahotic prevalences: %s%d.png<br>\
-   */
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+    } /* end i1 */
-   int *popage;
+  }/* End k1 */
-   double agec; /* generic age */
+  fprintf(fichtm,"</ul>");
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  fflush(fichtm);
-   double *popeffectif,*popcount;
+ }
-   double ***p3mat;
-   double ***mobaverage;
+ /******************* Gnuplot file **************/
-   char fileresf[FILENAMELENGTH];
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   agelim=AGESUP;
+   char dirfileres[132],optfileres[132];
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int ng=0;
-   strcpy(fileresf,"f");
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-   strcat(fileresf,fileres);
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+ /*   } */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   }
+   /*#ifdef windows */
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+     /*#endif */
+   m=pow(2,cptcoveff);
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   strcpy(dirfileres,optionfilefiname);
-   if (mobilav!=0) {
+   strcpy(optfileres,"vpl");
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  /* 1eme*/
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-     }
+      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
-   }
+      fprintf(ficgp,"set xlabel \"Age\" \n\
+ set ylabel \"Probability\" \n\
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ set ter png small size 320, 240\n\
-   if (stepm<=12) stepsize=1;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+      for (i=1; i<= nlstate ; i ++) {
-   }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   else  hstepm=estepm;
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-   hstepm=hstepm/stepm;
+      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);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+      for (i=1; i<= nlstate ; i ++) {
-                                fractional in yp1 */
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   anprojmean=yp;
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-   yp2=modf((yp1*12),&yp);
+      }
-   mprojmean=yp;
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-   yp1=modf((yp2*30.5),&yp);
+      for (i=1; i<= nlstate ; i ++) {
-   jprojmean=yp;
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-   if(jprojmean==0) jprojmean=1;
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-   if(mprojmean==0) jprojmean=1;
+      }
+      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-   i1=cptcoveff;
+    }
-   if (cptcovn < 1){i1=1;}
+   }
+   /*2 eme*/
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   for (k1=1; k1<= m ; k1 ++) {
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
- /*            if (h==(int)(YEARM*yearp)){ */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+     for (i=1; i<= nlstate+1 ; i ++) {
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=2*i;
-       k=k+1;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%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," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       fprintf(ficresf,"******\n");
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-       for(j=1; j<=nlstate+ndeath;j++){
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-         for(i=1; i<=nlstate;i++)
+       for (j=1; j<= nlstate+1 ; j ++) {
-           fprintf(ficresf," p%d%d",i,j);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         fprintf(ficresf," p.%d",j);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficresf,"\n");
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       }
-           nhstepm = nhstepm/hstepm;
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
-           oldm=oldms;savm=savms;
+     }
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+   }
-           for (h=0; h<=nhstepm; h++){
+   /*3eme*/
-             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
+   for (k1=1; k1<= m ; k1 ++) {
-               for(j=1;j<=cptcoveff;j++)
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       /*       k=2+nlstate*(2*cpt-2); */
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+       k=2+(nlstate+1)*(cpt-1);
-             }
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-             for(j=1; j<=nlstate+ndeath;j++) {
+       fprintf(ficgp,"set ter png small size 320, 240\n\
-               ppij=0.;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-               for(i=1; i<=nlstate;i++) {
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-                 if (mobilav==1)
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-                 else {
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-                 }
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-                 if (h*hstepm/YEARM*stepm== yearp) {
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+       */
-                 }
+       for (i=1; i< nlstate ; i ++) {
-               } /* end 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 (h*hstepm/YEARM*stepm==yearp) {
+         /*      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(ficresf," %.3f", ppij);
-               }
+       }
-             }/* end j */
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-           } /* end h */
+     }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   }
-         } /* end agec */
-       } /* end yearp */
+   /* CV preval stable (period) */
-     } /* end cptcod */
+   for (k1=1; k1<= m ; k1 ++) {
-   } /* end  cptcov */
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
+       k=3;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-   fclose(ficresf);
+ set ter png small size 320, 240\n\
- }
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
- /************** Forecasting *****not tested NB*************/
- populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+       for (i=1; i< nlstate ; i ++)
+         fprintf(ficgp,"+$%d",k+i+1);
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-   int *popage;
-   double calagedatem, agelim, kk1, kk2;
+       l=3+(nlstate+ndeath)*cpt;
-   double *popeffectif,*popcount;
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-   double ***p3mat,***tabpop,***tabpopprev;
+       for (i=1; i< nlstate ; i ++) {
-   double ***mobaverage;
+         l=3+(nlstate+ndeath)*cpt;
-   char filerespop[FILENAMELENGTH];
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     }
-   agelim=AGESUP;
+   }
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   /* proba elementaires */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   for(i=1,jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
-   strcpy(filerespop,"pop");
+         for(j=1; j <=ncovmodel; j++){
-   strcat(filerespop,fileres);
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+           jk++;
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+           fprintf(ficgp,"\n");
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+         }
-   }
+       }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+     }
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+    }
+   /*goto avoid;*/
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
-   if (mobilav!=0) {
+        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+        if (ng==2)
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+        else
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     }
+        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   }
+        i=1;
+        for(k2=1; k2<=nlstate; k2++) {
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+          k3=i;
-   if (stepm<=12) stepsize=1;
+          for(k=1; k<=(nlstate+ndeath); k++) {
+            if (k != k2){
-   agelim=AGESUP;
+              if(ng==2)
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-   hstepm=1;
+              else
-   hstepm=hstepm/stepm;
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-   if (popforecast==1) {
+              for(j=3; j <=ncovmodel; j++) {
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+                /*        ij++; */
-     }
+                /* } */
-     popage=ivector(0,AGESUP);
+                /* else */
-     popeffectif=vector(0,AGESUP);
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-     popcount=vector(0,AGESUP);
+              }
+              fprintf(ficgp,")/(1");
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+              for(k1=1; k1 <=nlstate; k1++){
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-     imx=i;
+                ij=1;
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+                for(j=3; j <=ncovmodel; j++){
-   }
+                  /* 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(cptcov=1,k=0;cptcov<=i2;cptcov++){
+                  /*   ij++; */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+                  /* } */
-       k=k+1;
+                  /* else */
-       fprintf(ficrespop,"\n#******");
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       for(j=1;j<=cptcoveff;j++) {
+                }
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                fprintf(ficgp,")");
-       }
+              }
-       fprintf(ficrespop,"******\n");
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-       fprintf(ficrespop,"# Age");
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+              i=i+ncovmodel;
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+            }
+          } /* end k */
-       for (cpt=0; cpt<=0;cpt++) {
+        } /* end k2 */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+      } /* end jk */
+    } /* end ng */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+  avoid:
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+    fflush(ficgp);
-           nhstepm = nhstepm/hstepm;
+ }  /* end gnuplot */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           oldm=oldms;savm=savms;
+ /*************** Moving average **************/
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-           for (h=0; h<=nhstepm; h++){
+   int i, cpt, cptcod;
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   int modcovmax =1;
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   int mobilavrange, mob;
-             }
+   double age;
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-               for(i=1; i<=nlstate;i++) {
+                            a covariate has 2 modalities */
-                 if (mobilav==1)
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+     if(mobilav==1) mobilavrange=5; /* default */
-                 }
+     else mobilavrange=mobilav;
-               }
+     for (age=bage; age<=fage; age++)
-               if (h==(int)(calagedatem+12*cpt)){
+       for (i=1; i<=nlstate;i++)
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-                   /*fprintf(ficrespop," %.3f", kk1);
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+     /* 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
-             }
+        we use a 5 terms etc. until the borders are no more concerned.
-             for(i=1; i<=nlstate;i++){
+     */
-               kk1=0.;
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-                 for(j=1; j<=nlstate;j++){
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+         for (i=1; i<=nlstate;i++){
-                 }
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-             }
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+               }
-           }
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           }
          }
-       }
+       }/* end age */
+     }/* end mob */
-   /******/
+   }else return -1;
+   return 0;
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+ }/* End movingaverage */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /************** Forecasting ******************/
-           nhstepm = nhstepm/hstepm;
+ 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
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+      agemin, agemax range of age
-           oldm=oldms;savm=savms;
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+      anproj2 year of en of projection (same day and month as proj1).
-           for (h=0; h<=nhstepm; h++){
+   */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   int *popage;
-             }
+   double agec; /* generic age */
-             for(j=1; j<=nlstate+ndeath;j++) {
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-               kk1=0.;kk2=0;
+   double *popeffectif,*popcount;
-               for(i=1; i<=nlstate;i++) {
+   double ***p3mat;
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+   double ***mobaverage;
-               }
+   char fileresf[FILENAMELENGTH];
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-             }
+   agelim=AGESUP;
-           }
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
+   strcpy(fileresf,"f");
-       }
+   strcat(fileresf,fileres);
-    }
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   }
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   if (popforecast==1) {
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     free_vector(popcount,0,AGESUP);
-   }
+   if (mobilav!=0) {
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   fclose(ficrespop);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- } /* End of popforecast */
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
- int fileappend(FILE *fichier, char *optionfich)
+   }
- {
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-     printf("Problem with file: %s\n", optionfich);
+   if (stepm<=12) stepsize=1;
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   if(estepm < stepm){
-     return (0);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
    }
-   fflush(fichier);
+   else  hstepm=estepm;
-   return (1);
- }
+   hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
- /**************** function prwizard **********************/
+   anprojmean=yp;
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+   yp2=modf((yp1*12),&yp);
- {
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
-   /* Wizard to print covariance matrix template */
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
-   char ca[32], cb[32], cc[32];
+   if(mprojmean==0) jprojmean=1;
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   int numlinepar;
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   for(i=1; i <=nlstate; i++){
-     jj=0;
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-     for(j=1; j <=nlstate+ndeath; j++){
-       if(j==i) continue;
+ /*            if (h==(int)(YEARM*yearp)){ */
-       jj++;
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       printf("%1d%1d",i,j);
+       k=k+1;
-       fprintf(ficparo,"%1d%1d",i,j);
+       fprintf(ficresf,"\n#******");
-       for(k=1; k<=ncovmodel;k++){
+       for(j=1;j<=cptcoveff;j++) {
-         /*        printf(" %lf",param[i][j][k]); */
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+       }
-         printf(" 0.");
+       fprintf(ficresf,"******\n");
-         fprintf(ficparo," 0.");
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       }
+       for(j=1; j<=nlstate+ndeath;j++){
-       printf("\n");
+         for(i=1; i<=nlstate;i++)
-       fprintf(ficparo,"\n");
+           fprintf(ficresf," p%d%d",i,j);
-     }
+         fprintf(ficresf," p.%d",j);
-   }
+       }
-   printf("# Scales (for hessian or gradient estimation)\n");
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+         fprintf(ficresf,"\n");
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-   for(i=1; i <=nlstate; i++){
-     jj=0;
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-     for(j=1; j <=nlstate+ndeath; j++){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-       if(j==i) continue;
+           nhstepm = nhstepm/hstepm;
-       jj++;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fprintf(ficparo,"%1d%1d",i,j);
+           oldm=oldms;savm=savms;
-       printf("%1d%1d",i,j);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-       fflush(stdout);
-       for(k=1; k<=ncovmodel;k++){
+           for (h=0; h<=nhstepm; h++){
-         /*      printf(" %le",delti3[i][j][k]); */
+             if (h*hstepm/YEARM*stepm ==yearp) {
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+               fprintf(ficresf,"\n");
-         printf(" 0.");
+               for(j=1;j<=cptcoveff;j++)
-         fprintf(ficparo," 0.");
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       }
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-       numlinepar++;
+             }
-       printf("\n");
+             for(j=1; j<=nlstate+ndeath;j++) {
-       fprintf(ficparo,"\n");
+               ppij=0.;
-     }
+               for(i=1; i<=nlstate;i++) {
-   }
+                 if (mobilav==1)
-   printf("# Covariance matrix\n");
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
- /* # 121 Var(a12)\n\ */
+                 else {
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+                 }
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+                 if (h*hstepm/YEARM*stepm== yearp) {
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
- /* # 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\ */
+               } /* end i */
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+               if (h*hstepm/YEARM*stepm==yearp) {
-   fflush(stdout);
+                 fprintf(ficresf," %.3f", ppij);
-   fprintf(ficparo,"# Covariance matrix\n");
+               }
-   /* # 121 Var(a12)\n\ */
+             }/* end j */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           } /* end h */
-   /* #   ...\n\ */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+         } /* end agec */
+       } /* end yearp */
-   for(itimes=1;itimes<=2;itimes++){
+     } /* end cptcod */
-     jj=0;
+   } /* end  cptcov */
-     for(i=1; i <=nlstate; i++){
-       for(j=1; j <=nlstate+ndeath; j++){
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         if(j==i) continue;
-         for(k=1; k<=ncovmodel;k++){
+   fclose(ficresf);
-           jj++;
+ }
-           ca[0]= k+'a'-1;ca[1]='\0';
-           if(itimes==1){
+ /************** Forecasting *****not tested NB*************/
-             printf("#%1d%1d%d",i,j,k);
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-           }else{
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-             printf("%1d%1d%d",i,j,k);
+   int *popage;
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+   double calagedatem, agelim, kk1, kk2;
-             /*  printf(" %.5le",matcov[i][j]); */
+   double *popeffectif,*popcount;
-           }
+   double ***p3mat,***tabpop,***tabpopprev;
-           ll=0;
+   double ***mobaverage;
-           for(li=1;li <=nlstate; li++){
+   char filerespop[FILENAMELENGTH];
-             for(lj=1;lj <=nlstate+ndeath; lj++){
-               if(lj==li) continue;
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               for(lk=1;lk<=ncovmodel;lk++){
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                 ll++;
+   agelim=AGESUP;
-                 if(ll<=jj){
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-                   cb[0]= lk +'a'-1;cb[1]='\0';
-                   if(ll<jj){
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-                     if(itimes==1){
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   strcpy(filerespop,"pop");
-                     }else{
+   strcat(filerespop,fileres);
-                       printf(" 0.");
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-                       fprintf(ficparo," 0.");
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-                     }
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-                   }else{
+   }
-                     if(itimes==1){
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-                     }else{
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-                       printf(" 0.");
-                       fprintf(ficparo," 0.");
+   if (mobilav!=0) {
-                     }
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                   }
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-                 }
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-               } /* end lk */
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-             } /* end lj */
+     }
-           } /* end li */
+   }
-           printf("\n");
-           fprintf(ficparo,"\n");
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-           numlinepar++;
+   if (stepm<=12) stepsize=1;
-         } /* end k*/
-       } /*end j */
+   agelim=AGESUP;
-     } /* end i */
-   } /* end itimes */
+   hstepm=1;
+   hstepm=hstepm/stepm;
- } /* end of prwizard */
- /******************* Gompertz Likelihood ******************************/
+   if (popforecast==1) {
- double gompertz(double x[])
+     if((ficpop=fopen(popfile,"r"))==NULL) {
- {
+       printf("Problem with population file : %s\n",popfile);exit(0);
-   double A,B,L=0.0,sump=0.,num=0.;
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-   int i,n=0; /* n is the size of the sample */
+     }
+     popage=ivector(0,AGESUP);
-   for (i=0;i<=imx-1 ; i++) {
+     popeffectif=vector(0,AGESUP);
-     sump=sump+weight[i];
+     popcount=vector(0,AGESUP);
-     /*    sump=sump+1;*/
-     num=num+1;
+     i=1;
-   }
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+     imx=i;
-   /* for (i=0; i<=imx; i++)
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+   }
-   for (i=1;i<=imx ; i++)
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-     {
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       if (cens[i] == 1 && wav[i]>1)
+       k=k+1;
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
-       if (cens[i] == 0 && wav[i]>1)
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+       }
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-       if (wav[i] > 1 ) { /* ??? */
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-         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 (cpt=0; cpt<=0;cpt++) {
-       }
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-     }
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
-   return -2*L*num/sump;
- }
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
- /******************* Printing html file ***********/
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-                   int lastpass, int stepm, int weightopt, char model[],\
+           for (h=0; h<=nhstepm; h++){
-                   int imx,  double p[],double **matcov,double agemortsup){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   int i,k;
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+             for(j=1; j<=nlstate+ndeath;j++) {
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+               kk1=0.;kk2=0;
-   for (i=1;i<=2;i++)
+               for(i=1; i<=nlstate;i++) {
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+                 if (mobilav==1)
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   fprintf(fichtm,"</ul>");
+                 else {
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+                 }
+               }
-  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+12*cpt)){
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-  for (k=agegomp;k<(agemortsup-2);k++)
+                   /*fprintf(ficrespop," %.3f", kk1);
-    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+               }
+             }
-   fflush(fichtm);
+             for(i=1; i<=nlstate;i++){
- }
+               kk1=0.;
+                 for(j=1; j<=nlstate;j++){
- /******************* Gnuplot file **************/
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+                 }
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   char dirfileres[132],optfileres[132];
+             }
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   int ng;
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+           }
-   /*#ifdef windows */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+         }
-     /*#endif */
+       }
+   /******/
-   strcpy(dirfileres,optionfilefiname);
-   strcpy(optfileres,"vpl");
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   fprintf(ficgp, "set ter png small\n set log y\n");
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   fprintf(ficgp, "set size 0.65,0.65\n");
+           nhstepm = nhstepm/hstepm;
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+           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);
+           for (h=0; h<=nhstepm; h++){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
- /***********************************************/
+             for(j=1; j<=nlstate+ndeath;j++) {
- /**************** Main Program *****************/
+               kk1=0.;kk2=0;
- /***********************************************/
+               for(i=1; i<=nlstate;i++) {
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
- int main(int argc, char *argv[])
+               }
- {
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+             }
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+           }
-   int linei, month, year,iout;
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   int jj, ll, li, lj, lk, imk;
+         }
-   int numlinepar=0; /* Current linenumber of parameter file */
+       }
-   int itimes;
+    }
-   int NDIM=2;
+   }
-   char ca[32], cb[32], cc[32];
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   char dummy[]="                         ";
-   /*  FILE *fichtm; *//* Html File */
+   if (popforecast==1) {
-   /* FILE *ficgp;*/ /*Gnuplot File */
+     free_ivector(popage,0,AGESUP);
-   struct stat info;
+     free_vector(popeffectif,0,AGESUP);
-   double agedeb, agefin,hf;
+     free_vector(popcount,0,AGESUP);
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   }
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double fret;
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double **xi,tmp,delta;
+   fclose(ficrespop);
+ } /* End of popforecast */
-   double dum; /* Dummy variable */
-   double ***p3mat;
+ int fileappend(FILE *fichier, char *optionfich)
-   double ***mobaverage;
+ {
-   int *indx;
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-   char line[MAXLINE], linepar[MAXLINE];
+     printf("Problem with file: %s\n", optionfich);
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     return (0);
-   char **bp, *tok, *val; /* pathtot */
+   }
-   int firstobs=1, lastobs=10;
+   fflush(fichier);
-   int sdeb, sfin; /* Status at beginning and end */
+   return (1);
-   int c,  h , cpt,l;
+ }
-   int ju,jl, mi;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+ /**************** function prwizard **********************/
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   int mobilav=0,popforecast=0;
+ {
-   int hstepm, nhstepm;
-   int agemortsup;
+   /* Wizard to print covariance matrix template */
-   float  sumlpop=0.;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+   char ca[32], cb[32], cc[32];
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   double **prlim;
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   double *severity;
+   for(i=1; i <=nlstate; i++){
-   double ***param; /* Matrix of parameters */
+     jj=0;
-   double  *p;
+     for(j=1; j <=nlstate+ndeath; j++){
-   double **matcov; /* Matrix of covariance */
+       if(j==i) continue;
-   double ***delti3; /* Scale */
+       jj++;
-   double *delti; /* Scale */
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-   double ***eij, ***vareij;
+       printf("%1d%1d",i,j);
-   double **varpl; /* Variances of prevalence limits by age */
+       fprintf(ficparo,"%1d%1d",i,j);
-   double *epj, vepp;
+       for(k=1; k<=ncovmodel;k++){
-   double kk1, kk2;
+         /*        printf(" %lf",param[i][j][k]); */
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-   double **ximort;
+         printf(" 0.");
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+         fprintf(ficparo," 0.");
-   int *dcwave;
+       }
+       printf("\n");
-   char z[1]="c", occ;
+       fprintf(ficparo,"\n");
+     }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+   }
-   char  *strt, strtend[80];
+   printf("# Scales (for hessian or gradient estimation)\n");
-   char *stratrunc;
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   int lstra;
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+   for(i=1; i <=nlstate; i++){
-   long total_usecs;
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
- /*   setlocale (LC_ALL, ""); */
+       if(j==i) continue;
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+       jj++;
- /*   textdomain (PACKAGE); */
+       fprintf(ficparo,"%1d%1d",i,j);
- /*   setlocale (LC_CTYPE, ""); */
+       printf("%1d%1d",i,j);
- /*   setlocale (LC_MESSAGES, ""); */
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+         /*      printf(" %le",delti3[i][j][k]); */
-   (void) gettimeofday(&start_time,&tzp);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   curr_time=start_time;
+         printf(" 0.");
-   tm = *localtime(&start_time.tv_sec);
+         fprintf(ficparo," 0.");
-   tmg = *gmtime(&start_time.tv_sec);
+       }
-   strcpy(strstart,asctime(&tm));
+       numlinepar++;
+       printf("\n");
- /*  printf("Localtime (at start)=%s",strstart); */
+       fprintf(ficparo,"\n");
- /*  tp.tv_sec = tp.tv_sec +86400; */
+     }
- /*  tm = *localtime(&start_time.tv_sec); */
+   }
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+   printf("# Covariance matrix\n");
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+ /* # 121 Var(a12)\n\ */
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
- /*   tp.tv_sec = mktime(&tmg); */
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
- /*   strt=asctime(&tmg); */
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
- /*   printf("Time(after) =%s",strstart);  */
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
- /*  (void) time (&time_value);
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
- *  tm = *localtime(&time_value);
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
- *  strstart=asctime(&tm);
+   fflush(stdout);
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+   fprintf(ficparo,"# Covariance matrix\n");
- */
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   nberr=0; /* Number of errors and warnings */
+   /* #   ...\n\ */
-   nbwarn=0;
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-   getcwd(pathcd, size);
+   for(itimes=1;itimes<=2;itimes++){
-   printf("\n%s\n%s",version,fullversion);
+     jj=0;
-   if(argc <=1){
+     for(i=1; i <=nlstate; i++){
-     printf("\nEnter the parameter file name: ");
+       for(j=1; j <=nlstate+ndeath; j++){
-     fgets(pathr,FILENAMELENGTH,stdin);
+         if(j==i) continue;
-     i=strlen(pathr);
+         for(k=1; k<=ncovmodel;k++){
-     if(pathr[i-1]=='\n')
+           jj++;
-       pathr[i-1]='\0';
+           ca[0]= k+'a'-1;ca[1]='\0';
-    for (tok = pathr; tok != NULL; ){
+           if(itimes==1){
-       printf("Pathr |%s|\n",pathr);
+             printf("#%1d%1d%d",i,j,k);
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-       printf("val= |%s| pathr=%s\n",val,pathr);
+           }else{
-       strcpy (pathtot, val);
+             printf("%1d%1d%d",i,j,k);
-       if(pathr[0] == '\0') break; /* Dirty */
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-     }
+             /*  printf(" %.5le",matcov[i][j]); */
-   }
+           }
-   else{
+           ll=0;
-     strcpy(pathtot,argv[1]);
+           for(li=1;li <=nlstate; li++){
-   }
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+               if(lj==li) continue;
-   /*cygwin_split_path(pathtot,path,optionfile);
+               for(lk=1;lk<=ncovmodel;lk++){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+                 ll++;
-   /* cutv(path,optionfile,pathtot,'\\');*/
+                 if(ll<=jj){
+                   cb[0]= lk +'a'-1;cb[1]='\0';
-   /* Split argv[0], imach program to get pathimach */
+                   if(ll<jj){
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+                     if(itimes==1){
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-  /*   strcpy(pathimach,argv[0]); */
+                     }else{
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+                       printf(" 0.");
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+                       fprintf(ficparo," 0.");
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+                     }
-   chdir(path); /* Can be a relative path */
+                   }else{
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+                     if(itimes==1){
-     printf("Current directory %s!\n",pathcd);
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-   strcpy(command,"mkdir ");
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-   strcat(command,optionfilefiname);
+                     }else{
-   if((outcmd=system(command)) != 0){
+                       printf(" 0.");
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+                       fprintf(ficparo," 0.");
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+                     }
-     /* fclose(ficlog); */
+                   }
- /*     exit(1); */
+                 }
-   }
+               } /* end lk */
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+             } /* end lj */
- /*     perror("mkdir"); */
+           } /* end li */
- /*   } */
+           printf("\n");
+           fprintf(ficparo,"\n");
-   /*-------- arguments in the command line --------*/
+           numlinepar++;
+         } /* end k*/
-   /* Log file */
+       } /*end j */
-   strcat(filelog, optionfilefiname);
+     } /* end i */
-   strcat(filelog,".log");    /* */
+   } /* end itimes */
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
-     printf("Problem with logfile %s\n",filelog);
+ } /* end of prwizard */
-     goto end;
+ /******************* Gompertz Likelihood ******************************/
-   }
+ double gompertz(double x[])
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+ {
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   double A,B,L=0.0,sump=0.,num=0.;
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   int i,n=0; /* n is the size of the sample */
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-  path=%s \n\
+   for (i=0;i<=imx-1 ; i++) {
-  optionfile=%s\n\
+     sump=sump+weight[i];
-  optionfilext=%s\n\
+     /*    sump=sump+1;*/
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+     num=num+1;
+   }
-   printf("Local time (at start):%s",strstart);
-   fprintf(ficlog,"Local time (at start): %s",strstart);
-   fflush(ficlog);
+   /* for (i=0; i<=imx; i++)
- /*   (void) gettimeofday(&curr_time,&tzp); */
+      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("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+   for (i=1;i<=imx ; i++)
-   /* */
+     {
-   strcpy(fileres,"r");
+       if (cens[i] == 1 && wav[i]>1)
-   strcat(fileres, optionfilefiname);
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   strcat(fileres,".txt");    /* Other files have txt extension */
+       if (cens[i] == 0 && wav[i]>1)
-   /*---------arguments file --------*/
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-     printf("Problem with optionfile %s\n",optionfile);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+       if (wav[i] > 1 ) { /* ??? */
-     fflush(ficlog);
+         L=L+A*weight[i];
-     goto end;
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-   }
+       }
+     }
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   return -2*L*num/sump;
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+ }
-     printf("Problem with Output resultfile: %s\n", filereso);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+ #ifdef GSL
-     fflush(ficlog);
+ /******************* Gompertz_f Likelihood ******************************/
-     goto end;
+ double gompertz_f(const gsl_vector *v, void *params)
-   }
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
-   /* Reads comments: lines beginning with '#' */
+   double *x= (double *) v->data;
-   numlinepar=0;
+   int i,n=0; /* n is the size of the sample */
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+   for (i=0;i<=imx-1 ; i++) {
-     fgets(line, MAXLINE, ficpar);
+     sump=sump+weight[i];
-     numlinepar++;
+     /*    sump=sump+1;*/
-     puts(line);
+     num=num+1;
-     fputs(line,ficparo);
+   }
-     fputs(line,ficlog);
-   }
-   ungetc(c,ficpar);
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-   numlinepar++;
+   for (i=1;i<=imx ; i++)
-   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);
+       if (cens[i] == 1 && wav[i]>1)
-   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);
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-   fflush(ficlog);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       if (cens[i] == 0 && wav[i]>1)
-     ungetc(c,ficpar);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-     fgets(line, MAXLINE, ficpar);
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-     numlinepar++;
-     puts(line);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-     fputs(line,ficparo);
+       if (wav[i] > 1 ) { /* ??? */
-     fputs(line,ficlog);
+         LL=LL+A*weight[i];
-   }
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-   ungetc(c,ficpar);
+       }
+     }
-   covar=matrix(0,NCOVMAX,1,n);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+   return -2*LL*num/sump;
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+ }
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+ #endif
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+ /******************* Printing html file ***********/
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   delti=delti3[1][1];
+                   int lastpass, int stepm, int weightopt, char model[],\
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+                   int imx,  double p[],double **matcov,double agemortsup){
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+   int i,k;
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   for (i=1;i<=2;i++)
-     fclose (ficparo);
+     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]));
-     fclose (ficlog);
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     goto end;
+   fprintf(fichtm,"</ul>");
-     exit(0);
-   }
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   else if(mle==-3) {
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+  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>");
-     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);
+  for (k=agegomp;k<(agemortsup-2);k++)
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+    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]);
-     matcov=matrix(1,npar,1,npar);
-   }
-   else{
+   fflush(fichtm);
-     /* Read guess parameters */
+ }
-     /* Reads comments: lines beginning with '#' */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+ /******************* Gnuplot file **************/
-       ungetc(c,ficpar);
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       fgets(line, MAXLINE, ficpar);
-       numlinepar++;
+   char dirfileres[132],optfileres[132];
-       puts(line);
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-       fputs(line,ficparo);
+   int ng;
-       fputs(line,ficlog);
-     }
-     ungetc(c,ficpar);
+   /*#ifdef windows */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     /*#endif */
-     for(i=1; i <=nlstate; i++){
-       j=0;
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+   strcpy(dirfileres,optionfilefiname);
-         if(jj==i) continue;
+   strcpy(optfileres,"vpl");
-         j++;
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-         if ((i1 != i) && (j1 != j)){
+   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+   /* fprintf(ficgp, "set size 0.65,0.65\n"); */
- It might be a problem of design; if ncovcol and the model are correct\n \
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           exit(1);
+ }
-         }
-         fprintf(ficparo,"%1d%1d",i1,j1);
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-         if(mle==1)
+ {
-           printf("%1d%1d",i,j);
-         fprintf(ficlog,"%1d%1d",i,j);
+   /*-------- data file ----------*/
-         for(k=1; k<=ncovmodel;k++){
+   FILE *fic;
-           fscanf(ficpar," %lf",&param[i][j][k]);
+   char dummy[]="                         ";
-           if(mle==1){
+   int i, j, n;
-             printf(" %lf",param[i][j][k]);
+   int linei, month, year,iout;
-             fprintf(ficlog," %lf",param[i][j][k]);
+   char line[MAXLINE], linetmp[MAXLINE];
-           }
+   char stra[80], strb[80];
-           else
+   char *stratrunc;
-             fprintf(ficlog," %lf",param[i][j][k]);
+   int lstra;
-           fprintf(ficparo," %lf",param[i][j][k]);
-         }
-         fscanf(ficpar,"\n");
+   if((fic=fopen(datafile,"r"))==NULL)    {
-         numlinepar++;
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-         if(mle==1)
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-           printf("\n");
+   }
-         fprintf(ficlog,"\n");
-         fprintf(ficparo,"\n");
+   i=1;
-       }
+   linei=0;
-     }
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-     fflush(ficlog);
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     p=param[1][1];
+       if(line[j] == '\t')
+         line[j] = ' ';
-     /* Reads comments: lines beginning with '#' */
+     }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-       ungetc(c,ficpar);
+       ;
-       fgets(line, MAXLINE, ficpar);
+     };
-       numlinepar++;
+     line[j+1]=0;  /* Trims blanks at end of line */
-       puts(line);
+     if(line[0]=='#'){
-       fputs(line,ficparo);
+       fprintf(ficlog,"Comment line\n%s\n",line);
-       fputs(line,ficlog);
+       printf("Comment line\n%s\n",line);
-     }
+       continue;
-     ungetc(c,ficpar);
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-     for(i=1; i <=nlstate; i++){
+     for (j=0; line[j]!='\0';j++){
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       line[j]=linetmp[j];
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+     }
-         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);
+     for (j=maxwav;j>=1;j--){
-         }
+       cutv(stra, strb, line, ' ');
-         printf("%1d%1d",i,j);
+       if(strb[0]=='.') { /* Missing status */
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         lval=-1;
-         fprintf(ficlog,"%1d%1d",i1,j1);
+       }else{
-         for(k=1; k<=ncovmodel;k++){
+         errno=0;
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+         lval=strtol(strb,&endptr,10);
-           printf(" %le",delti3[i][j][k]);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-           fprintf(ficparo," %le",delti3[i][j][k]);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-           fprintf(ficlog," %le",delti3[i][j][k]);
+           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);
-         fscanf(ficpar,"\n");
+           return 1;
-         numlinepar++;
+         }
-         printf("\n");
+       }
-         fprintf(ficparo,"\n");
+       s[j][i]=lval;
-         fprintf(ficlog,"\n");
-       }
+       strcpy(line,stra);
-     }
+       cutv(stra, strb,line,' ');
-     fflush(ficlog);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       }
-     delti=delti3[1][1];
+       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+         month=99;
+         year=9999;
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+       }else{
+         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-     /* Reads comments: lines beginning with '#' */
+         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);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         return 1;
-       ungetc(c,ficpar);
+       }
-       fgets(line, MAXLINE, ficpar);
+       anint[j][i]= (double) year;
-       numlinepar++;
+       mint[j][i]= (double)month;
-       puts(line);
+       strcpy(line,stra);
-       fputs(line,ficparo);
+     } /* ENd Waves */
-       fputs(line,ficlog);
-     }
+     cutv(stra, strb,line,' ');
-     ungetc(c,ficpar);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
-     matcov=matrix(1,npar,1,npar);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-     for(i=1; i <=npar; i++){
+       month=99;
-       fscanf(ficpar,"%s",&str);
+       year=9999;
-       if(mle==1)
+     }else{
-         printf("%s",str);
+       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);
-       fprintf(ficlog,"%s",str);
+         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);
-       fprintf(ficparo,"%s",str);
+         return 1;
-       for(j=1; j <=i; j++){
+     }
-         fscanf(ficpar," %le",&matcov[i][j]);
+     andc[i]=(double) year;
-         if(mle==1){
+     moisdc[i]=(double) month;
-           printf(" %.5le",matcov[i][j]);
+     strcpy(line,stra);
-         }
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     cutv(stra, strb,line,' ');
-         fprintf(ficparo," %.5le",matcov[i][j]);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       }
+     }
-       fscanf(ficpar,"\n");
+     else  if(iout=sscanf(strb,"%s.", dummy) != 0){
-       numlinepar++;
+       month=99;
-       if(mle==1)
+       year=9999;
-         printf("\n");
+     }else{
-       fprintf(ficlog,"\n");
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-       fprintf(ficparo,"\n");
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     }
+         return 1;
-     for(i=1; i <=npar; i++)
+     }
-       for(j=i+1;j<=npar;j++)
+     if (year==9999) {
-         matcov[i][j]=matcov[j][i];
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     if(mle==1)
+         return 1;
-       printf("\n");
-     fprintf(ficlog,"\n");
+     }
+     annais[i]=(double)(year);
-     fflush(ficlog);
+     moisnais[i]=(double)(month);
+     strcpy(line,stra);
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+     cutv(stra, strb,line,' ');
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     errno=0;
-     strcat(rfileres,".");    /* */
+     dval=strtod(strb,&endptr);
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if( strb[0]=='\0' || (*endptr != '\0')){
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       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);
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       fflush(ficlog);
-     }
+       return 1;
-     fprintf(ficres,"#%s\n",version);
+     }
-   }    /* End of mle != -3 */
+     weight[i]=dval;
+     strcpy(line,stra);
-   /*-------- data file ----------*/
-   if((fic=fopen(datafile,"r"))==NULL)    {
+     for (j=ncovcol;j>=1;j--){
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+       cutv(stra, strb,line,' ');
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+       if(strb[0]=='.') { /* Missing status */
-   }
+         lval=-1;
+       }else{
-   n= lastobs;
+         errno=0;
-   severity = vector(1,maxwav);
+         lval=strtol(strb,&endptr,10);
-   outcome=imatrix(1,maxwav+1,1,n);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   num=lvector(1,n);
+           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);
-   moisnais=vector(1,n);
+           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);
-   annais=vector(1,n);
+           return 1;
-   moisdc=vector(1,n);
+         }
-   andc=vector(1,n);
+       }
-   agedc=vector(1,n);
+       if(lval <-1 || lval >1){
-   cod=ivector(1,n);
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-   weight=vector(1,n);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-   mint=matrix(1,maxwav,1,n);
+  For example, for multinomial values like 1, 2 and 3,\n \
-   anint=matrix(1,maxwav,1,n);
+  build V1=0 V2=0 for the reference value (1),\n \
-   s=imatrix(1,maxwav+1,1,n);
+         V1=1 V2=0 for (2) \n \
-   tab=ivector(1,NCOVMAX);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-   ncodemax=ivector(1,8);
+  output of IMaCh is often meaningless.\n \
+  Exiting.\n",lval,linei, i,line,j);
-   i=1;
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-   linei=0;
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     linei=linei+1;
+  For example, for multinomial values like 1, 2 and 3,\n \
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+  build V1=0 V2=0 for the reference value (1),\n \
-       if(line[j] == '\t')
+         V1=1 V2=0 for (2) \n \
-         line[j] = ' ';
+  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 \
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       ;
+         return 1;
-     };
+       }
-     line[j+1]=0;  /* Trims blanks at end of line */
+       covar[j][i]=(double)(lval);
-     if(line[0]=='#'){
+       strcpy(line,stra);
-       fprintf(ficlog,"Comment line\n%s\n",line);
+     }
-       printf("Comment line\n%s\n",line);
+     lstra=strlen(stra);
-       continue;
-     }
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       stratrunc = &(stra[lstra-9]);
-     for (j=maxwav;j>=1;j--){
+       num[i]=atol(stratrunc);
-       cutv(stra, strb,line,' ');
+     }
-       errno=0;
+     else
-       lval=strtol(strb,&endptr,10);
+       num[i]=atol(stra);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-         printf("Error reading data around '%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);
-         exit(1);
+     i=i+1;
-       }
+   } /* End loop reading  data */
-       s[j][i]=lval;
+   *imax=i-1; /* Number of individuals */
-       strcpy(line,stra);
+   fclose(fic);
-       cutv(stra, strb,line,' ');
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+   return (0);
-       }
+   endread:
-       else  if(iout=sscanf(strb,"%s.") != 0){
+     printf("Exiting readdata: ");
-         month=99;
+     fclose(fic);
-         year=9999;
+     return (1);
-       }else{
-         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-         exit(1);
-       }
+ }
-       anint[j][i]= (double) year;
+ void removespace(char *str) {
-       mint[j][i]= (double)month;
+   char *p1 = str, *p2 = str;
-       strcpy(line,stra);
+   do
-     } /* ENd Waves */
+     while (*p2 == ' ')
+       p2++;
-     cutv(stra, strb,line,' ');
+   while (*p1++ = *p2++);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
-     }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+ int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
-       month=99;
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
-       year=9999;
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
-     }else{
+    * - cptcovn or number of covariates k of the models excluding age*products =6
-       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);
+    * - cptcovage number of covariates with age*products =2
-       exit(1);
+    * - cptcovs number of simple covariates
-     }
+    * - 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
-     andc[i]=(double) year;
+    *     which is a new column after the 9 (ncovcol) variables.
-     moisdc[i]=(double) month;
+    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-     strcpy(line,stra);
+    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-     cutv(stra, strb,line,' ');
+    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+  */
-     }
+ {
-     else  if(iout=sscanf(strb,"%s.") != 0){
+   int i, j, k, ks;
-       month=99;
+   int i1, j1, k1, k2;
-       year=9999;
+   char modelsav[80];
-     }else{
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
-       exit(1);
+   /*removespace(model);*/
-     }
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-     annais[i]=(double)(year);
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     moisnais[i]=(double)(month);
+     j=nbocc(model,'+'); /**< j=Number of '+' */
-     strcpy(line,stra);
+     j1=nbocc(model,'*'); /**< j1=Number of '*' */
+     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     cutv(stra, strb,line,' ');
+     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-     errno=0;
+                   /* including age products which are counted in cptcovage.
-     dval=strtod(strb,&endptr);
+                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-     if( strb[0]=='\0' || (*endptr != '\0')){
+     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-       exit(1);
+     strcpy(modelsav,model);
-     }
+     if (strstr(model,"AGE") !=0){
-     weight[i]=dval;
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-     strcpy(line,stra);
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       return 1;
-     for (j=ncovcol;j>=1;j--){
+     }
-       cutv(stra, strb,line,' ');
+     if (strstr(model,"v") !=0){
-       errno=0;
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-       lval=strtol(strb,&endptr,10);
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       return 1;
-         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);
+     }
-         exit(1);
-       }
+     /*   Design
-       if(lval <-1 || lval >1){
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+      *  <          ncovcol=8                >
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+      *   k=  1    2      3       4     5       6      7        8
-  For example, for multinomial values like 1, 2 and 3,\n \
+      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-  build V1=0 V2=0 for the reference value (1),\n \
+      *  covar[k,i], value of kth covariate if not including age for individual i:
-         V1=1 V2=0 for (2) \n \
+      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-  output of IMaCh is often meaningless.\n \
+      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-  Exiting.\n",lval,linei, i,line,j);
+      *  Tage[++cptcovage]=k
-         exit(1);
+      *       if products, new covar are created after ncovcol with k1
-       }
+      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-       covar[j][i]=(double)(lval);
+      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-       strcpy(line,stra);
+      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
-     }
+      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-     lstra=strlen(stra);
+      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+      *  <          ncovcol=8                >
-       stratrunc = &(stra[lstra-9]);
+      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-       num[i]=atol(stratrunc);
+      *          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
-     else
+      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-       num[i]=atol(stra);
+      * p Tprod[1]@2={                         6, 5}
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+      *p Tvard[1][1]@4= {7, 8, 5, 6}
-       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;}*/
+      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     i=i+1;
+      *How to reorganize?
-   } /* End loop reading  data */
+      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-   fclose(fic);
+      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-   /* printf("ii=%d", ij);
+      *       {2,   1,     4,      8,    5,      6,     3,       7}
-      scanf("%d",i);*/
+      * Struct []
-   imx=i-1; /* Number of individuals */
+      */
-   /* for (i=1; i<=imx; i++){
+     /* This loop fills the array Tvar from the string 'model'.*/
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-     }*/
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-    /*  for (i=1; i<=imx; i++){
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-      if (s[4][i]==9)  s[4][i]=-1;
+     /*  k=1 Tvar[1]=2 (from V2) */
-      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]));}*/
+     /*  k=5 Tvar[5] */
+     /* for (k=1; k<=cptcovn;k++) { */
-   /* for (i=1; i<=imx; i++) */
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+     /*  } */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-      else weight[i]=1;*/
+     /*
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-   /* Calculation of the number of parameters from char model */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+         Tvar[k]=0;
-   Tprod=ivector(1,15);
+     cptcovage=0;
-   Tvaraff=ivector(1,15);
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-   Tvard=imatrix(1,15,1,2);
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-   Tage=ivector(1,15);
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-     j=0, j1=0, k1=1, k2=1;
+       /*scanf("%d",i);*/
-     j=nbocc(model,'+'); /* j=Number of '+' */
+       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-     cptcovn=j+1;
+         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-     cptcovprod=j1; /*Number of products */
+           /* covar is not filled and then is empty */
+           cptcovprod--;
-     strcpy(modelsav,model);
+           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
-       printf("Error. Non available option model=%s ",model);
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-       goto end;
+           /*printf("stre=%s ", stre);*/
-     }
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           cptcovprod--;
-     /* This loop fills the array Tvar from the string 'model'.*/
+           cutl(stre,strb,strc,'V');
+           Tvar[k]=atoi(stre);
-     for(i=(j+1); i>=1;i--){
+           cptcovage++;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+           Tage[cptcovage]=k;
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-       /*scanf("%d",i);*/
+           cptcovn++;
-       if (strchr(strb,'*')) {  /* Model includes a product */
+           cptcovprodnoage++;k1++;
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+           cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+           Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
-           cptcovprod--;
+                                   because this model-covariate is a construction we invent a new column
-           cutv(strb,stre,strd,'V');
+                                   ncovcol + k1
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-           cptcovage++;
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-             Tage[cptcovage]=i;
+           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
-             /*printf("stre=%s ", stre);*/
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-         }
+           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-           cptcovprod--;
+           k2=k2+2;
-           cutv(strb,stre,strc,'V');
+           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-           Tvar[i]=atoi(stre);
+           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-           cptcovage++;
+           for (i=1; i<=lastobs;i++){
-           Tage[cptcovage]=i;
+             /* Computes the new covariate which is a product of
-         }
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-         else {  /* Age is not in the model */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+           }
-           Tvar[i]=ncovcol+k1;
+         } /* End age is not in the model */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+       } /* End if model includes a product */
-           Tprod[k1]=i;
+       else { /* no more sum */
-           Tvard[k1][1]=atoi(strc); /* m*/
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-           Tvard[k1][2]=atoi(stre); /* n */
+        /*  scanf("%d",i);*/
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+         cutl(strd,strc,strb,'V');
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+         ks++; /**< Number of simple covariates */
-           for (k=1; k<=lastobs;k++)
+         cptcovn++;
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+         Tvar[k]=atoi(strd);
-           k1++;
+       }
-           k2=k2+2;
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-         }
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-       }
+         scanf("%d",i);*/
-       else { /* no more sum */
+     } /* end of loop + */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+   } /* end model */
-        /*  scanf("%d",i);*/
-       cutv(strd,strc,strb,'V');
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-       Tvar[i]=atoi(strc);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-       }
-       strcpy(modelsav,stra);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+   printf("cptcovprod=%d ", cptcovprod);
-         scanf("%d",i);*/
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-     } /* end of loop + */
-   } /* end model */
+   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.
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
+   endread:
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+     printf("Exiting decodemodel: ");
-   printf("cptcovprod=%d ", cptcovprod);
+     return (1);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+ }
-   scanf("%d ",i);*/
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ {
-     /*  if(mle==1){*/
+   int i, m;
-   if (weightopt != 1) { /* Maximisation without weights*/
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   for (i=1; i<=imx; i++) {
-   }
+     for(m=2; (m<= maxwav); m++) {
-     /*-calculation of age at interview from date of interview and age at death -*/
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-   agev=matrix(1,maxwav,1,imx);
+         anint[m][i]=9999;
+         s[m][i]=-1;
-   for (i=1; i<=imx; i++) {
+       }
-     for(m=2; (m<= maxwav); m++) {
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         *nberr++;
-         anint[m][i]=9999;
+         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;
+         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++;
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-         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);
+         *nberr++;
-         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);
+         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]);
-         s[m][i]=-1;
+         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]);
-       }
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+       }
-         nberr++;
+     }
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+   }
-         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]);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+   for (i=1; i<=imx; i++)  {
-       }
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     }
+     for(m=firstpass; (m<= lastpass); m++){
-   }
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+         if (s[m][i] >= nlstate+1) {
-   for (i=1; i<=imx; i++)  {
+           if(agedc[i]>0)
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-     for(m=firstpass; (m<= lastpass); m++){
+               agev[m][i]=agedc[i];
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-         if (s[m][i] >= nlstate+1) {
+             else {
-           if(agedc[i]>0)
+               if ((int)andc[i]!=9999){
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+                 nbwarn++;
-               agev[m][i]=agedc[i];
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-             else {
+                 agev[m][i]=-1;
-               if ((int)andc[i]!=9999){
+               }
-                 nbwarn++;
+             }
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+         }
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-                 agev[m][i]=-1;
+                                  years but with the precision of a month */
-               }
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-             }
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-         }
+             agev[m][i]=1;
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+           else if(agev[m][i] < *agemin){
-                                  years but with the precision of a month */
+             *agemin=agev[m][i];
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+           }
-             agev[m][i]=1;
+           else if(agev[m][i] >*agemax){
-           else if(agev[m][i] <agemin){
+             *agemax=agev[m][i];
-             agemin=agev[m][i];
+             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+           }
-           }
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-           else if(agev[m][i] >agemax){
+           /*     agev[m][i] = age[i]+2*m;*/
-             agemax=agev[m][i];
+         }
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+         else { /* =9 */
-           }
+           agev[m][i]=1;
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+           s[m][i]=-1;
-           /*     agev[m][i] = age[i]+2*m;*/
+         }
-         }
+       }
-         else { /* =9 */
+       else /*= 0 Unknown */
-           agev[m][i]=1;
+         agev[m][i]=1;
-           s[m][i]=-1;
+     }
-         }
-       }
+   }
-       else /*= 0 Unknown */
+   for (i=1; i<=imx; i++)  {
-         agev[m][i]=1;
+     for(m=firstpass; (m<=lastpass); m++){
-     }
+       if (s[m][i] > (nlstate+ndeath)) {
+         *nberr++;
-   }
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-   for (i=1; i<=imx; i++)  {
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-     for(m=firstpass; (m<=lastpass); m++){
+         return 1;
-       if (s[m][i] > (nlstate+ndeath)) {
+       }
-         nberr++;
+     }
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+   }
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+   /*for (i=1; i<=imx; i++){
-       }
+   for (m=firstpass; (m<lastpass); m++){
-     }
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-   }
+ }
-   /*for (i=1; i<=imx; i++){
+ }*/
-   for (m=firstpass; (m<lastpass); m++){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
- }
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
- }*/
+   return (0);
+   endread:
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     printf("Exiting calandcheckages: ");
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     return (1);
+ }
-   agegomp=(int)agemin;
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
+ /***********************************************/
-   free_vector(moisnais,1,n);
+ /**************** Main Program *****************/
-   free_vector(annais,1,n);
+ /***********************************************/
-   /* free_matrix(mint,1,maxwav,1,n);
-      free_matrix(anint,1,maxwav,1,n);*/
+ int main(int argc, char *argv[])
-   free_vector(moisdc,1,n);
+ {
-   free_vector(andc,1,n);
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
-   wav=ivector(1,imx);
+   int rval = GSL_CONTINUE;
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   int status = GSL_SUCCESS;
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   double ssval;
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+ #endif
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   /* Concatenates waves */
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   int linei, month, year,iout;
+   int jj, ll, li, lj, lk, imk;
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
-   Tcode=ivector(1,100);
+   int NDIM=2;
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   int vpopbased=0;
-   ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   char ca[32], cb[32], cc[32];
+   /*  FILE *fichtm; *//* Html File */
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+   /* FILE *ficgp;*/ /*Gnuplot File */
-                                  the estimations*/
+   struct stat info;
-   h=0;
+   double agedeb, agefin,hf;
-   m=pow(2,cptcoveff);
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   for(k=1;k<=cptcoveff; k++){
+   double fret;
-     for(i=1; i <=(m/pow(2,k));i++){
+   double **xi,tmp,delta;
-       for(j=1; j <= ncodemax[k]; j++){
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   double dum; /* Dummy variable */
-           h++;
+   double ***p3mat;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   double ***mobaverage;
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   int *indx;
-         }
+   char line[MAXLINE], linepar[MAXLINE];
-       }
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     }
+   char pathr[MAXLINE], pathimach[MAXLINE];
-   }
+   char **bp, *tok, *val; /* pathtot */
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+   int firstobs=1, lastobs=10;
-      codtab[1][2]=1;codtab[2][2]=2; */
+   int sdeb, sfin; /* Status at beginning and end */
-   /* for(i=1; i <=m ;i++){
+   int c,  h , cpt,l;
-      for(k=1; k <=cptcovn; k++){
+   int ju,jl, mi;
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   int i1,j1, jk,aa,bb, stepsize, ij;
-      }
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-      printf("\n");
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-      }
+   int mobilav=0,popforecast=0;
-      scanf("%d",i);*/
+   int hstepm, nhstepm;
+   int agemortsup;
-   /*------------ gnuplot -------------*/
+   float  sumlpop=0.;
-   strcpy(optionfilegnuplot,optionfilefiname);
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-   if(mle==-3)
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-     strcat(optionfilegnuplot,"-mort");
-   strcat(optionfilegnuplot,".gp");
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   double **prlim;
-     printf("Problem with file %s",optionfilegnuplot);
+   double ***param; /* Matrix of parameters */
-   }
+   double  *p;
-   else{
+   double **matcov; /* Matrix of covariance */
-     fprintf(ficgp,"\n# %s\n", version);
+   double ***delti3; /* Scale */
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   double *delti; /* Scale */
-     fprintf(ficgp,"set missing 'NaNq'\n");
+   double ***eij, ***vareij;
-   }
+   double **varpl; /* Variances of prevalence limits by age */
-   /*  fclose(ficgp);*/
+   double *epj, vepp;
-   /*--------- index.htm --------*/
+   double kk1, kk2;
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   double **ximort;
-   if(mle==-3)
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
-     strcat(optionfilehtm,"-mort");
+   int *dcwave;
-   strcat(optionfilehtm,".htm");
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+   char z[1]="c", occ;
-     printf("Problem with %s \n",optionfilehtm), exit(0);
-   }
+   /*char  *strt;*/
+   char strtend[80];
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-   strcat(optionfilehtmcov,"-cov.htm");
+   long total_usecs;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+ /*   setlocale (LC_ALL, ""); */
-   }
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-   else{
+ /*   textdomain (PACKAGE); */
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ /*   setlocale (LC_CTYPE, ""); */
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ /*   setlocale (LC_MESSAGES, ""); */
- 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);
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   }
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   tm = *localtime(&start_time.tv_sec);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+   tmg = *gmtime(&start_time.tv_sec);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+   strcpy(strstart,asctime(&tm));
- \n\
- <hr  size=\"2\" color=\"#EC5E5E\">\
+ /*  printf("Localtime (at start)=%s",strstart); */
-  <ul><li><h4>Parameter files</h4>\n\
+ /*  tp.tv_sec = tp.tv_sec +86400; */
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+ /*  tm = *localtime(&start_time.tv_sec); */
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-  - Date and time at start: %s</ul>\n",\
+ /*   tp.tv_sec = mktime(&tmg); */
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ /*   strt=asctime(&tmg); */
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+ /*   printf("Time(after) =%s",strstart);  */
-           fileres,fileres,\
+ /*  (void) time (&time_value);
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-   fflush(fichtm);
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
-   strcpy(pathr,path);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-   strcat(pathr,optionfilefiname);
+ */
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+   nberr=0; /* Number of errors and warnings */
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+   nbwarn=0;
-      and prints on file fileres'p'. */
+   getcwd(pathcd, size);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   printf("\n%s\n%s",version,fullversion);
-   fprintf(fichtm,"\n");
+   if(argc <=1){
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+     printf("\nEnter the parameter file name: ");
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+     fgets(pathr,FILENAMELENGTH,stdin);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+     i=strlen(pathr);
-           imx,agemin,agemax,jmin,jmax,jmean);
+     if(pathr[i-1]=='\n')
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       pathr[i-1]='\0';
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+    for (tok = pathr; tok != NULL; ){
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       printf("Pathr |%s|\n",pathr);
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+       printf("val= |%s| pathr=%s\n",val,pathr);
+       strcpy (pathtot, val);
+       if(pathr[0] == '\0') break; /* Dirty */
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+     }
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+   }
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+   else{
+     strcpy(pathtot,argv[1]);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   }
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-   if (mle==-3){
+   /*cygwin_split_path(pathtot,path,optionfile);
-     ximort=matrix(1,NDIM,1,NDIM);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-     cens=ivector(1,n);
+   /* cutv(path,optionfile,pathtot,'\\');*/
-     ageexmed=vector(1,n);
-     agecens=vector(1,n);
+   /* Split argv[0], imach program to get pathimach */
-     dcwave=ivector(1,n);
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-     for (i=1; i<=imx; i++){
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-       dcwave[i]=-1;
+  /*   strcpy(pathimach,argv[0]); */
-       for (m=firstpass; m<=lastpass; m++)
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-         if (s[m][i]>nlstate) {
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-           dcwave[i]=m;
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+   chdir(path); /* Can be a relative path */
-           break;
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-         }
+     printf("Current directory %s!\n",pathcd);
-     }
+   strcpy(command,"mkdir ");
+   strcat(command,optionfilefiname);
-     for (i=1; i<=imx; i++) {
+   if((outcmd=system(command)) != 0){
-       if (wav[i]>0){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-         ageexmed[i]=agev[mw[1][i]][i];
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-         j=wav[i];
+     /* fclose(ficlog); */
-         agecens[i]=1.;
+ /*     exit(1); */
+   }
-         if (ageexmed[i]> 1 && wav[i] > 0){
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-           agecens[i]=agev[mw[j][i]][i];
+ /*     perror("mkdir"); */
-           cens[i]= 1;
+ /*   } */
-         }else if (ageexmed[i]< 1)
-           cens[i]= -1;
+   /*-------- arguments in the command line --------*/
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           cens[i]=0 ;
+   /* Log file */
-       }
+   strcat(filelog, optionfilefiname);
-       else cens[i]=-1;
+   strcat(filelog,".log");    /* */
-     }
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
-     for (i=1;i<=NDIM;i++) {
+     goto end;
-       for (j=1;j<=NDIM;j++)
+   }
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     }
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-     p[1]=0.0268; p[NDIM]=0.083;
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-     /*printf("%lf %lf", p[1], p[2]);*/
+  path=%s \n\
+  optionfile=%s\n\
+  optionfilext=%s\n\
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-     strcpy(filerespow,"pow-mort");
-     strcat(filerespow,fileres);
+   printf("Local time (at start):%s",strstart);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-       printf("Problem with resultfile: %s\n", filerespow);
+   fflush(ficlog);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     }
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     /*  for (i=1;i<=nlstate;i++)
+   /* */
-         for(j=1;j<=nlstate+ndeath;j++)
+   strcpy(fileres,"r");
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   strcat(fileres, optionfilefiname);
-     */
+   strcat(fileres,".txt");    /* Other files have txt extension */
-     fprintf(ficrespow,"\n");
+   /*---------arguments file --------*/
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-     fclose(ficrespow);
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
+     fflush(ficlog);
-     for(i=1; i <=NDIM; i++)
+     /* goto end; */
-       for(j=i+1;j<=NDIM;j++)
+     exit(70);
-         matcov[i][j]=matcov[j][i];
+   }
-     printf("\nCovariance matrix\n ");
-     for(i=1; i <=NDIM; i++) {
-       for(j=1;j<=NDIM;j++){
+   strcpy(filereso,"o");
-         printf("%f ",matcov[i][j]);
+   strcat(filereso,fileres);
-       }
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-       printf("\n ");
+     printf("Problem with Output resultfile: %s\n", filereso);
-     }
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
+     goto end;
-     for (i=1;i<=NDIM;i++)
+   }
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   /* Reads comments: lines beginning with '#' */
-     lsurv=vector(1,AGESUP);
+   numlinepar=0;
-     lpop=vector(1,AGESUP);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     tpop=vector(1,AGESUP);
+     ungetc(c,ficpar);
-     lsurv[agegomp]=100000;
+     fgets(line, MAXLINE, ficpar);
+     numlinepar++;
-     for (k=agegomp;k<=AGESUP;k++) {
+     fputs(line,stdout);
-       agemortsup=k;
+     fputs(line,ficparo);
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     fputs(line,ficlog);
-     }
+   }
+   ungetc(c,ficpar);
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   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++;
-     for (k=agegomp;k<agemortsup;k++){
+   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);
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   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);
-       sumlpop=sumlpop+lpop[k];
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-     }
+   fflush(ficlog);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-     tpop[agegomp]=sumlpop;
+     ungetc(c,ficpar);
-     for (k=agegomp;k<(agemortsup-3);k++){
+     fgets(line, MAXLINE, ficpar);
-       /*  tpop[k+1]=2;*/
+     numlinepar++;
-       tpop[k+1]=tpop[k]-lpop[k];
+     fputs(line, stdout);
-     }
+     //puts(line);
+     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]);
+   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+      v1+v2*age+v2*v3 makes cptcovn = 3
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+   */
-                      stepm, weightopt,\
+   if (strlen(model)>1)
-                      model,imx,p,matcov,agemortsup);
+     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+   else
-     free_vector(lsurv,1,AGESUP);
+     ncovmodel=2;
-     free_vector(lpop,1,AGESUP);
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-     free_vector(tpop,1,AGESUP);
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-   } /* Endof if mle==-3 */
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-   else{ /* For mle >=1 */
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     fflush(stdout);
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     fclose (ficlog);
-     for (k=1; k<=npar;k++)
+     goto end;
-       printf(" %d %8.5f",k,p[k]);
+   }
-     printf("\n");
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     globpr=1; /* to print the contributions */
+   delti=delti3[1][1];
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-     for (k=1; k<=npar;k++)
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-       printf(" %d %8.5f",k,p[k]);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     printf("\n");
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     if(mle>=1){ /* Could be 1 or 2 */
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     fclose (ficparo);
-     }
+     fclose (ficlog);
+     goto end;
-     /*--------- results files --------------*/
+     exit(0);
-     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(mle==-3) {
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1,jk=1; i <=nlstate; i++){
+     matcov=matrix(1,npar,1,npar);
-       for(k=1; k <=(nlstate+ndeath); k++){
+   }
-         if (k != i) {
+   else{
-           printf("%d%d ",i,k);
+     /* Read guessed parameters */
-           fprintf(ficlog,"%d%d ",i,k);
+     /* Reads comments: lines beginning with '#' */
-           fprintf(ficres,"%1d%1d ",i,k);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-           for(j=1; j <=ncovmodel; j++){
+       ungetc(c,ficpar);
-             printf("%lf ",p[jk]);
+       fgets(line, MAXLINE, ficpar);
-             fprintf(ficlog,"%lf ",p[jk]);
+       numlinepar++;
-             fprintf(ficres,"%lf ",p[jk]);
+       fputs(line,stdout);
-             jk++;
+       fputs(line,ficparo);
-           }
+       fputs(line,ficlog);
-           printf("\n");
+     }
-           fprintf(ficlog,"\n");
+     ungetc(c,ficpar);
-           fprintf(ficres,"\n");
-         }
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-       }
+     for(i=1; i <=nlstate; i++){
-     }
+       j=0;
-     if(mle!=0){
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-       /* Computing hessian and covariance matrix */
+         if(jj==i) continue;
-       ftolhess=ftol; /* Usually correct */
+         j++;
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     }
+         if ((i1 != i) && (j1 != j)){
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-     printf("# Scales (for hessian or gradient estimation)\n");
+ It might be a problem of design; if ncovcol and the model are correct\n \
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-     for(i=1,jk=1; i <=nlstate; i++){
+           exit(1);
-       for(j=1; j <=nlstate+ndeath; j++){
+         }
-         if (j!=i) {
+         fprintf(ficparo,"%1d%1d",i1,j1);
-           fprintf(ficres,"%1d%1d",i,j);
+         if(mle==1)
            printf("%1d%1d",i,j);
-           fprintf(ficlog,"%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,j);
-           for(k=1; k<=ncovmodel;k++){
+         for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-             fprintf(ficlog," %.5e",delti[jk]);
+           if(mle==1){
-             fprintf(ficres," %.5e",delti[jk]);
+             printf(" %lf",param[i][j][k]);
-             jk++;
+             fprintf(ficlog," %lf",param[i][j][k]);
            }
-           printf("\n");
+           else
-           fprintf(ficlog,"\n");
+             fprintf(ficlog," %lf",param[i][j][k]);
-           fprintf(ficres,"\n");
+           fprintf(ficparo," %lf",param[i][j][k]);
          }
-       }
+         fscanf(ficpar,"\n");
-     }
+         numlinepar++;
+         if(mle==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");
+           printf("\n");
-     if(mle>=1)
+         fprintf(ficlog,"\n");
-       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+         fprintf(ficparo,"\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\ */
+     fflush(ficlog);
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* Reads scales values */
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     p=param[1][1];
-     /* # 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\ */
+     /* Reads comments: lines beginning with '#' */
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-     /* Just to have a covariance matrix which will be more understandable
+       numlinepar++;
-        even is we still don't want to manage dictionary of variables
+       fputs(line,stdout);
-     */
+       fputs(line,ficparo);
-     for(itimes=1;itimes<=2;itimes++){
+       fputs(line,ficlog);
-       jj=0;
+     }
-       for(i=1; i <=nlstate; i++){
+     ungetc(c,ficpar);
-         for(j=1; j <=nlstate+ndeath; j++){
-           if(j==i) continue;
+     for(i=1; i <=nlstate; i++){
-           for(k=1; k<=ncovmodel;k++){
+       for(j=1; j <=nlstate+ndeath-1; j++){
-             jj++;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-             ca[0]= k+'a'-1;ca[1]='\0';
+         if ((i1-i)*(j1-j)!=0){
-             if(itimes==1){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-               if(mle>=1)
+           exit(1);
-                 printf("#%1d%1d%d",i,j,k);
+         }
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+         printf("%1d%1d",i,j);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-             }else{
+         fprintf(ficlog,"%1d%1d",i1,j1);
-               if(mle>=1)
+         for(k=1; k<=ncovmodel;k++){
-                 printf("%1d%1d%d",i,j,k);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+           printf(" %le",delti3[i][j][k]);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-             }
+           fprintf(ficlog," %le",delti3[i][j][k]);
-             ll=0;
+         }
-             for(li=1;li <=nlstate; li++){
+         fscanf(ficpar,"\n");
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+         numlinepar++;
-                 if(lj==li) continue;
+         printf("\n");
-                 for(lk=1;lk<=ncovmodel;lk++){
+         fprintf(ficparo,"\n");
-                   ll++;
+         fprintf(ficlog,"\n");
-                   if(ll<=jj){
+       }
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+     }
-                     if(ll<jj){
+     fflush(ficlog);
-                       if(itimes==1){
-                         if(mle>=1)
+     /* Reads covariance matrix */
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     delti=delti3[1][1];
-                         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{
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+     /* Reads comments: lines beginning with '#' */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+       ungetc(c,ficpar);
-                       }
+       fgets(line, MAXLINE, ficpar);
-                     }else{
+       numlinepar++;
-                       if(itimes==1){
+       fputs(line,stdout);
-                         if(mle>=1)
+       fputs(line,ficparo);
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+       fputs(line,ficlog);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+     }
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     ungetc(c,ficpar);
-                       }else{
-                         if(mle>=1)
+     matcov=matrix(1,npar,1,npar);
-                           printf(" %.5e",matcov[jj][ll]);
+     for(i=1; i <=npar; i++)
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+     for(i=1; i <=npar; i++){
-                     }
+       fscanf(ficpar,"%s",str);
-                   }
+       if(mle==1)
-                 } /* end lk */
+         printf("%s",str);
-               } /* end lj */
+       fprintf(ficlog,"%s",str);
-             } /* end li */
+       fprintf(ficparo,"%s",str);
-             if(mle>=1)
+       for(j=1; j <=i; j++){
-               printf("\n");
+         fscanf(ficpar," %le",&matcov[i][j]);
-             fprintf(ficlog,"\n");
+         if(mle==1){
-             fprintf(ficres,"\n");
+           printf(" %.5le",matcov[i][j]);
-             numlinepar++;
+         }
-           } /* end k*/
+         fprintf(ficlog," %.5le",matcov[i][j]);
-         } /*end j */
+         fprintf(ficparo," %.5le",matcov[i][j]);
-       } /* end i */
+       }
-     } /* end itimes */
+       fscanf(ficpar,"\n");
+       numlinepar++;
-     fflush(ficlog);
+       if(mle==1)
-     fflush(ficres);
+         printf("\n");
+       fprintf(ficlog,"\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficparo,"\n");
-       ungetc(c,ficpar);
+     }
-       fgets(line, MAXLINE, ficpar);
+     for(i=1; i <=npar; i++)
-       puts(line);
+       for(j=i+1;j<=npar;j++)
-       fputs(line,ficparo);
+         matcov[i][j]=matcov[j][i];
-     }
-     ungetc(c,ficpar);
+     if(mle==1)
+       printf("\n");
-     estepm=0;
+     fprintf(ficlog,"\n");
-     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;
+     fflush(ficlog);
-     if (fage <= 2) {
-       bage = ageminpar;
+     /*-------- Rewriting parameter file ----------*/
-       fage = agemaxpar;
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     }
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-       ungetc(c,ficpar);
+     fprintf(ficres,"#%s\n",version);
-       fgets(line, MAXLINE, ficpar);
+   }    /* End of mle != -3 */
-       puts(line);
-       fputs(line,ficparo);
-     }
+   n= lastobs;
-     ungetc(c,ficpar);
+   num=lvector(1,n);
+   moisnais=vector(1,n);
-     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);
+   annais=vector(1,n);
-     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);
+   moisdc=vector(1,n);
-     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);
+   andc=vector(1,n);
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+   agedc=vector(1,n);
-     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);
+   cod=ivector(1,n);
+   weight=vector(1,n);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-       ungetc(c,ficpar);
+   mint=matrix(1,maxwav,1,n);
-       fgets(line, MAXLINE, ficpar);
+   anint=matrix(1,maxwav,1,n);
-       puts(line);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-       fputs(line,ficparo);
+   tab=ivector(1,NCOVMAX);
-     }
+   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
-     ungetc(c,ficpar);
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+     goto end;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+   /* Calculation of the number of parameters from char model */
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-     fprintf(ficres,"pop_based=%d\n",popbased);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         k=1 Tvar[1]=2 (from V2)
-       ungetc(c,ficpar);
+     */
-       fgets(line, MAXLINE, ficpar);
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-       puts(line);
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-       fputs(line,ficparo);
+       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.
-     ungetc(c,ficpar);
+   */
+   /* For model-covariate k tells which data-covariate to use but
-     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);
+     because this model-covariate is a construction we invent a new column
-     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);
+     ncovcol + k1
-     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);
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     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);
+     Tvar[3=V1*V4]=4+1 etc */
-     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);
+   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
-     /* day and month of proj2 are not used but only year anproj2.*/
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+   */
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+   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
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+                       */
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
-    /*------------ free_vector  -------------*/
-    /*  chdir(path); */
+   if((double)(lastobs-imx)/(double)imx > 1.10){
+     nbwarn++;
-     free_ivector(wav,1,imx);
+     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);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+   }
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     /*  if(mle==1){*/
-     free_lvector(num,1,n);
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     free_vector(agedc,1,n);
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+   }
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     fclose(ficparo);
+     /*-calculation of age at interview from date of interview and age at death -*/
-     fclose(ficres);
+   agev=matrix(1,maxwav,1,imx);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     goto end;
-     strcpy(filerespl,"pl");
-     strcat(filerespl,fileres);
+   agegomp=(int)agemin;
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+   free_vector(moisnais,1,n);
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   free_vector(annais,1,n);
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+   /* free_matrix(mint,1,maxwav,1,n);
-     }
+      free_matrix(anint,1,maxwav,1,n);*/
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   free_vector(moisdc,1,n);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   free_vector(andc,1,n);
-     pstamp(ficrespl);
+   /* */
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
-     fprintf(ficrespl,"#Age ");
+   wav=ivector(1,imx);
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     fprintf(ficrespl,"\n");
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     prlim=matrix(1,nlstate,1,nlstate);
+   /* Concatenates waves */
-     agebase=ageminpar;
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     agelim=agemaxpar;
+   /* */
-     ftolpl=1.e-10;
-     i1=cptcoveff;
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     if (cptcovn < 1){i1=1;}
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   ncodemax[1]=1;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+   Ndum =ivector(-1,NCOVMAX);
-         k=k+1;
+   if (ncovmodel > 2)
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-         fprintf(ficlog,"\n#******");
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
-         for(j=1;j<=cptcoveff;j++) {
+   h=0;
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           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]]);
+   /*if (cptcovn > 0) */
-         }
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
+   m=pow(2,cptcoveff);
-         fprintf(ficlog,"******\n");
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-         for (age=agebase; age<=agelim; age++){
+     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 */
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-           fprintf(ficrespl,"%.0f ",age );
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-           for(j=1;j<=cptcoveff;j++)
+           h++;
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           if (h>m)
-           for(i=1; i<=nlstate;i++)
+             h=1;
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-           fprintf(ficrespl,"\n");
+            *     h     1     2     3     4
-         }
+            *______________________________
-       }
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-     }
+            *     2     2     1     1     1
-     fclose(ficrespl);
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
-     /*------------- h Pij x at various ages ------------*/
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+            *     7 i=4 1     2     2     1
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+            *     8     2     2     2     1
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+            *     9 i=5 1 i=3 1 i=2 1     1
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+            *    10     2     1     1     1
-     }
+            *    11 i=6 1     2     1     1
-     printf("Computing pij: result on file '%s' \n", filerespij);
+            *    12     2     2     1     1
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+            *    15 i=8 1     2     2     1
-     /*if (stepm<=24) stepsize=2;*/
+            *    16     2     2     2     1
+            */
-     agelim=AGESUP;
+           codtab[h][k]=j;
-     hstepm=stepsize*YEARM; /* Every year of age */
+           /*codtab[h][Tvar[k]]=j;*/
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+           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]]);
+         }
-     /* hstepm=1;   aff par mois*/
+       }
-     pstamp(ficrespij);
+     }
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+   }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+      codtab[1][2]=1;codtab[2][2]=2; */
-         k=k+1;
+   /* for(i=1; i <=m ;i++){
-         fprintf(ficrespij,"\n#****** ");
+      for(k=1; k <=cptcovn; k++){
-         for(j=1;j<=cptcoveff;j++)
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
-         fprintf(ficrespij,"******\n");
+      printf("\n");
+      }
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+      scanf("%d",i);*/
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+  free_ivector(Ndum,-1,NCOVMAX);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /*------------ gnuplot -------------*/
-           oldm=oldms;savm=savms;
+   strcpy(optionfilegnuplot,optionfilefiname);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   if(mle==-3)
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     strcat(optionfilegnuplot,"-mort");
-           for(i=1; i<=nlstate;i++)
+   strcat(optionfilegnuplot,".gp");
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-           fprintf(ficrespij,"\n");
+     printf("Problem with file %s",optionfilegnuplot);
-           for (h=0; h<=nhstepm; h++){
+   }
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+   else{
-             for(i=1; i<=nlstate;i++)
+     fprintf(ficgp,"\n# %s\n", version);
-               for(j=1; j<=nlstate+ndeath;j++)
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-             fprintf(ficrespij,"\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-           }
+   }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /*  fclose(ficgp);*/
-           fprintf(ficrespij,"\n");
+   /*--------- index.htm --------*/
-         }
-       }
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-     }
+   if(mle==-3)
+     strcat(optionfilehtm,"-mort");
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+   strcat(optionfilehtm,".htm");
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     fclose(ficrespij);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }
-     for(i=1;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-         for(k=1;k<=NCOVMAX;k++)
+   strcat(optionfilehtmcov,"-cov.htm");
-           probs[i][j][k]=0.;
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-     /*---------- Forecasting ------------------*/
+   }
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+   else{
-     if(prevfcast==1){
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-       /*    if(stepm ==1){*/
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-       /*      }  */
+   }
-       /*      else{ */
-       /*        erreur=108; */
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-       /*        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); */
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-       /*        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); */
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-       /*      } */
+ \n\
-     }
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-     /*---------- Health expectancies and variances ------------*/
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-     strcpy(filerest,"t");
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-     strcat(filerest,fileres);
+  - Date and time at start: %s</ul>\n",\
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+           fileres,fileres,\
-     }
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   fflush(fichtm);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+   strcpy(pathr,path);
+   strcat(pathr,optionfilefiname);
-     strcpy(filerese,"e");
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     strcat(filerese,fileres);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+      and prints on file fileres'p'. */
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-     }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+   fprintf(fichtm,"\n");
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-     strcpy(fileresstde,"stde");
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-     strcat(fileresstde,fileres);
+           imx,agemin,agemax,jmin,jmax,jmean);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     }
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     strcpy(filerescve,"cve");
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-     strcat(filerescve,fileres);
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-       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);
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+   if (mle==-3){
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     strcpy(fileresv,"v");
+     cens=ivector(1,n);
-     strcat(fileresv,fileres);
+     ageexmed=vector(1,n);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+     agecens=vector(1,n);
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+     dcwave=ivector(1,n);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-     }
+     for (i=1; i<=imx; i++){
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       dcwave[i]=-1;
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+       for (m=firstpass; m<=lastpass; m++)
+         if (s[m][i]>nlstate) {
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+           dcwave[i]=m;
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     /*  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",\
+           break;
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+         }
-     */
+     }
-     if (mobilav!=0) {
+     for (i=1; i<=imx; i++) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       if (wav[i]>0){
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         ageexmed[i]=agev[mw[1][i]][i];
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         j=wav[i];
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         agecens[i]=1.;
-       }
-     }
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+           cens[i]= 1;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         }else if (ageexmed[i]< 1)
-         k=k+1;
+           cens[i]= -1;
-         fprintf(ficrest,"\n#****** ");
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-         for(j=1;j<=cptcoveff;j++)
+           cens[i]=0 ;
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-         fprintf(ficrest,"******\n");
+       else cens[i]=-1;
+     }
-         fprintf(ficreseij,"\n#****** ");
-         fprintf(ficresstdeij,"\n#****** ");
+     for (i=1;i<=NDIM;i++) {
-         fprintf(ficrescveij,"\n#****** ");
+       for (j=1;j<=NDIM;j++)
-         for(j=1;j<=cptcoveff;j++) {
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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]]);
+     /*p[1]=0.0268; p[NDIM]=0.083;*/
-         }
+     /*printf("%lf %lf", p[1], p[2]);*/
-         fprintf(ficreseij,"******\n");
-         fprintf(ficresstdeij,"******\n");
-         fprintf(ficrescveij,"******\n");
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-         fprintf(ficresvij,"\n#****** ");
+ #elsedef
-         for(j=1;j<=cptcoveff;j++)
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ #endif
-         fprintf(ficresvij,"******\n");
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-         oldm=oldms;savm=savms;
+       printf("Problem with resultfile: %s\n", filerespow);
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+     }
+ #ifdef GSL
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-         oldm=oldms;savm=savms;
+ #elsedef
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-         if(popbased==1){
+ #endif
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+     /*  for (i=1;i<=nlstate;i++)
-         }
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-         pstamp(ficrest);
+     */
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+     fprintf(ficrespow,"\n");
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+ #ifdef GSL
-         fprintf(ficrest,"\n");
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
-         epj=vector(1,nlstate+1);
+     gsl_multimin_fminimizer *sfm = NULL;
-         for(age=bage; age <=fage ;age++){
+     gsl_vector *ss, *x;
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     gsl_multimin_function minex_func;
-           if (popbased==1) {
-             if(mobilav ==0){
+     /* Initial vertex size vector */
-               for(i=1; i<=nlstate;i++)
+     ss = gsl_vector_alloc (NDIM);
-                 prlim[i][i]=probs[(int)age][i][k];
-             }else{ /* mobilav */
+     if (ss == NULL){
-               for(i=1; i<=nlstate;i++)
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+     }
-             }
+     /* Set all step sizes to 1 */
-           }
+     gsl_vector_set_all (ss, 0.001);
-           fprintf(ficrest," %4.0f",age);
+     /* Starting point */
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     x = gsl_vector_alloc (NDIM);
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     if (x == NULL){
-             }
+       gsl_vector_free(ss);
-             epj[nlstate+1] +=epj[j];
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-           }
+     }
-           for(i=1, vepp=0.;i <=nlstate;i++)
+     /* Initialize method and iterate */
-             for(j=1;j <=nlstate;j++)
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-               vepp += vareij[i][j][(int)age];
+ /*     gsl_vector_set(x, 0, 0.0268); */
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+ /*     gsl_vector_set(x, 1, 0.083); */
-           for(j=1;j <=nlstate;j++){
+     gsl_vector_set(x, 0, p[1]);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     gsl_vector_set(x, 1, p[2]);
-           }
-           fprintf(ficrest,"\n");
+     minex_func.f = &gompertz_f;
-         }
+     minex_func.n = NDIM;
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     minex_func.params = (void *)&p; /* ??? */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_vector(epj,1,nlstate+1);
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-       }
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-     }
-     free_vector(weight,1,n);
+     printf("Iterations beginning .....\n\n");
-     free_imatrix(Tvard,1,15,1,2);
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-     free_imatrix(s,1,maxwav+1,1,n);
-     free_matrix(anint,1,maxwav,1,n);
+     iteri=0;
-     free_matrix(mint,1,maxwav,1,n);
+     while (rval == GSL_CONTINUE){
-     free_ivector(cod,1,n);
+       iteri++;
-     free_ivector(tab,1,NCOVMAX);
+       status = gsl_multimin_fminimizer_iterate(sfm);
-     fclose(ficreseij);
-     fclose(ficresstdeij);
+       if (status) printf("error: %s\n", gsl_strerror (status));
-     fclose(ficrescveij);
+       fflush(0);
-     fclose(ficresvij);
-     fclose(ficrest);
+       if (status)
-     fclose(ficpar);
+         break;
-     /*------- Variance of period (stable) prevalence------*/
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
-     strcpy(fileresvpl,"vpl");
-     strcat(fileresvpl,fileres);
+       if (rval == GSL_SUCCESS)
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+         printf ("converged to a local maximum at\n");
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
+       printf("%5d ", iteri);
-     }
+       for (it = 0; it < NDIM; it++){
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     }
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     gsl_vector_free(x); /* initial values */
-         fprintf(ficresvpl,"******\n");
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       p[it+1]=gsl_vector_get(sfm->x,it);
-         oldm=oldms;savm=savms;
+       fprintf(ficrespow," %.12lf", p[it]);
-         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);
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
-       }
+ #endif
-     }
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-     fclose(ficresvpl);
+ #endif
+     fclose(ficrespow);
-     /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     for(i=1; i <=NDIM; i++)
-   }  /* mle==-3 arrives here for freeing */
+       for(j=i+1;j<=NDIM;j++)
-   free_matrix(prlim,1,nlstate,1,nlstate);
+         matcov[i][j]=matcov[j][i];
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     printf("\nCovariance matrix\n ");
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     for(i=1; i <=NDIM; i++) {
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+       for(j=1;j<=NDIM;j++){
-     free_matrix(covar,0,NCOVMAX,1,n);
+         printf("%f ",matcov[i][j]);
-     free_matrix(matcov,1,npar,1,npar);
+       }
-     /*free_vector(delti,1,npar);*/
+       printf("\n ");
-     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);
+     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++)
-     free_ivector(ncodemax,1,8);
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-     free_ivector(Tvar,1,15);
-     free_ivector(Tprod,1,15);
+     lsurv=vector(1,AGESUP);
-     free_ivector(Tvaraff,1,15);
+     lpop=vector(1,AGESUP);
-     free_ivector(Tage,1,15);
+     tpop=vector(1,AGESUP);
-     free_ivector(Tcode,1,100);
+     lsurv[agegomp]=100000;
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     for (k=agegomp;k<=AGESUP;k++) {
-     free_imatrix(codtab,1,100,1,10);
+       agemortsup=k;
-   fflush(fichtm);
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-   fflush(ficgp);
+     }
+     for (k=agegomp;k<agemortsup;k++)
-   if((nberr >0) || (nbwarn>0)){
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-     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);
+     for (k=agegomp;k<agemortsup;k++){
-   }else{
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
-     printf("End of Imach\n");
+       sumlpop=sumlpop+lpop[k];
-     fprintf(ficlog,"End of Imach\n");
+     }
-   }
-   printf("See log file on %s\n",filelog);
+     tpop[agegomp]=sumlpop;
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     for (k=agegomp;k<(agemortsup-3);k++){
-   (void) gettimeofday(&end_time,&tzp);
+       /*  tpop[k+1]=2;*/
-   tm = *localtime(&end_time.tv_sec);
+       tpop[k+1]=tpop[k]-lpop[k];
-   tmg = *gmtime(&end_time.tv_sec);
+     }
-   strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     for (k=agegomp;k<(agemortsup-2);k++)
+       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
- /*   if(fileappend(fichtm,optionfilehtm)){ */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
-   fclose(fichtm);
+                      stepm, weightopt,\
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+                      model,imx,p,matcov,agemortsup);
-   fclose(fichtmcov);
-   fclose(ficgp);
+     free_vector(lsurv,1,AGESUP);
-   fclose(ficlog);
+     free_vector(lpop,1,AGESUP);
-   /*------ End -----------*/
+     free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
-    printf("Before Current directory %s!\n",pathcd);
+     free_vector(agecens,1,n);
-    if(chdir(pathcd) != 0)
+     free_ivector(dcwave,1,n);
-     printf("Can't move to directory %s!\n",path);
+     free_matrix(ximort,1,NDIM,1,NDIM);
-   if(getcwd(pathcd,MAXLINE) > 0)
+ #endif
-     printf("Current directory %s!\n",pathcd);
+   } /* Endof if mle==-3 */
-   /*strcat(plotcmd,CHARSEPARATOR);*/
-   sprintf(plotcmd,"gnuplot");
+   else{ /* For mle >=1 */
- #ifndef UNIX
+     globpr=0;/* debug */
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
- #endif
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-   if(!stat(plotcmd,&info)){
+     for (k=1; k<=npar;k++)
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       printf(" %d %8.5f",k,p[k]);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     printf("\n");
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     globpr=1; /* to print the contributions */
-     }else
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-       strcpy(pplotcmd,plotcmd);
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
- #ifdef UNIX
+     for (k=1; k<=npar;k++)
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+       printf(" %d %8.5f",k,p[k]);
-     if(!stat(plotcmd,&info)){
+     printf("\n");
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(mle>=1){ /* Could be 1 or 2 */
-     }else
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-       strcpy(pplotcmd,plotcmd);
+     }
- #endif
-   }else
+     /*--------- results files --------------*/
-     strcpy(pplotcmd,plotcmd);
+     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);
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   if((outcmd=system(plotcmd)) != 0){
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("\n Problem with gnuplot\n");
+     for(i=1,jk=1; i <=nlstate; i++){
-   }
+       for(k=1; k <=(nlstate+ndeath); k++){
-   printf(" Wait...");
+         if (k != i) {
-   while (z[0] != 'q') {
+           printf("%d%d ",i,k);
-     /* chdir(path); */
+           fprintf(ficlog,"%d%d ",i,k);
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+           fprintf(ficres,"%1d%1d ",i,k);
-     scanf("%s",z);
+           for(j=1; j <=ncovmodel; j++){
- /*     if (z[0] == 'c') system("./imach"); */
+             printf("%lf ",p[jk]);
-     if (z[0] == 'e') {
+             fprintf(ficlog,"%lf ",p[jk]);
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+             fprintf(ficres,"%lf ",p[jk]);
-       system(optionfilehtm);
+             jk++;
-     }
+           }
-     else if (z[0] == 'g') system(plotcmd);
+           printf("\n");
-     else if (z[0] == 'q') exit(0);
+           fprintf(ficlog,"\n");
-   }
+           fprintf(ficres,"\n");
-   end:
+         }
-   while (z[0] != 'q') {
+       }
-     printf("\nType  q for exiting: ");
+     }
-     scanf("%s",z);
+     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);
+   tm = *localtime(&end_time.tv_sec);
+   tmg = *gmtime(&end_time.tv_sec);
+   strcpy(strtend,asctime(&tm));
+   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  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");
+ #ifndef UNIX
+   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+ #endif
+   if(!stat(plotcmd,&info)){
+     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     if(!stat(getenv("GNUPLOTBIN"),&info)){
+       printf("Error 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("\n Problem with gnuplot command %s\n", plotcmd);
+     printf("\n Trying on same directory\n");
+     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+     if((outcmd=system(plotcmd)) != 0)
+       printf("\n Still a problem with gnuplot command %s\n", plotcmd);
+   }
+   printf(" Wait...");
+   while (z[0] != 'q') {
+     /* chdir(path); */
+     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     scanf("%s",z);
+ /*     if (z[0] == 'c') system("./imach"); */
+     if (z[0] == 'e') {
+ #ifdef OSX
+       sprintf(pplotcmd, "open %s", optionfilehtm);
+ #elsedef
+       sprintf(pplotcmd, "%s", optionfilehtm);
+ #enddef
+       printf("Starting browser with: %s",plotcmd);fflush(stdout);
+       system(plotcmd);
+     }
+     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
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	Added in v.1.152