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Diff for /imach/src/imach.c between versions 1.125 and 1.143

-version 1.125, 2006/04/04 15:20:31
+version 1.143, 2014/01/26 09:45:38
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
     for age prevalim()
    h Pij x
    variance of p varprob
    forecasting if prevfcast==1 prevforecast call prevalence()
    health expectancies
    Variance-covariance of DFLE
    prevalence()
     movingaverage()
    varevsij()
    if popbased==1 varevsij(,popbased)
    total life expectancies
    Variance of period (stable) prevalence
   end
  */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
  #include <unistd.h>
  #include <limits.h>
  #include <sys/types.h>
  #include <sys/stat.h>
  #include <errno.h>
  extern int errno;
- /* #include <sys/time.h> */
+ #ifdef LINUX
  #include <time.h>
  #include "timeval.h"
+ #else
- /* #include <libintl.h> */
+ #include <sys/time.h>
- /* #define _(String) gettext (String) */
+ #endif
- #define MAXLINE 256
+ #ifdef GSL
+ #include <gsl/gsl_errno.h>
- #define GNUPLOTPROGRAM "gnuplot"
+ #include <gsl/gsl_multimin.h>
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ #endif
- #define FILENAMELENGTH 132
+ /* #include <libintl.h> */
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
+ /* #define _(String) gettext (String) */
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define NINTERVMAX 8
+ #define FILENAMELENGTH 132
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #define MAXPARM 128 /* Maximum number of parameters for the optimization */
- #define AGESUP 130
+ #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
- #define AGEBASE 40
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #define NINTERVMAX 8
- #ifdef UNIX
+ #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define DIRSEPARATOR '/'
+ #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
- #define CHARSEPARATOR "/"
+ #define NCOVMAX 20 /* Maximum number of covariates */
- #define ODIRSEPARATOR '\\'
+ #define MAXN 20000
- #else
+ #define YEARM 12. /* Number of months per year */
- #define DIRSEPARATOR '\\'
+ #define AGESUP 130
- #define CHARSEPARATOR "\\"
+ #define AGEBASE 40
- #define ODIRSEPARATOR '/'
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #endif
+ #ifdef UNIX
+ #define DIRSEPARATOR '/'
- /* $Id$ */
+ #define CHARSEPARATOR "/"
- /* $State$ */
+ #define ODIRSEPARATOR '\\'
+ #else
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #define DIRSEPARATOR '\\'
- char fullversion[]="$Revision$ $Date$";
+ #define CHARSEPARATOR "\\"
- char strstart[80];
+ #define ODIRSEPARATOR '/'
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ #endif
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ /* $Id$ */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ /* $State$ */
- int npar=NPARMAX;
- int nlstate=2; /* Number of live states */
+ char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
- int ndeath=1; /* Number of dead states */
+ char fullversion[]="$Revision$ $Date$";
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ char strstart[80];
- int popbased=0;
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int *wav; /* Number of waves for this individuual 0 is possible */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- int maxwav; /* Maxim number of waves */
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ int npar=NPARMAX;
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ int nlstate=2; /* Number of live states */
- int gipmx, gsw; /* Global variables on the number of contributions
+ int ndeath=1; /* Number of dead states */
-                    to the likelihood and the sum of weights (done by funcone)*/
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- int mle, weightopt;
+ int popbased=0;
- 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 */
+ int *wav; /* Number of waves for this individuual 0 is possible */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ int maxwav=0; /* Maxim number of waves */
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- double jmean; /* Mean space between 2 waves */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+                    to the likelihood and the sum of weights (done by funcone)*/
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ int mle=1, weightopt=0;
- FILE *ficlog, *ficrespow;
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- int globpr; /* Global variable for printing or not */
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- double fretone; /* Only one call to likelihood */
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- long ipmx; /* Number of contributions */
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- double sw; /* Sum of weights */
+ double jmean=1; /* Mean space between 2 waves */
- char filerespow[FILENAMELENGTH];
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- FILE *ficresilk;
+ /*FILE *fic ; */ /* Used in readdata only */
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- FILE *ficresprobmorprev;
+ FILE *ficlog, *ficrespow;
- FILE *fichtm, *fichtmcov; /* Html File */
+ int globpr=0; /* Global variable for printing or not */
- FILE *ficreseij;
+ double fretone; /* Only one call to likelihood */
- char filerese[FILENAMELENGTH];
+ long ipmx=0; /* Number of contributions */
- FILE *ficresstdeij;
+ double sw; /* Sum of weights */
- char fileresstde[FILENAMELENGTH];
+ char filerespow[FILENAMELENGTH];
- FILE *ficrescveij;
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- char filerescve[FILENAMELENGTH];
+ FILE *ficresilk;
- FILE  *ficresvij;
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- char fileresv[FILENAMELENGTH];
+ FILE *ficresprobmorprev;
- FILE  *ficresvpl;
+ FILE *fichtm, *fichtmcov; /* Html File */
- char fileresvpl[FILENAMELENGTH];
+ FILE *ficreseij;
- char title[MAXLINE];
+ char filerese[FILENAMELENGTH];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ FILE *ficresstdeij;
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ char fileresstde[FILENAMELENGTH];
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ FILE *ficrescveij;
- char command[FILENAMELENGTH];
+ char filerescve[FILENAMELENGTH];
- int  outcmd=0;
+ FILE  *ficresvij;
+ char fileresv[FILENAMELENGTH];
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ FILE  *ficresvpl;
+ char fileresvpl[FILENAMELENGTH];
- char filelog[FILENAMELENGTH]; /* Log file */
+ char title[MAXLINE];
- char filerest[FILENAMELENGTH];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
- char fileregp[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- char popfile[FILENAMELENGTH];
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ int  outcmd=0;
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- struct timezone tzp;
- extern int gettimeofday();
+ char filelog[FILENAMELENGTH]; /* Log file */
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
+ char filerest[FILENAMELENGTH];
- long time_value;
+ char fileregp[FILENAMELENGTH];
- extern long time();
+ char popfile[FILENAMELENGTH];
- char strcurr[80], strfor[80];
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- char *endptr;
- long lval;
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
- double dval;
+ struct timezone tzp;
+ extern int gettimeofday();
- #define NR_END 1
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
- #define FREE_ARG char*
+ long time_value;
- #define FTOL 1.0e-10
+ extern long time();
+ char strcurr[80], strfor[80];
- #define NRANSI
- #define ITMAX 200
+ char *endptr;
+ long lval;
- #define TOL 2.0e-4
+ double dval;
- #define CGOLD 0.3819660
+ #define NR_END 1
- #define ZEPS 1.0e-10
+ #define FREE_ARG char*
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ #define FTOL 1.0e-10
- #define GOLD 1.618034
+ #define NRANSI
- #define GLIMIT 100.0
+ #define ITMAX 200
- #define TINY 1.0e-20
+ #define TOL 2.0e-4
- static double maxarg1,maxarg2;
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #define CGOLD 0.3819660
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ #define ZEPS 1.0e-10
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
- #define rint(a) floor(a+0.5)
+ #define GOLD 1.618034
+ #define GLIMIT 100.0
- static double sqrarg;
+ #define TINY 1.0e-20
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+ static double maxarg1,maxarg2;
- int agegomp= AGEGOMP;
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- int imx;
- int stepm=1;
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
- /* Stepm, step in month: minimum step interpolation*/
+ #define rint(a) floor(a+0.5)
- int estepm;
+ static double sqrarg;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- int m,nb;
+ int agegomp= AGEGOMP;
- long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ int imx;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ int stepm=1;
- double **pmmij, ***probs;
+ /* Stepm, step in month: minimum step interpolation*/
- double *ageexmed,*agecens;
- double dateintmean=0;
+ int estepm;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- double *weight;
- int **s; /* Status */
+ int m,nb;
- double *agedc, **covar, idx;
+ long *num;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- double *lsurv, *lpop, *tpop;
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ double **pmmij, ***probs;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ double *ageexmed,*agecens;
- double ftolhess; /* Tolerance for computing hessian */
+ double dateintmean=0;
- /**************** split *************************/
+ double *weight;
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ int **s; /* Status */
- {
+ double *agedc;
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ double  **covar; /**< covar[i,j], value of jth covariate for individual i,
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+                   * covar=matrix(0,NCOVMAX,1,n);
-   */
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
-   char  *ss;                            /* pointer */
+ double  idx;
-   int   l1, l2;                         /* length counters */
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
-   l1 = strlen(path );                   /* length of path */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ double *lsurv, *lpop, *tpop;
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+ double ftolhess; /**< Tolerance for computing hessian */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+ /**************** split *************************/
-     /* get current working directory */
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
-     /*    extern  char* getcwd ( char *buf , int len);*/
+ {
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-       return( GLOCK_ERROR_GETCWD );
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-     }
+   */
-     /* got dirc from getcwd*/
+   char  *ss;                            /* pointer */
-     printf(" DIRC = %s \n",dirc);
+   int   l1, l2;                         /* length counters */
-   } else {                              /* strip direcotry from path */
-     ss++;                               /* after this, the filename */
+   l1 = strlen(path );                   /* length of path */
-     l2 = strlen( ss );                  /* length of filename */
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-     strcpy( name, ss );         /* save file name */
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     strcpy( name, path );               /* we got the fullname name because no directory */
-     dirc[l1-l2] = 0;                    /* add zero */
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-     printf(" DIRC2 = %s \n",dirc);
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-   }
+     /* get current working directory */
-   /* We add a separator at the end of dirc if not exists */
+     /*    extern  char* getcwd ( char *buf , int len);*/
-   l1 = strlen( dirc );                  /* length of directory */
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-   if( dirc[l1-1] != DIRSEPARATOR ){
+       return( GLOCK_ERROR_GETCWD );
-     dirc[l1] =  DIRSEPARATOR;
+     }
-     dirc[l1+1] = 0;
+     /* got dirc from getcwd*/
-     printf(" DIRC3 = %s \n",dirc);
+     printf(" DIRC = %s \n",dirc);
-   }
+   } else {                              /* strip direcotry from path */
-   ss = strrchr( name, '.' );            /* find last / */
+     ss++;                               /* after this, the filename */
-   if (ss >0){
+     l2 = strlen( ss );                  /* length of filename */
-     ss++;
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-     strcpy(ext,ss);                     /* save extension */
+     strcpy( name, ss );         /* save file name */
-     l1= strlen( name);
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     l2= strlen(ss)+1;
+     dirc[l1-l2] = 0;                    /* add zero */
-     strncpy( finame, name, l1-l2);
+     printf(" DIRC2 = %s \n",dirc);
-     finame[l1-l2]= 0;
+   }
-   }
+   /* We add a separator at the end of dirc if not exists */
+   l1 = strlen( dirc );                  /* length of directory */
-   return( 0 );                          /* we're done */
+   if( dirc[l1-1] != DIRSEPARATOR ){
- }
+     dirc[l1] =  DIRSEPARATOR;
+     dirc[l1+1] = 0;
+     printf(" DIRC3 = %s \n",dirc);
- /******************************************/
+   }
+   ss = strrchr( name, '.' );            /* find last / */
- void replace_back_to_slash(char *s, char*t)
+   if (ss >0){
- {
+     ss++;
-   int i;
+     strcpy(ext,ss);                     /* save extension */
-   int lg=0;
+     l1= strlen( name);
-   i=0;
+     l2= strlen(ss)+1;
-   lg=strlen(t);
+     strncpy( finame, name, l1-l2);
-   for(i=0; i<= lg; i++) {
+     finame[l1-l2]= 0;
-     (s[i] = t[i]);
+   }
-     if (t[i]== '\\') s[i]='/';
-   }
+   return( 0 );                          /* we're done */
  }
- int nbocc(char *s, char occ)
- {
+ /******************************************/
-   int i,j=0;
-   int lg=20;
+ void replace_back_to_slash(char *s, char*t)
-   i=0;
+ {
-   lg=strlen(s);
+   int i;
-   for(i=0; i<= lg; i++) {
+   int lg=0;
-   if  (s[i] == occ ) j++;
+   i=0;
-   }
+   lg=strlen(t);
-   return j;
+   for(i=0; i<= lg; i++) {
- }
+     (s[i] = t[i]);
+     if (t[i]== '\\') s[i]='/';
- void cutv(char *u,char *v, char*t, char occ)
+   }
- {
+ }
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+ char *trimbb(char *out, char *in)
-      gives u="abcedf" and v="ghi2j" */
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   int i,lg,j,p=0;
+   char *s;
-   i=0;
+   s=out;
-   for(j=0; j<=strlen(t)-1; j++) {
+   while (*in != '\0'){
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
-   }
+       in++;
+     }
-   lg=strlen(t);
+     *out++ = *in++;
-   for(j=0; j<p; j++) {
+   }
-     (u[j] = t[j]);
+   *out='\0';
-   }
+   return s;
-      u[p]='\0';
+ }
-    for(j=0; j<= lg; j++) {
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ {
-   }
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
- }
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
+      gives blocc="abcdef2ghi" and alocc="j".
- /********************** nrerror ********************/
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
+   */
- void nrerror(char error_text[])
+   char *s, *t;
- {
+   t=in;s=in;
-   fprintf(stderr,"ERREUR ...\n");
+   while (*in != '\0'){
-   fprintf(stderr,"%s\n",error_text);
+     while( *in == occ){
-   exit(EXIT_FAILURE);
+       *blocc++ = *in++;
- }
+       s=in;
- /*********************** vector *******************/
+     }
- double *vector(int nl, int nh)
+     *blocc++ = *in++;
- {
+   }
-   double *v;
+   if (s == t) /* occ not found */
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+     *(blocc-(in-s))='\0';
-   if (!v) nrerror("allocation failure in vector");
+   else
-   return v-nl+NR_END;
+     *(blocc-(in-s)-1)='\0';
- }
+   in=s;
+   while ( *in != '\0'){
- /************************ free vector ******************/
+     *alocc++ = *in++;
- void free_vector(double*v, int nl, int nh)
+   }
- {
-   free((FREE_ARG)(v+nl-NR_END));
+   *alocc='\0';
- }
+   return s;
+ }
- /************************ivector *******************************/
- int *ivector(long nl,long nh)
+ int nbocc(char *s, char occ)
  {
-   int *v;
+   int i,j=0;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+   int lg=20;
-   if (!v) nrerror("allocation failure in ivector");
+   i=0;
-   return v-nl+NR_END;
+   lg=strlen(s);
- }
+   for(i=0; i<= lg; i++) {
+   if  (s[i] == occ ) j++;
- /******************free ivector **************************/
+   }
- void free_ivector(int *v, long nl, long nh)
+   return j;
- {
+ }
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ /* void cutv(char *u,char *v, char*t, char occ) */
+ /* { */
- /************************lvector *******************************/
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- long *lvector(long nl,long nh)
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
- {
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
-   long *v;
+ /*   int i,lg,j,p=0; */
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ /*   i=0; */
-   if (!v) nrerror("allocation failure in ivector");
+ /*   lg=strlen(t); */
-   return v-nl+NR_END;
+ /*   for(j=0; j<=lg-1; j++) { */
- }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
- /******************free lvector **************************/
- void free_lvector(long *v, long nl, long nh)
+ /*   for(j=0; j<p; j++) { */
- {
+ /*     (u[j] = t[j]); */
-   free((FREE_ARG)(v+nl-NR_END));
+ /*   } */
- }
+ /*      u[p]='\0'; */
- /******************* imatrix *******************************/
+ /*    for(j=0; j<= lg; j++) { */
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+ /*   } */
- {
+ /* } */
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   int **m;
+ /********************** nrerror ********************/
-   /* allocate pointers to rows */
+ void nrerror(char error_text[])
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+ {
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   fprintf(stderr,"ERREUR ...\n");
-   m += NR_END;
+   fprintf(stderr,"%s\n",error_text);
-   m -= nrl;
+   exit(EXIT_FAILURE);
+ }
+ /*********************** vector *******************/
-   /* allocate rows and set pointers to them */
+ double *vector(int nl, int nh)
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ {
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   double *v;
-   m[nrl] += NR_END;
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   m[nrl] -= ncl;
+   if (!v) nrerror("allocation failure in vector");
+   return v-nl+NR_END;
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ }
-   /* return pointer to array of pointers to rows */
+ /************************ free vector ******************/
-   return m;
+ void free_vector(double*v, int nl, int nh)
- }
+ {
+   free((FREE_ARG)(v+nl-NR_END));
- /****************** free_imatrix *************************/
+ }
- void free_imatrix(m,nrl,nrh,ncl,nch)
-       int **m;
+ /************************ivector *******************************/
-       long nch,ncl,nrh,nrl;
+ int *ivector(long nl,long nh)
-      /* free an int matrix allocated by imatrix() */
+ {
- {
+   int *v;
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
-   free((FREE_ARG) (m+nrl-NR_END));
+   if (!v) nrerror("allocation failure in ivector");
- }
+   return v-nl+NR_END;
+ }
- /******************* matrix *******************************/
- double **matrix(long nrl, long nrh, long ncl, long nch)
+ /******************free ivector **************************/
- {
+ void free_ivector(int *v, long nl, long nh)
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ {
-   double **m;
+   free((FREE_ARG)(v+nl-NR_END));
+ }
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /************************lvector *******************************/
-   m += NR_END;
+ long *lvector(long nl,long nh)
-   m -= nrl;
+ {
+   long *v;
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   if (!v) nrerror("allocation failure in ivector");
-   m[nrl] += NR_END;
+   return v-nl+NR_END;
-   m[nrl] -= ncl;
+ }
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ /******************free lvector **************************/
-   return m;
+ void free_lvector(long *v, long nl, long nh)
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ {
-    */
+   free((FREE_ARG)(v+nl-NR_END));
  }
- /*************************free matrix ************************/
+ /******************* imatrix *******************************/
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
- {
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ {
-   free((FREE_ARG)(m+nrl-NR_END));
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
- }
+   int **m;
- /******************* ma3x *******************************/
+   /* allocate pointers to rows */
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- {
+   if (!m) nrerror("allocation failure 1 in matrix()");
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   m += NR_END;
-   double ***m;
+   m -= nrl;
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   /* allocate rows and set pointers to them */
-   m += NR_END;
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
-   m -= nrl;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+   m[nrl] += NR_END;
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+   m[nrl] -= ncl;
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   m[nrl] -= ncl;
+   /* return pointer to array of pointers to rows */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   return m;
+ }
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ /****************** free_imatrix *************************/
-   m[nrl][ncl] += NR_END;
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   m[nrl][ncl] -= nll;
+       int **m;
-   for (j=ncl+1; j<=nch; j++)
+       long nch,ncl,nrh,nrl;
-     m[nrl][j]=m[nrl][j-1]+nlay;
+      /* free an int matrix allocated by imatrix() */
+ {
-   for (i=nrl+1; i<=nrh; i++) {
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   free((FREE_ARG) (m+nrl-NR_END));
-     for (j=ncl+1; j<=nch; j++)
+ }
-       m[i][j]=m[i][j-1]+nlay;
-   }
+ /******************* matrix *******************************/
-   return m;
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+ {
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
-   */
+   double **m;
- }
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- /*************************free ma3x ************************/
+   if (!m) nrerror("allocation failure 1 in matrix()");
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   m += NR_END;
- {
+   m -= nrl;
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   free((FREE_ARG)(m+nrl-NR_END));
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- }
+   m[nrl] += NR_END;
+   m[nrl] -= ncl;
- /*************** function subdirf ***********/
- char *subdirf(char fileres[])
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- {
+   return m;
-   /* Caution optionfilefiname is hidden */
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
-   strcpy(tmpout,optionfilefiname);
+    */
-   strcat(tmpout,"/"); /* Add to the right */
+ }
-   strcat(tmpout,fileres);
-   return tmpout;
+ /*************************free matrix ************************/
- }
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ {
- /*************** function subdirf2 ***********/
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- char *subdirf2(char fileres[], char *preop)
+   free((FREE_ARG)(m+nrl-NR_END));
- {
+ }
-   /* Caution optionfilefiname is hidden */
+ /******************* ma3x *******************************/
-   strcpy(tmpout,optionfilefiname);
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-   strcat(tmpout,"/");
+ {
-   strcat(tmpout,preop);
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-   strcat(tmpout,fileres);
+   double ***m;
-   return tmpout;
- }
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   if (!m) nrerror("allocation failure 1 in matrix()");
- /*************** function subdirf3 ***********/
+   m += NR_END;
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   m -= nrl;
- {
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   /* Caution optionfilefiname is hidden */
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   strcpy(tmpout,optionfilefiname);
+   m[nrl] += NR_END;
-   strcat(tmpout,"/");
+   m[nrl] -= ncl;
-   strcat(tmpout,preop);
-   strcat(tmpout,preop2);
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   strcat(tmpout,fileres);
-   return tmpout;
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
- }
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+   m[nrl][ncl] += NR_END;
- /***************** f1dim *************************/
+   m[nrl][ncl] -= nll;
- extern int ncom;
+   for (j=ncl+1; j<=nch; j++)
- extern double *pcom,*xicom;
+     m[nrl][j]=m[nrl][j-1]+nlay;
- extern double (*nrfunc)(double []);
+   for (i=nrl+1; i<=nrh; i++) {
- double f1dim(double x)
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- {
+     for (j=ncl+1; j<=nch; j++)
-   int j;
+       m[i][j]=m[i][j-1]+nlay;
-   double f;
+   }
-   double *xt;
+   return m;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
-   xt=vector(1,ncom);
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   */
-   f=(*nrfunc)(xt);
+ }
-   free_vector(xt,1,ncom);
-   return f;
+ /*************************free ma3x ************************/
- }
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+ {
- /*****************brent *************************/
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- {
+   free((FREE_ARG)(m+nrl-NR_END));
-   int iter;
+ }
-   double a,b,d,etemp;
-   double fu,fv,fw,fx;
+ /*************** function subdirf ***********/
-   double ftemp;
+ char *subdirf(char fileres[])
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ {
-   double e=0.0;
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
-   a=(ax < cx ? ax : cx);
+   strcat(tmpout,"/"); /* Add to the right */
-   b=(ax > cx ? ax : cx);
+   strcat(tmpout,fileres);
-   x=w=v=bx;
+   return tmpout;
-   fw=fv=fx=(*f)(x);
+ }
-   for (iter=1;iter<=ITMAX;iter++) {
-     xm=0.5*(a+b);
+ /*************** function subdirf2 ***********/
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ char *subdirf2(char fileres[], char *preop)
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ {
-     printf(".");fflush(stdout);
-     fprintf(ficlog,".");fflush(ficlog);
+   /* Caution optionfilefiname is hidden */
- #ifdef DEBUG
+   strcpy(tmpout,optionfilefiname);
-     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);
+   strcat(tmpout,"/");
-     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);
+   strcat(tmpout,preop);
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   strcat(tmpout,fileres);
- #endif
+   return tmpout;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ }
-       *xmin=x;
-       return fx;
+ /*************** function subdirf3 ***********/
-     }
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-     ftemp=fu;
+ {
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+   /* Caution optionfilefiname is hidden */
-       q=(x-v)*(fx-fw);
+   strcpy(tmpout,optionfilefiname);
-       p=(x-v)*q-(x-w)*r;
+   strcat(tmpout,"/");
-       q=2.0*(q-r);
+   strcat(tmpout,preop);
-       if (q > 0.0) p = -p;
+   strcat(tmpout,preop2);
-       q=fabs(q);
+   strcat(tmpout,fileres);
-       etemp=e;
+   return tmpout;
-       e=d;
+ }
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ /***************** f1dim *************************/
-       else {
+ extern int ncom;
-         d=p/q;
+ extern double *pcom,*xicom;
-         u=x+d;
+ extern double (*nrfunc)(double []);
-         if (u-a < tol2 || b-u < tol2)
-           d=SIGN(tol1,xm-x);
+ double f1dim(double x)
-       }
+ {
-     } else {
+   int j;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   double f;
-     }
+   double *xt;
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-     fu=(*f)(u);
+   xt=vector(1,ncom);
-     if (fu <= fx) {
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-       if (u >= x) a=x; else b=x;
+   f=(*nrfunc)(xt);
-       SHFT(v,w,x,u)
+   free_vector(xt,1,ncom);
-         SHFT(fv,fw,fx,fu)
+   return f;
-         } else {
+ }
-           if (u < x) a=u; else b=u;
-           if (fu <= fw || w == x) {
+ /*****************brent *************************/
-             v=w;
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-             w=u;
+ {
-             fv=fw;
+   int iter;
-             fw=fu;
+   double a,b,d,etemp;
-           } else if (fu <= fv || v == x || v == w) {
+   double fu,fv,fw,fx;
-             v=u;
+   double ftemp;
-             fv=fu;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-           }
+   double e=0.0;
-         }
-   }
+   a=(ax < cx ? ax : cx);
-   nrerror("Too many iterations in brent");
+   b=(ax > cx ? ax : cx);
-   *xmin=x;
+   x=w=v=bx;
-   return fx;
+   fw=fv=fx=(*f)(x);
- }
+   for (iter=1;iter<=ITMAX;iter++) {
+     xm=0.5*(a+b);
- /****************** mnbrak ***********************/
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+     printf(".");fflush(stdout);
-             double (*func)(double))
+     fprintf(ficlog,".");fflush(ficlog);
- {
+ #ifdef DEBUG
-   double ulim,u,r,q, dum;
+     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-   double fu;
+     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-   *fa=(*func)(*ax);
+ #endif
-   *fb=(*func)(*bx);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-   if (*fb > *fa) {
+       *xmin=x;
-     SHFT(dum,*ax,*bx,dum)
+       return fx;
-       SHFT(dum,*fb,*fa,dum)
+     }
-       }
+     ftemp=fu;
-   *cx=(*bx)+GOLD*(*bx-*ax);
+     if (fabs(e) > tol1) {
-   *fc=(*func)(*cx);
+       r=(x-w)*(fx-fv);
-   while (*fb > *fc) {
+       q=(x-v)*(fx-fw);
-     r=(*bx-*ax)*(*fb-*fc);
+       p=(x-v)*q-(x-w)*r;
-     q=(*bx-*cx)*(*fb-*fa);
+       q=2.0*(q-r);
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+       if (q > 0.0) p = -p;
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+       q=fabs(q);
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+       etemp=e;
-     if ((*bx-u)*(u-*cx) > 0.0) {
+       e=d;
-       fu=(*func)(u);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-       fu=(*func)(u);
+       else {
-       if (fu < *fc) {
+         d=p/q;
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+         u=x+d;
-           SHFT(*fb,*fc,fu,(*func)(u))
+         if (u-a < tol2 || b-u < tol2)
-           }
+           d=SIGN(tol1,xm-x);
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+       }
-       u=ulim;
+     } else {
-       fu=(*func)(u);
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     } else {
+     }
-       u=(*cx)+GOLD*(*cx-*bx);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-       fu=(*func)(u);
+     fu=(*f)(u);
-     }
+     if (fu <= fx) {
-     SHFT(*ax,*bx,*cx,u)
+       if (u >= x) a=x; else b=x;
-       SHFT(*fa,*fb,*fc,fu)
+       SHFT(v,w,x,u)
-       }
+         SHFT(fv,fw,fx,fu)
- }
+         } else {
+           if (u < x) a=u; else b=u;
- /*************** linmin ************************/
+           if (fu <= fw || w == x) {
+             v=w;
- int ncom;
+             w=u;
- double *pcom,*xicom;
+             fv=fw;
- double (*nrfunc)(double []);
+             fw=fu;
+           } else if (fu <= fv || v == x || v == w) {
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+             v=u;
- {
+             fv=fu;
-   double brent(double ax, double bx, double cx,
+           }
-                double (*f)(double), double tol, double *xmin);
+         }
-   double f1dim(double x);
+   }
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+   nrerror("Too many iterations in brent");
-               double *fc, double (*func)(double));
+   *xmin=x;
-   int j;
+   return fx;
-   double xx,xmin,bx,ax;
+ }
-   double fx,fb,fa;
+ /****************** mnbrak ***********************/
-   ncom=n;
-   pcom=vector(1,n);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-   xicom=vector(1,n);
+             double (*func)(double))
-   nrfunc=func;
+ {
-   for (j=1;j<=n;j++) {
+   double ulim,u,r,q, dum;
-     pcom[j]=p[j];
+   double fu;
-     xicom[j]=xi[j];
-   }
+   *fa=(*func)(*ax);
-   ax=0.0;
+   *fb=(*func)(*bx);
-   xx=1.0;
+   if (*fb > *fa) {
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+     SHFT(dum,*ax,*bx,dum)
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+       SHFT(dum,*fb,*fa,dum)
- #ifdef DEBUG
+       }
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   *cx=(*bx)+GOLD*(*bx-*ax);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   *fc=(*func)(*cx);
- #endif
+   while (*fb > *fc) {
-   for (j=1;j<=n;j++) {
+     r=(*bx-*ax)*(*fb-*fc);
-     xi[j] *= xmin;
+     q=(*bx-*cx)*(*fb-*fa);
-     p[j] += xi[j];
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-   }
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-   free_vector(xicom,1,n);
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
-   free_vector(pcom,1,n);
+     if ((*bx-u)*(u-*cx) > 0.0) {
- }
+       fu=(*func)(u);
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
- char *asc_diff_time(long time_sec, char ascdiff[])
+       fu=(*func)(u);
- {
+       if (fu < *fc) {
-   long sec_left, days, hours, minutes;
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-   days = (time_sec) / (60*60*24);
+           SHFT(*fb,*fc,fu,(*func)(u))
-   sec_left = (time_sec) % (60*60*24);
+           }
-   hours = (sec_left) / (60*60) ;
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-   sec_left = (sec_left) %(60*60);
+       u=ulim;
-   minutes = (sec_left) /60;
+       fu=(*func)(u);
-   sec_left = (sec_left) % (60);
+     } else {
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+       u=(*cx)+GOLD*(*cx-*bx);
-   return ascdiff;
+       fu=(*func)(u);
- }
+     }
+     SHFT(*ax,*bx,*cx,u)
- /*************** powell ************************/
+       SHFT(*fa,*fb,*fc,fu)
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+       }
-             double (*func)(double []))
+ }
- {
-   void linmin(double p[], double xi[], int n, double *fret,
+ /*************** linmin ************************/
-               double (*func)(double []));
-   int i,ibig,j;
+ int ncom;
-   double del,t,*pt,*ptt,*xit;
+ double *pcom,*xicom;
-   double fp,fptt;
+ double (*nrfunc)(double []);
-   double *xits;
-   int niterf, itmp;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+ {
-   pt=vector(1,n);
+   double brent(double ax, double bx, double cx,
-   ptt=vector(1,n);
+                double (*f)(double), double tol, double *xmin);
-   xit=vector(1,n);
+   double f1dim(double x);
-   xits=vector(1,n);
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-   *fret=(*func)(p);
+               double *fc, double (*func)(double));
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   int j;
-   for (*iter=1;;++(*iter)) {
+   double xx,xmin,bx,ax;
-     fp=(*fret);
+   double fx,fb,fa;
-     ibig=0;
-     del=0.0;
+   ncom=n;
-     last_time=curr_time;
+   pcom=vector(1,n);
-     (void) gettimeofday(&curr_time,&tzp);
+   xicom=vector(1,n);
-     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);
+   nrfunc=func;
-     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); */
+     pcom[j]=p[j];
-    for (i=1;i<=n;i++) {
+     xicom[j]=xi[j];
-       printf(" %d %.12f",i, p[i]);
+   }
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   ax=0.0;
-       fprintf(ficrespow," %.12lf", p[i]);
+   xx=1.0;
-     }
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-     printf("\n");
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-     fprintf(ficlog,"\n");
+ #ifdef DEBUG
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-     if(*iter <=3){
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-       tm = *localtime(&curr_time.tv_sec);
+ #endif
-       strcpy(strcurr,asctime(&tm));
+   for (j=1;j<=n;j++) {
- /*       asctime_r(&tm,strcurr); */
+     xi[j] *= xmin;
-       forecast_time=curr_time;
+     p[j] += xi[j];
-       itmp = strlen(strcurr);
+   }
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   free_vector(xicom,1,n);
-         strcurr[itmp-1]='\0';
+   free_vector(pcom,1,n);
-       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);
-       for(niterf=10;niterf<=30;niterf+=10){
+ char *asc_diff_time(long time_sec, char ascdiff[])
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ {
-         tmf = *localtime(&forecast_time.tv_sec);
+   long sec_left, days, hours, minutes;
- /*      asctime_r(&tmf,strfor); */
+   days = (time_sec) / (60*60*24);
-         strcpy(strfor,asctime(&tmf));
+   sec_left = (time_sec) % (60*60*24);
-         itmp = strlen(strfor);
+   hours = (sec_left) / (60*60) ;
-         if(strfor[itmp-1]=='\n')
+   sec_left = (sec_left) %(60*60);
-         strfor[itmp-1]='\0';
+   minutes = (sec_left) /60;
-         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);
+   sec_left = (sec_left) % (60);
-         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);
+   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
-       }
+   return ascdiff;
-     }
+ }
-     for (i=1;i<=n;i++) {
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+ /*************** powell ************************/
-       fptt=(*fret);
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
- #ifdef DEBUG
+             double (*func)(double []))
-       printf("fret=%lf \n",*fret);
+ {
-       fprintf(ficlog,"fret=%lf \n",*fret);
+   void linmin(double p[], double xi[], int n, double *fret,
- #endif
+               double (*func)(double []));
-       printf("%d",i);fflush(stdout);
+   int i,ibig,j;
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+   double del,t,*pt,*ptt,*xit;
-       linmin(p,xit,n,fret,func);
+   double fp,fptt;
-       if (fabs(fptt-(*fret)) > del) {
+   double *xits;
-         del=fabs(fptt-(*fret));
+   int niterf, itmp;
-         ibig=i;
-       }
+   pt=vector(1,n);
- #ifdef DEBUG
+   ptt=vector(1,n);
-       printf("%d %.12e",i,(*fret));
+   xit=vector(1,n);
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+   xits=vector(1,n);
-       for (j=1;j<=n;j++) {
+   *fret=(*func)(p);
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+   for (j=1;j<=n;j++) pt[j]=p[j];
-         printf(" x(%d)=%.12e",j,xit[j]);
+   for (*iter=1;;++(*iter)) {
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+     fp=(*fret);
-       }
+     ibig=0;
-       for(j=1;j<=n;j++) {
+     del=0.0;
-         printf(" p=%.12e",p[j]);
+     last_time=curr_time;
-         fprintf(ficlog," p=%.12e",p[j]);
+     (void) gettimeofday(&curr_time,&tzp);
-       }
+     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);
-       printf("\n");
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
-       fprintf(ficlog,"\n");
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
- #endif
+    for (i=1;i<=n;i++) {
-     }
+       printf(" %d %.12f",i, p[i]);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+       fprintf(ficlog," %d %.12lf",i, p[i]);
- #ifdef DEBUG
+       fprintf(ficrespow," %.12lf", p[i]);
-       int k[2],l;
+     }
-       k[0]=1;
+     printf("\n");
-       k[1]=-1;
+     fprintf(ficlog,"\n");
-       printf("Max: %.12e",(*func)(p));
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+     if(*iter <=3){
-       for (j=1;j<=n;j++) {
+       tm = *localtime(&curr_time.tv_sec);
-         printf(" %.12e",p[j]);
+       strcpy(strcurr,asctime(&tm));
-         fprintf(ficlog," %.12e",p[j]);
+ /*       asctime_r(&tm,strcurr); */
-       }
+       forecast_time=curr_time;
-       printf("\n");
+       itmp = strlen(strcurr);
-       fprintf(ficlog,"\n");
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       for(l=0;l<=1;l++) {
+         strcurr[itmp-1]='\0';
-         for (j=1;j<=n;j++) {
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       for(niterf=10;niterf<=30;niterf+=10){
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
-         }
+         tmf = *localtime(&forecast_time.tv_sec);
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ /*      asctime_r(&tmf,strfor); */
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+         strcpy(strfor,asctime(&tmf));
-       }
+         itmp = strlen(strfor);
- #endif
+         if(strfor[itmp-1]=='\n')
+         strfor[itmp-1]='\0';
+         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);
-       free_vector(xit,1,n);
+         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);
-       free_vector(xits,1,n);
+       }
-       free_vector(ptt,1,n);
+     }
-       free_vector(pt,1,n);
+     for (i=1;i<=n;i++) {
-       return;
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-     }
+       fptt=(*fret);
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ #ifdef DEBUG
-     for (j=1;j<=n;j++) {
+       printf("fret=%lf \n",*fret);
-       ptt[j]=2.0*p[j]-pt[j];
+       fprintf(ficlog,"fret=%lf \n",*fret);
-       xit[j]=p[j]-pt[j];
+ #endif
-       pt[j]=p[j];
+       printf("%d",i);fflush(stdout);
-     }
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     fptt=(*func)(ptt);
+       linmin(p,xit,n,fret,func);
-     if (fptt < fp) {
+       if (fabs(fptt-(*fret)) > del) {
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+         del=fabs(fptt-(*fret));
-       if (t < 0.0) {
+         ibig=i;
-         linmin(p,xit,n,fret,func);
+       }
-         for (j=1;j<=n;j++) {
+ #ifdef DEBUG
-           xi[j][ibig]=xi[j][n];
+       printf("%d %.12e",i,(*fret));
-           xi[j][n]=xit[j];
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-         }
+       for (j=1;j<=n;j++) {
- #ifdef DEBUG
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-         for(j=1;j<=n;j++){
+       }
-           printf(" %.12e",xit[j]);
+       for(j=1;j<=n;j++) {
-           fprintf(ficlog," %.12e",xit[j]);
+         printf(" p=%.12e",p[j]);
-         }
+         fprintf(ficlog," p=%.12e",p[j]);
-         printf("\n");
+       }
-         fprintf(ficlog,"\n");
+       printf("\n");
- #endif
+       fprintf(ficlog,"\n");
-       }
+ #endif
      }
-   }
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
- }
+ #ifdef DEBUG
+       int k[2],l;
- /**** Prevalence limit (stable or period prevalence)  ****************/
+       k[0]=1;
+       k[1]=-1;
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+       printf("Max: %.12e",(*func)(p));
- {
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+       for (j=1;j<=n;j++) {
-      matrix by transitions matrix until convergence is reached */
+         printf(" %.12e",p[j]);
+         fprintf(ficlog," %.12e",p[j]);
-   int i, ii,j,k;
+       }
-   double min, max, maxmin, maxmax,sumnew=0.;
+       printf("\n");
-   double **matprod2();
+       fprintf(ficlog,"\n");
-   double **out, cov[NCOVMAX], **pmij();
+       for(l=0;l<=1;l++) {
-   double **newm;
+         for (j=1;j<=n;j++) {
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+           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]);
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     for (j=1;j<=nlstate+ndeath;j++){
+         }
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         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)));
+       }
-    cov[1]=1.;
+ #endif
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+       free_vector(xit,1,n);
-     newm=savm;
+       free_vector(xits,1,n);
-     /* Covariates have to be included here again */
+       free_vector(ptt,1,n);
-      cov[2]=agefin;
+       free_vector(pt,1,n);
+       return;
-       for (k=1; k<=cptcovn;k++) {
+     }
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+     for (j=1;j<=n;j++) {
-       }
+       ptt[j]=2.0*p[j]-pt[j];
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       xit[j]=p[j]-pt[j];
-       for (k=1; k<=cptcovprod;k++)
+       pt[j]=p[j];
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     }
+     fptt=(*func)(ptt);
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     if (fptt < fp) {
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+       if (t < 0.0) {
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+         linmin(p,xit,n,fret,func);
+         for (j=1;j<=n;j++) {
-     savm=oldm;
+           xi[j][ibig]=xi[j][n];
-     oldm=newm;
+           xi[j][n]=xit[j];
-     maxmax=0.;
+         }
-     for(j=1;j<=nlstate;j++){
+ #ifdef DEBUG
-       min=1.;
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       max=0.;
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       for(i=1; i<=nlstate; i++) {
+         for(j=1;j<=n;j++){
-         sumnew=0;
+           printf(" %.12e",xit[j]);
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+           fprintf(ficlog," %.12e",xit[j]);
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+         }
-         max=FMAX(max,prlim[i][j]);
+         printf("\n");
-         min=FMIN(min,prlim[i][j]);
+         fprintf(ficlog,"\n");
-       }
+ #endif
-       maxmin=max-min;
+       }
-       maxmax=FMAX(maxmax,maxmin);
+     }
-     }
+   }
-     if(maxmax < ftolpl){
+ }
-       return prlim;
-     }
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-   }
- }
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+ {
- /*************** transition probabilities ***************/
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+      matrix by transitions matrix until convergence is reached */
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
- {
+   int i, ii,j,k;
-   double s1, s2;
+   double min, max, maxmin, maxmax,sumnew=0.;
-   /*double t34;*/
+   double **matprod2();
-   int i,j,j1, nc, ii, jj;
+   double **out, cov[NCOVMAX+1], **pmij();
+   double **newm;
-     for(i=1; i<= nlstate; i++){
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-       for(j=1; j<i;j++){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-           /*s2 += param[i][j][nc]*cov[nc];*/
+     for (j=1;j<=nlstate+ndeath;j++){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+     }
-         }
-         ps[i][j]=s2;
+    cov[1]=1.;
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
-       }
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     newm=savm;
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+     /* Covariates have to be included here again */
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+     cov[2]=agefin;
-         }
-         ps[i][j]=s2;
+     for (k=1; k<=cptcovn;k++) {
-       }
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-     }
+       /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
-     /*ps[3][2]=1;*/
+     }
+     for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-     for(i=1; i<= nlstate; i++){
+     for (k=1; k<=cptcovprod;k++)
-       s1=0;
+       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       for(j=1; j<i; j++)
-         s1+=exp(ps[i][j]);
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       for(j=i+1; j<=nlstate+ndeath; j++)
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-         s1+=exp(ps[i][j]);
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-       ps[i][i]=1./(s1+1.);
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
-       for(j=1; j<i; j++)
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     savm=oldm;
-       for(j=i+1; j<=nlstate+ndeath; j++)
+     oldm=newm;
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+     maxmax=0.;
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     for(j=1;j<=nlstate;j++){
-     } /* end i */
+       min=1.;
+       max=0.;
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(i=1; i<=nlstate; i++) {
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+         sumnew=0;
-         ps[ii][jj]=0;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         ps[ii][ii]=1;
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-       }
+         max=FMAX(max,prlim[i][j]);
-     }
+         min=FMIN(min,prlim[i][j]);
+       }
+       maxmin=max-min;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       maxmax=FMAX(maxmax,maxmin);
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     }
- /*         printf("ddd %lf ",ps[ii][jj]); */
+     if(maxmax < ftolpl){
- /*       } */
+       return prlim;
- /*       printf("\n "); */
+     }
- /*        } */
+   }
- /*        printf("\n ");printf("%lf ",cov[2]); */
+ }
-        /*
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ /*************** transition probabilities ***************/
-       goto end;*/
-     return ps;
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
- }
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
- /**************** Product of 2 matrices ******************/
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+      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
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+      ncth covariate in the global vector x is given by the formula:
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-   /* in, b, out are matrice of pointers which should have been initialized
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
-      before: only the contents of out is modified. The function returns
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
-      a pointer to pointers identical to out */
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-   long i, j, k;
+      Outputs ps[i][j] the probability to be observed in j being in j according to
-   for(i=nrl; i<= nrh; i++)
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
-     for(k=ncolol; k<=ncoloh; k++)
+   */
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+   double s1, lnpijopii;
-         out[i][k] +=in[i][j]*b[j][k];
+   /*double t34;*/
+   int i,j,j1, nc, ii, jj;
-   return out;
- }
+     for(i=1; i<= nlstate; i++){
+       for(j=1; j<i;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- /************* Higher Matrix Product ***************/
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
- {
+         }
-   /* Computes the transition matrix starting at age 'age' over
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-      'nhstepm*hstepm*stepm' months (i.e. until
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+       }
-      nhstepm*hstepm matrices.
+       for(j=i+1; j<=nlstate+ndeath;j++){
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-      (typically every 2 years instead of every month which is too big
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-      for the memory).
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-      Model is determined by parameters x and covariates have to be
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-      included manually here.
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-      */
+       }
+     }
-   int i, j, d, h, k;
-   double **out, cov[NCOVMAX];
+     for(i=1; i<= nlstate; i++){
-   double **newm;
+       s1=0;
+       for(j=1; j<i; j++){
-   /* Hstepm could be zero and should return the unit matrix */
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   for (i=1;i<=nlstate+ndeath;i++)
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-     for (j=1;j<=nlstate+ndeath;j++){
+       }
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       for(j=i+1; j<=nlstate+ndeath; j++){
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-     }
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       }
-   for(h=1; h <=nhstepm; h++){
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-     for(d=1; d <=hstepm; d++){
+       ps[i][i]=1./(s1+1.);
-       newm=savm;
+       /* Computing other pijs */
-       /* Covariates have to be included here again */
+       for(j=1; j<i; j++)
-       cov[1]=1.;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       for(j=i+1; j<=nlstate+ndeath; j++)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       for (k=1; k<=cptcovage;k++)
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     } /* end 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]]];
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
+         ps[ii][jj]=0;
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+         ps[ii][ii]=1;
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       }
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+     }
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-       savm=oldm;
-       oldm=newm;
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-     }
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
-     for(i=1; i<=nlstate+ndeath; i++)
+ /*         printf("ddd %lf ",ps[ii][jj]); */
-       for(j=1;j<=nlstate+ndeath;j++) {
+ /*       } */
-         po[i][j][h]=newm[i][j];
+ /*       printf("\n "); */
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+ /*        } */
-          */
+ /*        printf("\n ");printf("%lf ",cov[2]); */
-       }
+        /*
-   } /* end h */
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-   return po;
+       goto end;*/
- }
+     return ps;
+ }
- /*************** log-likelihood *************/
+ /**************** Product of 2 matrices ******************/
- double func( double *x)
- {
+ double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
-   int i, ii, j, k, mi, d, kk;
+ {
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-   double **out;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-   double sw; /* Sum of weights */
+   /* in, b, out are matrice of pointers which should have been initialized
-   double lli; /* Individual log likelihood */
+      before: only the contents of out is modified. The function returns
-   int s1, s2;
+      a pointer to pointers identical to out */
-   double bbh, survp;
+   long i, j, k;
-   long ipmx;
+   for(i=nrl; i<= nrh; i++)
-   /*extern weight */
+     for(k=ncolol; k<=ncoloh; k++)
-   /* We are differentiating ll according to initial status */
+       for(j=ncl,out[i][k]=0.; j<=nch; j++)
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         out[i][k] +=in[i][j]*b[j][k];
-   /*for(i=1;i<imx;i++)
-     printf(" %d\n",s[4][i]);
+   return out;
-   */
+ }
-   cov[1]=1.;
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+ /************* Higher Matrix Product ***************/
-   if(mle==1){
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ {
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   /* Computes the transition matrix starting at age 'age' over
-       for(mi=1; mi<= wav[i]-1; mi++){
+      'nhstepm*hstepm*stepm' months (i.e. until
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-           for (j=1;j<=nlstate+ndeath;j++){
+      nhstepm*hstepm matrices.
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+      (typically every 2 years instead of every month which is too big
-           }
+      for the memory).
-         for(d=0; d<dh[mi][i]; d++){
+      Model is determined by parameters x and covariates have to be
-           newm=savm;
+      included manually here.
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           for (kk=1; kk<=cptcovage;kk++) {
+      */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+   int i, j, d, h, k;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   double **out, cov[NCOVMAX+1];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   double **newm;
-           savm=oldm;
-           oldm=newm;
+   /* Hstepm could be zero and should return the unit matrix */
-         } /* end mult */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+     }
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+   for(h=1; h <=nhstepm; h++){
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+     for(d=1; d <=hstepm; d++){
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+       newm=savm;
-          * probability in order to take into account the bias as a fraction of the way
+       /* Covariates have to be included here again */
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+       cov[1]=1.;
-          * -stepm/2 to stepm/2 .
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       for (k=1; k<=cptcovn;k++)
-          * For stepm > 1 the results are less biased than in previous versions.
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-          */
+       for (k=1; k<=cptcovage;k++)
-         s1=s[mw[mi][i]][i];
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         s2=s[mw[mi+1][i]][i];
+       for (k=1; k<=cptcovprod;k++)
-         bbh=(double)bh[mi][i]/(double)stepm;
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-         /* bias bh is positive if real duration
-          * is higher than the multiple of stepm and negative otherwise.
-          */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-         if( s2 > nlstate){
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-           /* i.e. if s2 is a death state and if the date of death is known
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-              then the contribution to the likelihood is the probability to
+       savm=oldm;
-              die between last step unit time and current  step unit time,
+       oldm=newm;
-              which is also equal to probability to die before dh
+     }
-              minus probability to die before dh-stepm .
+     for(i=1; i<=nlstate+ndeath; i++)
-              In version up to 0.92 likelihood was computed
+       for(j=1;j<=nlstate+ndeath;j++) {
-         as if date of death was unknown. Death was treated as any other
+         po[i][j][h]=newm[i][j];
-         health state: the date of the interview describes the actual state
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-         and not the date of a change in health state. The former idea was
+       }
-         to consider that at each interview the state was recorded
+     /*printf("h=%d ",h);*/
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   } /* end h */
-         introduced the exact date of death then we should have modified
+ /*     printf("\n H=%d \n",h); */
-         the contribution of an exact death to the likelihood. This new
+   return po;
-         contribution is smaller and very dependent of the step unit
+ }
-         stepm. It is no more the probability to die between last interview
-         and month of death but the probability to survive from last
-         interview up to one month before death multiplied by the
+ /*************** log-likelihood *************/
-         probability to die within a month. Thanks to Chris
+ double func( double *x)
-         Jackson for correcting this bug.  Former versions increased
+ {
-         mortality artificially. The bad side is that we add another loop
+   int i, ii, j, k, mi, d, kk;
-         which slows down the processing. The difference can be up to 10%
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-         lower mortality.
+   double **out;
-           */
+   double sw; /* Sum of weights */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   double lli; /* Individual log likelihood */
+   int s1, s2;
+   double bbh, survp;
-         } else if  (s2==-2) {
+   long ipmx;
-           for (j=1,survp=0. ; j<=nlstate; j++)
+   /*extern weight */
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   /* We are differentiating ll according to initial status */
-           /*survp += out[s1][j]; */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-           lli= log(survp);
+   /*for(i=1;i<imx;i++)
-         }
+     printf(" %d\n",s[4][i]);
+   */
-         else if  (s2==-4) {
+   cov[1]=1.;
-           for (j=3,survp=0. ; j<=nlstate; j++)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-           lli= log(survp);
-         }
+   if(mle==1){
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         else if  (s2==-5) {
+       /* Computes the values of the ncovmodel covariates of the model
-           for (j=1,survp=0. ; j<=2; j++)
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-           lli= log(survp);
+          to be observed in j being in i according to the model.
-         }
+        */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         else{
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
-           /*  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 */
+          has been calculated etc */
-         }
+       for(mi=1; mi<= wav[i]-1; mi++){
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         /*if(lli ==000.0)*/
+           for (j=1;j<=nlstate+ndeath;j++){
-         /*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); */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         ipmx +=1;
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         sw += weight[i];
+           }
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         for(d=0; d<dh[mi][i]; d++){
-       } /* end of wave */
+           newm=savm;
-     } /* end of individual */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   }  else if(mle==2){
+           for (kk=1; kk<=cptcovage;kk++) {
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+           }
-       for(mi=1; mi<= wav[i]-1; mi++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           for (j=1;j<=nlstate+ndeath;j++){
+           savm=oldm;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           oldm=newm;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         } /* end mult */
-           }
-         for(d=0; d<=dh[mi][i]; d++){
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-           newm=savm;
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-           for (kk=1; kk<=cptcovage;kk++) {
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-           }
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+          * probability in order to take into account the bias as a fraction of the way
-           savm=oldm;
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-           oldm=newm;
+          * -stepm/2 to stepm/2 .
-         } /* end mult */
+          * For stepm=1 the results are the same as for previous versions of Imach.
+          * For stepm > 1 the results are less biased than in previous versions.
-         s1=s[mw[mi][i]][i];
+          */
-         s2=s[mw[mi+1][i]][i];
+         s1=s[mw[mi][i]][i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+         s2=s[mw[mi+1][i]][i];
-         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 */
+         bbh=(double)bh[mi][i]/(double)stepm;
-         ipmx +=1;
+         /* bias bh is positive if real duration
-         sw += weight[i];
+          * is higher than the multiple of stepm and negative otherwise.
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+          */
-       } /* end of wave */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-     } /* end of individual */
+         if( s2 > nlstate){
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+           /* i.e. if s2 is a death state and if the date of death is known
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+              then the contribution to the likelihood is the probability to
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+              die between last step unit time and current  step unit time,
-       for(mi=1; mi<= wav[i]-1; mi++){
+              which is also equal to probability to die before dh
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+              minus probability to die before dh-stepm .
-           for (j=1;j<=nlstate+ndeath;j++){
+              In version up to 0.92 likelihood was computed
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         as if date of death was unknown. Death was treated as any other
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         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
-         for(d=0; d<dh[mi][i]; d++){
+         to consider that at each interview the state was recorded
-           newm=savm;
+         (healthy, disable or death) and IMaCh was corrected; but when we
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         introduced the exact date of death then we should have modified
-           for (kk=1; kk<=cptcovage;kk++) {
+         the contribution of an exact death to the likelihood. This new
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         contribution is smaller and very dependent of the step unit
-           }
+         stepm. It is no more the probability to die between last interview
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         and month of death but the probability to survive from last
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         interview up to one month before death multiplied by the
-           savm=oldm;
+         probability to die within a month. Thanks to Chris
-           oldm=newm;
+         Jackson for correcting this bug.  Former versions increased
-         } /* end mult */
+         mortality artificially. The bad side is that we add another loop
+         which slows down the processing. The difference can be up to 10%
-         s1=s[mw[mi][i]][i];
+         lower mortality.
-         s2=s[mw[mi+1][i]][i];
+           */
-         bbh=(double)bh[mi][i]/(double)stepm;
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         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;
-         sw += weight[i];
+         } else if  (s2==-2) {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           for (j=1,survp=0. ; j<=nlstate; j++)
-       } /* end of wave */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-     } /* end of individual */
+           /*survp += out[s1][j]; */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+           lli= log(survp);
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+         else if  (s2==-4) {
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+           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[ii][j]=(ii==j ? 1.0 : 0.0);
+           lli= log(survp);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         }
-           }
-         for(d=0; d<dh[mi][i]; d++){
+         else if  (s2==-5) {
-           newm=savm;
+           for (j=1,survp=0. ; j<=2; j++)
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-           for (kk=1; kk<=cptcovage;kk++) {
+           lli= log(survp);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
-           }
+         else{
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-,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;
+         }
-           oldm=newm;
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         } /* end mult */
+         /*if(lli ==000.0)*/
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-         s1=s[mw[mi][i]][i];
+         ipmx +=1;
-         s2=s[mw[mi+1][i]][i];
+         sw += weight[i];
-         if( s2 > nlstate){
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-           lli=log(out[s1][s2] - savm[s1][s2]);
+       } /* end of wave */
-         }else{
+     } /* end of individual */
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+   }  else if(mle==2){
-         }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         ipmx +=1;
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         sw += weight[i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
- /*      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 (j=1;j<=nlstate+ndeath;j++){
-       } /* end of wave */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     } /* end of individual */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+           }
-     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];
+         bbh=(double)bh[mi][i]/(double)stepm;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         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 */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         ipmx +=1;
-           savm=oldm;
+         sw += weight[i];
-           oldm=newm;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         } /* end mult */
+       } /* end of wave */
+     } /* end of individual */
-         s1=s[mw[mi][i]][i];
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-         s2=s[mw[mi+1][i]][i];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         ipmx +=1;
+       for(mi=1; mi<= wav[i]-1; mi++){
-         sw += weight[i];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           for (j=1;j<=nlstate+ndeath;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]);*/
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } /* end of wave */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     } /* end of individual */
+           }
-   } /* End of if */
+         for(d=0; d<dh[mi][i]; d++){
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+           newm=savm;
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           for (kk=1; kk<=cptcovage;kk++) {
-   return -l;
+             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 funcone( double *x)
+           savm=oldm;
- {
+           oldm=newm;
-   /* Same as likeli but slower because of a lot of printf and if */
+         } /* end mult */
-   int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+         s1=s[mw[mi][i]][i];
-   double **out;
+         s2=s[mw[mi+1][i]][i];
-   double lli; /* Individual log likelihood */
+         bbh=(double)bh[mi][i]/(double)stepm;
-   double llt;
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   int s1, s2;
+         ipmx +=1;
-   double bbh, survp;
+         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==4){  /* ml=4 no 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);
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+           }
-     for(mi=1; mi<= wav[i]-1; mi++){
+         for(d=0; d<dh[mi][i]; d++){
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+           newm=savm;
-         for (j=1;j<=nlstate+ndeath;j++){
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           for (kk=1; kk<=cptcovage;kk++) {
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         }
+           }
-       for(d=0; d<dh[mi][i]; d++){
-         newm=savm;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         for (kk=1; kk<=cptcovage;kk++) {
+           savm=oldm;
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           oldm=newm;
-         }
+         } /* end mult */
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         s1=s[mw[mi][i]][i];
-         savm=oldm;
+         s2=s[mw[mi+1][i]][i];
-         oldm=newm;
+         if( s2 > nlstate){
-       } /* end mult */
+           lli=log(out[s1][s2] - savm[s1][s2]);
+         }else{
-       s1=s[mw[mi][i]][i];
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       s2=s[mw[mi+1][i]][i];
+         }
-       bbh=(double)bh[mi][i]/(double)stepm;
+         ipmx +=1;
-       /* bias is positive if real duration
+         sw += weight[i];
-        * is higher than the multiple of stepm and negative otherwise.
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-        */
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+       } /* end of wave */
-         lli=log(out[s1][s2] - savm[s1][s2]);
+     } /* end of individual */
-       } else if  (s2==-2) {
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-         for (j=1,survp=0. ; j<=nlstate; j++)
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         lli= log(survp);
+       for(mi=1; mi<= wav[i]-1; mi++){
-       }else if (mle==1){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           for (j=1;j<=nlstate+ndeath;j++){
-       } else if(mle==2){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } else if(mle==3){  /* exponential inter-extrapolation */
+           }
-         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+         for(d=0; d<dh[mi][i]; d++){
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+           newm=savm;
-         lli=log(out[s1][s2]); /* Original formula */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+           for (kk=1; kk<=cptcovage;kk++) {
-         lli=log(out[s1][s2]); /* Original formula */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       } /* End of if */
+           }
-       ipmx +=1;
-       sw += weight[i];
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- /*       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]); */
+           savm=oldm;
-       if(globpr){
+           oldm=newm;
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         } /* end mult */
-  %11.6f %11.6f %11.6f ", \
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+         s1=s[mw[mi][i]][i];
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         s2=s[mw[mi+1][i]][i];
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-           llt +=ll[k]*gipmx/gsw;
+         ipmx +=1;
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+         sw += weight[i];
-         }
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         fprintf(ficresilk," %10.6f\n", -llt);
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-       }
+       } /* end of wave */
-     } /* end of wave */
+     } /* end of individual */
-   } /* end of individual */
+   } /* End of if */
    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   if(globpr==0){ /* First time we count the contributions and weights */
+   return -l;
-     gipmx=ipmx;
+ }
-     gsw=sw;
-   }
+ /*************** log-likelihood *************/
-   return -l;
+ double funcone( double *x)
- }
+ {
+   /* Same as likeli but slower because of a lot of printf and if */
+   int i, ii, j, k, mi, d, kk;
- /*************** function likelione ***********/
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+   double **out;
- {
+   double lli; /* Individual log likelihood */
-   /* This routine should help understanding what is done with
+   double llt;
-      the selection of individuals/waves and
+   int s1, s2;
-      to check the exact contribution to the likelihood.
+   double bbh, survp;
-      Plotting could be done.
+   /*extern weight */
-    */
+   /* We are differentiating ll according to initial status */
-   int k;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+     printf(" %d\n",s[4][i]);
-     strcpy(fileresilk,"ilk");
+   */
-     strcat(fileresilk,fileres);
+   cov[1]=1.;
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-       printf("Problem with resultfile: %s\n", fileresilk);
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-     }
+   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);
+         }
-   }
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   return;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- }
+         savm=oldm;
+         oldm=newm;
+       } /* end mult */
- /*********** Maximum Likelihood Estimation ***************/
+       s1=s[mw[mi][i]][i];
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+       s2=s[mw[mi+1][i]][i];
- {
+       bbh=(double)bh[mi][i]/(double)stepm;
-   int i,j, iter;
+       /* bias is positive if real duration
-   double **xi;
+        * is higher than the multiple of stepm and negative otherwise.
-   double fret;
+        */
-   double fretone; /* Only one call to likelihood */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-   /*  char filerespow[FILENAMELENGTH];*/
+         lli=log(out[s1][s2] - savm[s1][s2]);
-   xi=matrix(1,npar,1,npar);
+       } else if  (s2==-2) {
-   for (i=1;i<=npar;i++)
+         for (j=1,survp=0. ; j<=nlstate; j++)
-     for (j=1;j<=npar;j++)
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+         lli= log(survp);
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+       }else if (mle==1){
-   strcpy(filerespow,"pow");
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   strcat(filerespow,fileres);
+       } else if(mle==2){
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+         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("Problem with resultfile: %s\n", filerespow);
+       } else if(mle==3){  /* exponential inter-extrapolation */
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+         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 */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+         lli=log(out[s1][s2]); /* Original formula */
-   for (i=1;i<=nlstate;i++)
+       } else{  /* mle=0 back to 1 */
-     for(j=1;j<=nlstate+ndeath;j++)
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   fprintf(ficrespow,"\n");
+       } /* End of if */
+       ipmx +=1;
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+       sw += weight[i];
+       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   free_matrix(xi,1,npar,1,npar);
+       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-   fclose(ficrespow);
+       if(globpr){
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+  %11.6f %11.6f %11.6f ", \
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
- }
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
- /**** Computes Hessian and covariance matrix ***/
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+         }
- {
+         fprintf(ficresilk," %10.6f\n", -llt);
-   double  **a,**y,*x,pd;
+       }
-   double **hess;
+     } /* end of wave */
-   int i, j,jk;
+   } /* end of individual */
-   int *indx;
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+   if(globpr==0){ /* First time we count the contributions and weights */
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+     gipmx=ipmx;
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+     gsw=sw;
-   double gompertz(double p[]);
+   }
-   hess=matrix(1,npar,1,npar);
+   return -l;
+ }
-   printf("\nCalculation of the hessian matrix. Wait...\n");
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-   for (i=1;i<=npar;i++){
+ /*************** function likelione ***********/
-     printf("%d",i);fflush(stdout);
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+ {
+   /* This routine should help understanding what is done with
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+      the selection of individuals/waves and
+      to check the exact contribution to the likelihood.
-     /*  printf(" %f ",p[i]);
+      Plotting could be done.
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+    */
-   }
+   int k;
-   for (i=1;i<=npar;i++) {
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     for (j=1;j<=npar;j++)  {
+     strcpy(fileresilk,"ilk");
-       if (j>i) {
+     strcat(fileresilk,fileres);
-         printf(".%d%d",i,j);fflush(stdout);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+       printf("Problem with resultfile: %s\n", fileresilk);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+     }
-         hess[j][i]=hess[i][j];
+     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");
-         /*printf(" %lf ",hess[i][j]);*/
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-       }
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-     }
+     for(k=1; k<=nlstate; k++)
-   }
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   printf("\n");
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   fprintf(ficlog,"\n");
+   }
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   *fretone=(*funcone)(p);
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+   if(*globpri !=0){
+     fclose(ficresilk);
-   a=matrix(1,npar,1,npar);
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   y=matrix(1,npar,1,npar);
+     fflush(fichtm);
-   x=vector(1,npar);
+   }
-   indx=ivector(1,npar);
+   return;
-   for (i=1;i<=npar;i++)
+ }
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   ludcmp(a,npar,indx,&pd);
+ /*********** Maximum Likelihood Estimation ***************/
-   for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-     x[j]=1;
+ {
-     lubksb(a,npar,indx,x);
+   int i,j, iter;
-     for (i=1;i<=npar;i++){
+   double **xi;
-       matcov[i][j]=x[i];
+   double fret;
-     }
+   double fretone; /* Only one call to likelihood */
-   }
+   /*  char filerespow[FILENAMELENGTH];*/
+   xi=matrix(1,npar,1,npar);
-   printf("\n#Hessian matrix#\n");
+   for (i=1;i<=npar;i++)
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+     for (j=1;j<=npar;j++)
-   for (i=1;i<=npar;i++) {
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     for (j=1;j<=npar;j++) {
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-       printf("%.3e ",hess[i][j]);
+   strcpy(filerespow,"pow");
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   strcat(filerespow,fileres);
-     }
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     printf("\n");
+     printf("Problem with resultfile: %s\n", filerespow);
-     fprintf(ficlog,"\n");
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
    }
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   /* Recompute Inverse */
+   for (i=1;i<=nlstate;i++)
-   for (i=1;i<=npar;i++)
+     for(j=1;j<=nlstate+ndeath;j++)
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   ludcmp(a,npar,indx,&pd);
+   fprintf(ficrespow,"\n");
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-   for (j=1;j<=npar;j++) {
+   free_matrix(xi,1,npar,1,npar);
-     for (i=1;i<=npar;i++) x[i]=0;
+   fclose(ficrespow);
-     x[j]=1;
+   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-     lubksb(a,npar,indx,x);
+   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-     for (i=1;i<=npar;i++){
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-       y[i][j]=x[i];
-       printf("%.3e ",y[i][j]);
+ }
-       fprintf(ficlog,"%.3e ",y[i][j]);
-     }
+ /**** Computes Hessian and covariance matrix ***/
-     printf("\n");
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-     fprintf(ficlog,"\n");
+ {
-   }
+   double  **a,**y,*x,pd;
-   */
+   double **hess;
+   int i, j,jk;
-   free_matrix(a,1,npar,1,npar);
+   int *indx;
-   free_matrix(y,1,npar,1,npar);
-   free_vector(x,1,npar);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-   free_ivector(indx,1,npar);
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-   free_matrix(hess,1,npar,1,npar);
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
+   double gompertz(double p[]);
- }
+   hess=matrix(1,npar,1,npar);
- /*************** hessian matrix ****************/
+   printf("\nCalculation of the hessian matrix. Wait...\n");
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
- {
+   for (i=1;i<=npar;i++){
-   int i;
+     printf("%d",i);fflush(stdout);
-   int l=1, lmax=20;
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-   double k1,k2;
-   double p2[NPARMAX+1];
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-   double res;
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+     /*  printf(" %f ",p[i]);
-   double fx;
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-   int k=0,kmax=10;
+   }
-   double l1;
+   for (i=1;i<=npar;i++) {
-   fx=func(x);
+     for (j=1;j<=npar;j++)  {
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+       if (j>i) {
-   for(l=0 ; l <=lmax; l++){
+         printf(".%d%d",i,j);fflush(stdout);
-     l1=pow(10,l);
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-     delts=delt;
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-     for(k=1 ; k <kmax; k=k+1){
-       delt = delta*(l1*k);
+         hess[j][i]=hess[i][j];
-       p2[theta]=x[theta] +delt;
+         /*printf(" %lf ",hess[i][j]);*/
-       k1=func(p2)-fx;
+       }
-       p2[theta]=x[theta]-delt;
+     }
-       k2=func(p2)-fx;
+   }
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   printf("\n");
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   fprintf(ficlog,"\n");
- #ifdef DEBUG
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
- #endif
+   a=matrix(1,npar,1,npar);
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   y=matrix(1,npar,1,npar);
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+   x=vector(1,npar);
-         k=kmax;
+   indx=ivector(1,npar);
-       }
+   for (i=1;i<=npar;i++)
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-         k=kmax; l=lmax*10.;
+   ludcmp(a,npar,indx,&pd);
-       }
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   for (j=1;j<=npar;j++) {
-         delts=delt;
+     for (i=1;i<=npar;i++) x[i]=0;
-       }
+     x[j]=1;
-     }
+     lubksb(a,npar,indx,x);
-   }
+     for (i=1;i<=npar;i++){
-   delti[theta]=delts;
+       matcov[i][j]=x[i];
-   return res;
+     }
+   }
- }
+   printf("\n#Hessian matrix#\n");
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+   fprintf(ficlog,"\n#Hessian matrix#\n");
- {
+   for (i=1;i<=npar;i++) {
-   int i;
+     for (j=1;j<=npar;j++) {
-   int l=1, l1, lmax=20;
+       printf("%.3e ",hess[i][j]);
-   double k1,k2,k3,k4,res,fx;
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-   double p2[NPARMAX+1];
+     }
-   int k;
+     printf("\n");
+     fprintf(ficlog,"\n");
-   fx=func(x);
+   }
-   for (k=1; k<=2; k++) {
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+   /* Recompute Inverse */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   for (i=1;i<=npar;i++)
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-     k1=func(p2)-fx;
+   ludcmp(a,npar,indx,&pd);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+   /*  printf("\n#Hessian matrix recomputed#\n");
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     k2=func(p2)-fx;
+   for (j=1;j<=npar;j++) {
+     for (i=1;i<=npar;i++) x[i]=0;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     x[j]=1;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     lubksb(a,npar,indx,x);
-     k3=func(p2)-fx;
+     for (i=1;i<=npar;i++){
+       y[i][j]=x[i];
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       printf("%.3e ",y[i][j]);
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       fprintf(ficlog,"%.3e ",y[i][j]);
-     k4=func(p2)-fx;
+     }
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     printf("\n");
- #ifdef DEBUG
+     fprintf(ficlog,"\n");
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+   }
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+   */
- #endif
-   }
+   free_matrix(a,1,npar,1,npar);
-   return res;
+   free_matrix(y,1,npar,1,npar);
- }
+   free_vector(x,1,npar);
+   free_ivector(indx,1,npar);
- /************** Inverse of matrix **************/
+   free_matrix(hess,1,npar,1,npar);
- void ludcmp(double **a, int n, int *indx, double *d)
- {
-   int i,imax,j,k;
+ }
-   double big,dum,sum,temp;
-   double *vv;
+ /*************** hessian matrix ****************/
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-   vv=vector(1,n);
+ {
-   *d=1.0;
+   int i;
-   for (i=1;i<=n;i++) {
+   int l=1, lmax=20;
-     big=0.0;
+   double k1,k2;
-     for (j=1;j<=n;j++)
+   double p2[MAXPARM+1]; /* identical to x */
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+   double res;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-     vv[i]=1.0/big;
+   double fx;
-   }
+   int k=0,kmax=10;
-   for (j=1;j<=n;j++) {
+   double l1;
-     for (i=1;i<j;i++) {
-       sum=a[i][j];
+   fx=func(x);
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-       a[i][j]=sum;
+   for(l=0 ; l <=lmax; l++){
-     }
+     l1=pow(10,l);
-     big=0.0;
+     delts=delt;
-     for (i=j;i<=n;i++) {
+     for(k=1 ; k <kmax; k=k+1){
-       sum=a[i][j];
+       delt = delta*(l1*k);
-       for (k=1;k<j;k++)
+       p2[theta]=x[theta] +delt;
-         sum -= a[i][k]*a[k][j];
+       k1=func(p2)-fx;
-       a[i][j]=sum;
+       p2[theta]=x[theta]-delt;
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+       k2=func(p2)-fx;
-         big=dum;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-         imax=i;
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-       }
-     }
+ #ifdef DEBUGHESS
-     if (j != imax) {
+       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);
-       for (k=1;k<=n;k++) {
+       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);
-         dum=a[imax][k];
+ #endif
-         a[imax][k]=a[j][k];
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-         a[j][k]=dum;
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-       }
+         k=kmax;
-       *d = -(*d);
+       }
-       vv[imax]=vv[j];
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-     }
+         k=kmax; l=lmax*10.;
-     indx[j]=imax;
+       }
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-     if (j != n) {
+         delts=delt;
-       dum=1.0/(a[j][j]);
+       }
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+     }
-     }
+   }
-   }
+   delti[theta]=delts;
-   free_vector(vv,1,n);  /* Doesn't work */
+   return res;
- ;
  }
- void lubksb(double **a, int n, int *indx, double b[])
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
-   int i,ii=0,ip,j;
+   int i;
-   double sum;
+   int l=1, l1, lmax=20;
+   double k1,k2,k3,k4,res,fx;
-   for (i=1;i<=n;i++) {
+   double p2[MAXPARM+1];
-     ip=indx[i];
+   int k;
-     sum=b[ip];
-     b[ip]=b[i];
+   fx=func(x);
-     if (ii)
+   for (k=1; k<=2; k++) {
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-     else if (sum) ii=i;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-     b[i]=sum;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-   }
+     k1=func(p2)-fx;
-   for (i=n;i>=1;i--) {
-     sum=b[i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     b[i]=sum/a[i][i];
+     k2=func(p2)-fx;
-   }
- }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
- void pstamp(FILE *fichier)
+     k3=func(p2)-fx;
- {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+     p2[thetai]=x[thetai]-delti[thetai]/k;
- }
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     k4=func(p2)-fx;
- /************ Frequencies ********************/
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
- 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[])
+ #ifdef DEBUG
- {  /* Some frequencies */
+     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+ #endif
-   int first;
+   }
-   double ***freq; /* Frequencies */
+   return res;
-   double *pp, **prop;
+ }
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   char fileresp[FILENAMELENGTH];
+ /************** Inverse of matrix **************/
+ void ludcmp(double **a, int n, int *indx, double *d)
-   pp=vector(1,nlstate);
+ {
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   int i,imax,j,k;
-   strcpy(fileresp,"p");
+   double big,dum,sum,temp;
-   strcat(fileresp,fileres);
+   double *vv;
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   vv=vector(1,n);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+   *d=1.0;
-     exit(0);
+   for (i=1;i<=n;i++) {
-   }
+     big=0.0;
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+     for (j=1;j<=n;j++)
-   j1=0;
+       if ((temp=fabs(a[i][j])) > big) big=temp;
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-   j=cptcoveff;
+     vv[i]=1.0/big;
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   }
+   for (j=1;j<=n;j++) {
-   first=1;
+     for (i=1;i<j;i++) {
+       sum=a[i][j];
-   for(k1=1; k1<=j;k1++){
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-     for(i1=1; i1<=ncodemax[k1];i1++){
+       a[i][j]=sum;
-       j1++;
+     }
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+     big=0.0;
-         scanf("%d", i);*/
+     for (i=j;i<=n;i++) {
-       for (i=-5; i<=nlstate+ndeath; i++)
+       sum=a[i][j];
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+       for (k=1;k<j;k++)
-           for(m=iagemin; m <= iagemax+3; m++)
+         sum -= a[i][k]*a[k][j];
-             freq[i][jk][m]=0;
+       a[i][j]=sum;
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-     for (i=1; i<=nlstate; i++)
+         big=dum;
-       for(m=iagemin; m <= iagemax+3; m++)
+         imax=i;
-         prop[i][m]=0;
+       }
+     }
-       dateintsum=0;
+     if (j != imax) {
-       k2cpt=0;
+       for (k=1;k<=n;k++) {
-       for (i=1; i<=imx; i++) {
+         dum=a[imax][k];
-         bool=1;
+         a[imax][k]=a[j][k];
-         if  (cptcovn>0) {
+         a[j][k]=dum;
-           for (z1=1; z1<=cptcoveff; z1++)
+       }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+       *d = -(*d);
-               bool=0;
+       vv[imax]=vv[j];
-         }
+     }
-         if (bool==1){
+     indx[j]=imax;
-           for(m=firstpass; m<=lastpass; m++){
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-             k2=anint[m][i]+(mint[m][i]/12.);
+     if (j != n) {
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+       dum=1.0/(a[j][j]);
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     }
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   }
-               if (m<lastpass) {
+   free_vector(vv,1,n);  /* Doesn't work */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+ ;
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+ }
-               }
+ void lubksb(double **a, int n, int *indx, double b[])
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+ {
-                 dateintsum=dateintsum+k2;
+   int i,ii=0,ip,j;
-                 k2cpt++;
+   double sum;
-               }
-               /*}*/
+   for (i=1;i<=n;i++) {
-           }
+     ip=indx[i];
-         }
+     sum=b[ip];
-       }
+     b[ip]=b[i];
+     if (ii)
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-       pstamp(ficresp);
+     else if (sum) ii=i;
-       if  (cptcovn>0) {
+     b[i]=sum;
-         fprintf(ficresp, "\n#********** Variable ");
+   }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   for (i=n;i>=1;i--) {
-         fprintf(ficresp, "**********\n#");
+     sum=b[i];
-       }
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       for(i=1; i<=nlstate;i++)
+     b[i]=sum/a[i][i];
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+   }
-       fprintf(ficresp, "\n");
+ }
-       for(i=iagemin; i <= iagemax+3; i++){
+ void pstamp(FILE *fichier)
-         if(i==iagemax+3){
+ {
-           fprintf(ficlog,"Total");
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-         }else{
+ }
-           if(first==1){
-             first=0;
+ /************ Frequencies ********************/
-             printf("See log file for details...\n");
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-           }
+ {  /* Some frequencies */
-           fprintf(ficlog,"Age %d", i);
-         }
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-         for(jk=1; jk <=nlstate ; jk++){
+   int first;
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   double ***freq; /* Frequencies */
-             pp[jk] += freq[jk][m][i];
+   double *pp, **prop;
-         }
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-         for(jk=1; jk <=nlstate ; jk++){
+   char fileresp[FILENAMELENGTH];
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
+   pp=vector(1,nlstate);
-           if(pp[jk]>=1.e-10){
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-             if(first==1){
+   strcpy(fileresp,"p");
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   strcat(fileresp,fileres);
-             }
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-           }else{
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-             if(first==1)
+     exit(0);
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   }
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-           }
+   j1=0;
-         }
+   j=cptcoveff;
-         for(jk=1; jk <=nlstate ; jk++){
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-             pp[jk] += freq[jk][m][i];
+   first=1;
-         }
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+   for(k1=1; k1<=j;k1++){   /* Loop on covariates */
-           pos += pp[jk];
+     for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-           posprop += prop[jk][i];
+       j1++;
-         }
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-         for(jk=1; jk <=nlstate ; jk++){
+         scanf("%d", i);*/
-           if(pos>=1.e-5){
+       for (i=-5; i<=nlstate+ndeath; i++)
-             if(first==1)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           for(m=iagemin; m <= iagemax+3; m++)
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             freq[i][jk][m]=0;
-           }else{
-             if(first==1)
+       for (i=1; i<=nlstate; i++)
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+         for(m=iagemin; m <= iagemax+3; m++)
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           prop[i][m]=0;
-           }
-           if( i <= iagemax){
+       dateintsum=0;
-             if(pos>=1.e-5){
+       k2cpt=0;
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+       for (i=1; i<=imx; i++) {
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+         bool=1;
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+         if  (cptcovn>0) {
-             }
+           for (z1=1; z1<=cptcoveff; z1++)
-             else
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+               bool=0;
-           }
+         }
-         }
+         if (bool==1){
+           for(m=firstpass; m<=lastpass; m++){
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+             k2=anint[m][i]+(mint[m][i]/12.);
-           for(m=-1; m <=nlstate+ndeath; m++)
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-             if(freq[jk][m][i] !=0 ) {
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-             if(first==1)
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+               if (m<lastpass) {
-             }
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-         if(i <= iagemax)
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-           fprintf(ficresp,"\n");
+               }
-         if(first==1)
-           printf("Others in log...\n");
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-         fprintf(ficlog,"\n");
+                 dateintsum=dateintsum+k2;
-       }
+                 k2cpt++;
-     }
+               }
-   }
+               /*}*/
-   dateintmean=dateintsum/k2cpt;
+           }
+         }
-   fclose(ficresp);
+       }
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   free_vector(pp,1,nlstate);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+       pstamp(ficresp);
-   /* End of Freq */
+       if  (cptcovn>0) {
- }
+         fprintf(ficresp, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- /************ Prevalence ********************/
+         fprintf(ficresp, "**********\n#");
- 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, "\n#********** Variable ");
- {
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+         fprintf(ficlog, "**********\n#");
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+       }
-      We still use firstpass and lastpass as another selection.
+       for(i=1; i<=nlstate;i++)
-   */
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, "\n");
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
-   double ***freq; /* Frequencies */
+       for(i=iagemin; i <= iagemax+3; i++){
-   double *pp, **prop;
+         if(i==iagemax+3){
-   double pos,posprop;
+           fprintf(ficlog,"Total");
-   double  y2; /* in fractional years */
+         }else{
-   int iagemin, iagemax;
+           if(first==1){
+             first=0;
-   iagemin= (int) agemin;
+             printf("See log file for details...\n");
-   iagemax= (int) agemax;
+           }
-   /*pp=vector(1,nlstate);*/
+           fprintf(ficlog,"Age %d", i);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+         }
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+         for(jk=1; jk <=nlstate ; jk++){
-   j1=0;
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+             pp[jk] += freq[jk][m][i];
-   j=cptcoveff;
+         }
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=-1, pos=0; m <=0 ; m++)
-   for(k1=1; k1<=j;k1++){
+             pos += freq[jk][m][i];
-     for(i1=1; i1<=ncodemax[k1];i1++){
+           if(pp[jk]>=1.e-10){
-       j1++;
+             if(first==1){
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-       for (i=1; i<=nlstate; i++)
+             }
-         for(m=iagemin; m <= iagemax+3; m++)
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           prop[i][m]=0.0;
+           }else{
+             if(first==1)
-       for (i=1; i<=imx; i++) { /* Each individual */
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         bool=1;
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-         if  (cptcovn>0) {
+           }
-           for (z1=1; z1<=cptcoveff; z1++)
+         }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               bool=0;
+         for(jk=1; jk <=nlstate ; jk++){
-         }
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-         if (bool==1) {
+             pp[jk] += freq[jk][m][i];
-           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 */
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+           pos += pp[jk];
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+           posprop += prop[jk][i];
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+         }
-               if((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);
+         for(jk=1; jk <=nlstate ; jk++){
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+           if(pos>=1.e-5){
-                 /*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(first==1)
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                 prop[s[m][i]][iagemax+3] += weight[i];
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-               }
+           }else{
-             }
+             if(first==1)
-           } /* end selection of waves */
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-         }
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-       }
+           }
-       for(i=iagemin; i <= iagemax+3; i++){
+           if( i <= iagemax){
+             if(pos>=1.e-5){
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-           posprop += prop[jk][i];
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-         }
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+             }
-         for(jk=1; jk <=nlstate ; jk++){
+             else
-           if( i <=  iagemax){
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-             if(posprop>=1.e-5){
+           }
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+         }
-             }
-           }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-         }/* end jk */
+           for(m=-1; m <=nlstate+ndeath; m++)
-       }/* end i */
+             if(freq[jk][m][i] !=0 ) {
-     } /* end i1 */
+             if(first==1)
-   } /* end k1 */
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+             }
-   /*free_vector(pp,1,nlstate);*/
+         if(i <= iagemax)
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+           fprintf(ficresp,"\n");
- }  /* End of prevalence */
+         if(first==1)
+           printf("Others in log...\n");
- /************* Waves Concatenation ***************/
+         fprintf(ficlog,"\n");
+       }
- void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
+     }
- {
+   }
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   dateintmean=dateintsum/k2cpt;
-      Death is a valid wave (if date is known).
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+   fclose(ficresp);
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-      and mw[mi+1][i]. dh depends on stepm.
+   free_vector(pp,1,nlstate);
-      */
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of Freq */
-   int i, mi, m;
+ }
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-      double sum=0., jmean=0.;*/
+ /************ Prevalence ********************/
-   int first;
+ 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)
-   int j, k=0,jk, ju, jl;
+ {
-   double sum=0.;
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-   first=0;
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-   jmin=1e+5;
+      We still use firstpass and lastpass as another selection.
-   jmax=-1;
+   */
-   jmean=0.;
-   for(i=1; i<=imx; i++){
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-     mi=0;
+   double ***freq; /* Frequencies */
-     m=firstpass;
+   double *pp, **prop;
-     while(s[m][i] <= nlstate){
+   double pos,posprop;
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+   double  y2; /* in fractional years */
-         mw[++mi][i]=m;
+   int iagemin, iagemax;
-       if(m >=lastpass)
-         break;
+   iagemin= (int) agemin;
-       else
+   iagemax= (int) agemax;
-         m++;
+   /*pp=vector(1,nlstate);*/
-     }/* end while */
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-     if (s[m][i] > nlstate){
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-       mi++;     /* Death is another wave */
+   j1=0;
-       /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
+   j=cptcoveff;
-       mw[mi][i]=m;
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-     }
+   for(k1=1; k1<=j;k1++){
-     wav[i]=mi;
+     for(i1=1; i1<=ncodemax[k1];i1++){
-     if(mi==0){
+       j1++;
-       nbwarn++;
-       if(first==0){
+       for (i=1; i<=nlstate; i++)
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         for(m=iagemin; m <= iagemax+3; m++)
-         first=1;
+           prop[i][m]=0.0;
-       }
-       if(first==1){
+       for (i=1; i<=imx; i++) { /* Each individual */
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         bool=1;
-       }
+         if  (cptcovn>0) {
-     } /* end mi==0 */
+           for (z1=1; z1<=cptcoveff; z1++)
-   } /* End individuals */
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               bool=0;
-   for(i=1; i<=imx; i++){
+         }
-     for(mi=1; mi<wav[i];mi++){
+         if (bool==1) {
-       if (stepm <=0)
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-         dh[mi][i]=1;
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-       else{
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-           if (agedc[i] < 2*AGESUP) {
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+               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(j==0) j=1;  /* Survives at least one month after exam */
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-             else if(j<0){
+                 /*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]]);*/
-               nberr++;
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+                 prop[s[m][i]][iagemax+3] += weight[i];
-               j=1; /* Temporary Dangerous patch */
+               }
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+             }
-               fprintf(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]);
+           } /* end selection of waves */
-               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+         }
-             }
+       }
-             k=k+1;
+       for(i=iagemin; i <= iagemax+3; i++){
-             if (j >= jmax){
-               jmax=j;
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-               ijmax=i;
+           posprop += prop[jk][i];
-             }
+         }
-             if (j <= jmin){
-               jmin=j;
+         for(jk=1; jk <=nlstate ; jk++){
-               ijmin=i;
+           if( i <=  iagemax){
-             }
+             if(posprop>=1.e-5){
-             sum=sum+j;
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             } else
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
            }
-         }
+         }/* end jk */
-         else{
+       }/* end i */
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+     } /* end i1 */
- /*        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]); */
+   } /* end k1 */
-           k=k+1;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-           if (j >= jmax) {
+   /*free_vector(pp,1,nlstate);*/
-             jmax=j;
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-             ijmax=i;
+ }  /* End of prevalence */
-           }
-           else if (j <= jmin){
+ /************* Waves Concatenation ***************/
-             jmin=j;
-             ijmin=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 (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual 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]);*/
+      Death is a valid wave (if date is known).
-           if(j<0){
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-             nberr++;
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+      and mw[mi+1][i]. dh depends on stepm.
-             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]);
+      */
-           }
-           sum=sum+j;
+   int i, mi, m;
-         }
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-         jk= j/stepm;
+      double sum=0., jmean=0.;*/
-         jl= j -jk*stepm;
+   int first;
-         ju= j -(jk+1)*stepm;
+   int j, k=0,jk, ju, jl;
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+   double sum=0.;
-           if(jl==0){
+   first=0;
-             dh[mi][i]=jk;
+   jmin=1e+5;
-             bh[mi][i]=0;
+   jmax=-1;
-           }else{ /* We want a negative bias in order to only have interpolation ie
+   jmean=0.;
-                   * at the price of an extra matrix product in likelihood */
+   for(i=1; i<=imx; i++){
-             dh[mi][i]=jk+1;
+     mi=0;
-             bh[mi][i]=ju;
+     m=firstpass;
-           }
+     while(s[m][i] <= nlstate){
-         }else{
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-           if(jl <= -ju){
+         mw[++mi][i]=m;
-             dh[mi][i]=jk;
+       if(m >=lastpass)
-             bh[mi][i]=jl;       /* bias is positive if real duration
+         break;
-                                  * is higher than the multiple of stepm and negative otherwise.
+       else
-                                  */
+         m++;
-           }
+     }/* end while */
-           else{
+     if (s[m][i] > nlstate){
-             dh[mi][i]=jk+1;
+       mi++;     /* Death is another wave */
-             bh[mi][i]=ju;
+       /* if(mi==0)  never been interviewed correctly before death */
-           }
+          /* Only death is a correct wave */
-           if(dh[mi][i]==0){
+       mw[mi][i]=m;
-             dh[mi][i]=1; /* At least one step */
+     }
-             bh[mi][i]=ju; /* At least one step */
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+     wav[i]=mi;
-           }
+     if(mi==0){
-         } /* end if mle */
+       nbwarn++;
-       }
+       if(first==0){
-     } /* end wave */
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-   }
+         first=1;
-   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);
+       if(first==1){
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-  }
+       }
+     } /* end mi==0 */
- /*********** Tricode ****************************/
+   } /* End individuals */
- void tricode(int *Tvar, int **nbcode, int imx)
- {
+   for(i=1; i<=imx; i++){
+     for(mi=1; mi<wav[i];mi++){
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+       if (stepm <=0)
-   int cptcode=0;
+         dh[mi][i]=1;
-   cptcoveff=0;
+       else{
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+           if (agedc[i] < 2*AGESUP) {
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             if(j==0) j=1;  /* Survives at least one month after exam */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+             else if(j<0){
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+               nberr++;
-                                modality*/
+               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]);
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+               j=1; /* Temporary Dangerous patch */
-       Ndum[ij]++; /*store the modality */
+               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);
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+               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 (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+               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);
-                                        Tvar[j]. If V=sex and male is 0 and
+             }
-                                        female is 1, then  cptcode=1.*/
+             k=k+1;
-     }
+             if (j >= jmax){
+               jmax=j;
-     for (i=0; i<=cptcode; i++) {
+               ijmax=i;
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+             }
-     }
+             if (j <= jmin){
+               jmin=j;
-     ij=1;
+               ijmin=i;
-     for (i=1; i<=ncodemax[j]; i++) {
+             }
-       for (k=0; k<= maxncov; k++) {
+             sum=sum+j;
-         if (Ndum[k] != 0) {
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-           nbcode[Tvar[j]][ij]=k;
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+           }
+         }
-           ij++;
+         else{
-         }
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-         if (ij > ncodemax[j]) break;
+ /*        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]); */
-       }
-     }
+           k=k+1;
-   }
+           if (j >= jmax) {
+             jmax=j;
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+             ijmax=i;
+           }
-  for (i=1; i<=ncovmodel-2; i++) {
+           else if (j <= jmin){
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+             jmin=j;
-    ij=Tvar[i];
+             ijmin=i;
-    Ndum[ij]++;
+           }
-  }
+           /*        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]);*/
-  ij=1;
+           if(j<0){
-  for (i=1; i<= maxncov; i++) {
+             nberr++;
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+             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]);
-      Tvaraff[ij]=i; /*For printing */
+             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]);
-      ij++;
+           }
-    }
+           sum=sum+j;
-  }
+         }
+         jk= j/stepm;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+         jl= j -jk*stepm;
- }
+         ju= j -(jk+1)*stepm;
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
- /*********** Health Expectancies ****************/
+           if(jl==0){
+             dh[mi][i]=jk;
- 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[] )
+             bh[mi][i]=0;
+           }else{ /* We want a negative bias in order to only have interpolation ie
- {
+                   * to avoid the price of an extra matrix product in likelihood */
-   /* Health expectancies, no variances */
+             dh[mi][i]=jk+1;
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+             bh[mi][i]=ju;
-   double age, agelim, hf;
+           }
-   double ***p3mat;
+         }else{
-   double eip;
+           if(jl <= -ju){
+             dh[mi][i]=jk;
-   pstamp(ficreseij);
+             bh[mi][i]=jl;       /* bias is positive if real duration
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+                                  * is higher than the multiple of stepm and negative otherwise.
-   fprintf(ficreseij,"# Age");
+                                  */
-   for(i=1; i<=nlstate;i++){
+           }
-     for(j=1; j<=nlstate;j++){
+           else{
-       fprintf(ficreseij," e%1d%1d ",i,j);
+             dh[mi][i]=jk+1;
-     }
+             bh[mi][i]=ju;
-     fprintf(ficreseij," e%1d. ",i);
+           }
-   }
+           if(dh[mi][i]==0){
-   fprintf(ficreseij,"\n");
+             dh[mi][i]=1; /* At least one step */
+             bh[mi][i]=ju; /* At least one step */
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-   if(estepm < stepm){
+           }
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+         } /* end if mle */
-   }
+       }
-   else  hstepm=estepm;
+     } /* end wave */
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   }
-    * This is mainly to measure the difference between two models: for example
+   jmean=sum/k;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-    * progression in between and thus overestimating or underestimating according
+  }
-    * to the curvature of the survival function. If, for the same date, we
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ /*********** Tricode ****************************/
-    * to compare the new estimate of Life expectancy with the same linear
+ void tricode(int *Tvar, int **nbcode, int imx)
-    * hypothesis. A more precise result, taking into account a more precise
+ {
-    * curvature will be obtained if estepm is as small as stepm. */
+   /* Uses cptcovn+2*cptcovprod as the number of covariates */
+   /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-      nhstepm is the number of hstepm from age to agelim
+   int modmaxcovj=0; /* Modality max of covariates j */
-      nstepm is the number of stepm from age to agelin.
+   cptcoveff=0;
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like estepm months */
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-      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
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
-      results. So we changed our mind and took the option of the best precision.
+                                modality of this covariate Vj*/
-   */
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+                                       modality of the nth covariate of individual i. */
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-   agelim=AGESUP;
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-   /* If stepm=6 months */
+       if (ij > modmaxcovj) modmaxcovj=ij;
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       /* getting the maximum value of the modality of the covariate
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+          female is 1, then modmaxcovj=1.*/
- /* nhstepm age range expressed in number of stepm */
+     }
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
-   /* if (stepm >= YEARM) hstepm=1;*/
+       if( Ndum[i] != 0 )
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         ncodemax[j]++;
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       /* Number of modalities of the j th covariate. In fact
+          ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   for (age=bage; age<=fage; age ++){
+          historical reasons */
+     } /* Ndum[-1] number of undefined modalities */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     ij=1;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
+       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
-     printf("%d|",(int)age);fflush(stdout);
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      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; */
-     /* Computing expectancies */
+           ij++;
-     for(i=1; i<=nlstate;i++)
+         }
-       for(j=1; j<=nlstate;j++)
+         if (ij > ncodemax[j]) break;
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+       }  /* end of loop on */
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+     } /* end of loop on modality */
+   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-           /*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 (k=0; k< maxncov; k++) Ndum[k]=0;
-         }
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
-     fprintf(ficreseij,"%3.0f",age );
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     for(i=1; i<=nlstate;i++){
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-       eip=0;
+    Ndum[ij]++;
-       for(j=1; j<=nlstate;j++){
+  }
-         eip +=eij[i][j][(int)age];
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+  ij=1;
-       }
+  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-       fprintf(ficreseij,"%9.4f", eip );
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-     }
+      Tvaraff[ij]=i; /*For printing */
-     fprintf(ficreseij,"\n");
+      ij++;
+    }
-   }
+  }
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  ij--;
-   printf("\n");
+  cptcoveff=ij; /*Number of simple covariates*/
-   fprintf(ficlog,"\n");
+ }
- }
+ /*********** Health Expectancies ****************/
- void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
  {
-   /* Covariances of health expectancies eij and of total life expectancies according
+   /* Health expectancies, no variances */
-    to initial status i, ei. .
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-   */
+   int nhstepma, nstepma; /* Decreasing with age */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   double age, agelim, hf;
-   double age, agelim, hf;
+   double ***p3mat;
-   double ***p3matp, ***p3matm, ***varhe;
+   double eip;
-   double **dnewm,**doldm;
-   double *xp, *xm;
+   pstamp(ficreseij);
-   double **gp, **gm;
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
-   double ***gradg, ***trgradg;
+   fprintf(ficreseij,"# Age");
-   int theta;
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++){
-   double eip, vip;
+       fprintf(ficreseij," e%1d%1d ",i,j);
+     }
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+     fprintf(ficreseij," e%1d. ",i);
-   xp=vector(1,npar);
+   }
-   xm=vector(1,npar);
+   fprintf(ficreseij,"\n");
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+   if(estepm < stepm){
-   pstamp(ficresstdeij);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+   }
-   fprintf(ficresstdeij,"# Age");
+   else  hstepm=estepm;
-   for(i=1; i<=nlstate;i++){
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     for(j=1; j<=nlstate;j++)
+    * This is mainly to measure the difference between two models: for example
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     fprintf(ficresstdeij," e%1d. ",i);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   }
+    * progression in between and thus overestimating or underestimating according
-   fprintf(ficresstdeij,"\n");
+    * to the curvature of the survival function. If, for the same date, we
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   pstamp(ficrescveij);
+    * to compare the new estimate of Life expectancy with the same linear
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+    * hypothesis. A more precise result, taking into account a more precise
-   fprintf(ficrescveij,"# Age");
+    * curvature will be obtained if estepm is as small as stepm. */
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++){
+   /* For example we decided to compute the life expectancy with the smallest unit */
-       cptj= (j-1)*nlstate+i;
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       for(i2=1; i2<=nlstate;i2++)
+      nhstepm is the number of hstepm from age to agelim
-         for(j2=1; j2<=nlstate;j2++){
+      nstepm is the number of stepm from age to agelin.
-           cptj2= (j2-1)*nlstate+i2;
+      Look at hpijx to understand the reason of that which relies in memory size
-           if(cptj2 <= cptj)
+      and note for a fixed period like estepm months */
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         }
+      survival function given by stepm (the optimization length). Unfortunately it
-     }
+      means that if the survival funtion is printed only each two years of age and if
-   fprintf(ficrescveij,"\n");
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+      results. So we changed our mind and took the option of the best precision.
-   if(estepm < stepm){
+   */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   }
-   else  hstepm=estepm;
+   agelim=AGESUP;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   /* If stepm=6 months */
-    * This is mainly to measure the difference between two models: for example
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
-    * progression in between and thus overestimating or underestimating according
+ /* nhstepm age range expressed in number of stepm */
-    * to the curvature of the survival function. If, for the same date, we
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-    * to compare the new estimate of Life expectancy with the same linear
+   /* if (stepm >= YEARM) hstepm=1;*/
-    * hypothesis. A more precise result, taking into account a more precise
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-    * curvature will be obtained if estepm is as small as stepm. */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   for (age=bage; age<=fage; age ++){
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-      nhstepm is the number of hstepm from age to agelim
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-      nstepm is the number of stepm from age to agelin.
+     /* if (stepm >= YEARM) hstepm=1;*/
-      Look at hpijx to understand the reason of that which relies in memory size
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-      and note for a fixed period like estepm months */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     /* If stepm=6 months */
-      survival function given by stepm (the optimization length). Unfortunately it
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-      means that if the survival funtion is printed only each two years of age and if
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   /* If stepm=6 months */
+     printf("%d|",(int)age);fflush(stdout);
-   /* nhstepm age range expressed in number of stepm */
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   agelim=AGESUP;
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+     /* Computing expectancies */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+     for(i=1; i<=nlstate;i++)
-   /* if (stepm >= YEARM) hstepm=1;*/
+       for(j=1; j<=nlstate;j++)
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         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;
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /* 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]);*/
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+         }
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+     fprintf(ficreseij,"%3.0f",age );
+     for(i=1; i<=nlstate;i++){
-   for (age=bage; age<=fage; age ++){
+       eip=0;
+       for(j=1; j<=nlstate;j++){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+         eip +=eij[i][j][(int)age];
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       fprintf(ficreseij,"%9.4f", eip );
+     }
-     /* Computing  Variances of health expectancies */
+     fprintf(ficreseij,"\n");
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-        decrease memory allocation */
+   }
-     for(theta=1; theta <=npar; theta++){
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(i=1; i<=npar; i++){
+   printf("\n");
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   fprintf(ficlog,"\n");
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-       }
+ }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+ void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-       for(j=1; j<= nlstate; j++){
+ {
-         for(i=1; i<=nlstate; i++){
+   /* Covariances of health expectancies eij and of total life expectancies according
-           for(h=0; h<=nhstepm-1; h++){
+    to initial status i, ei. .
-             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.;
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-           }
+   int nhstepma, nstepma; /* Decreasing with age */
-         }
+   double age, agelim, hf;
-       }
+   double ***p3matp, ***p3matm, ***varhe;
+   double **dnewm,**doldm;
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+   double *xp, *xm;
-         for(h=0; h<=nhstepm-1; h++){
+   double **gp, **gm;
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+   double ***gradg, ***trgradg;
-         }
+   int theta;
-     }/* End theta */
+   double eip, vip;
-     for(h=0; h<=nhstepm-1; h++)
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-       for(j=1; j<=nlstate*nlstate;j++)
+   xp=vector(1,npar);
-         for(theta=1; theta <=npar; theta++)
+   xm=vector(1,npar);
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   pstamp(ficresstdeij);
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-         varhe[ij][ji][(int)age] =0.;
+   fprintf(ficresstdeij,"# Age");
+   for(i=1; i<=nlstate;i++){
-      printf("%d|",(int)age);fflush(stdout);
+     for(j=1; j<=nlstate;j++)
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-      for(h=0;h<=nhstepm-1;h++){
+     fprintf(ficresstdeij," e%1d. ",i);
-       for(k=0;k<=nhstepm-1;k++){
+   }
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+   fprintf(ficresstdeij,"\n");
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+   pstamp(ficrescveij);
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+   fprintf(ficrescveij,"# Age");
-       }
+   for(i=1; i<=nlstate;i++)
-     }
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
-     /* Computing expectancies */
+       for(i2=1; i2<=nlstate;i2++)
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+         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)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+         }
+     }
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+   fprintf(ficrescveij,"\n");
-         }
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     fprintf(ficresstdeij,"%3.0f",age );
+   }
-     for(i=1; i<=nlstate;i++){
+   else  hstepm=estepm;
-       eip=0.;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-       vip=0.;
+    * 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
-         eip += eij[i][j][(int)age];
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+    * progression in between and thus overestimating or underestimating according
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+    * to the curvature of the survival function. If, for the same date, we
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-       }
+    * to compare the new estimate of Life expectancy with the same linear
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+    * hypothesis. A more precise result, taking into account a more precise
-     }
+    * curvature will be obtained if estepm is as small as stepm. */
-     fprintf(ficresstdeij,"\n");
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     fprintf(ficrescveij,"%3.0f",age );
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     for(i=1; i<=nlstate;i++)
+      nhstepm is the number of hstepm from age to agelim
-       for(j=1; j<=nlstate;j++){
+      nstepm is the number of stepm from age to agelin.
-         cptj= (j-1)*nlstate+i;
+      Look at hpijx to understand the reason of that which relies in memory size
-         for(i2=1; i2<=nlstate;i2++)
+      and note for a fixed period like estepm months */
-           for(j2=1; j2<=nlstate;j2++){
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-             cptj2= (j2-1)*nlstate+i2;
+      survival function given by stepm (the optimization length). Unfortunately it
-             if(cptj2 <= cptj)
+      means that if the survival funtion is printed only each two years of age and if
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+      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.
-       }
+   */
-     fprintf(ficrescveij,"\n");
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   }
+   /* If stepm=6 months */
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   /* nhstepm age range expressed in number of stepm */
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+   agelim=AGESUP;
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* if (stepm >= YEARM) hstepm=1;*/
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-   printf("\n");
-   fprintf(ficlog,"\n");
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_vector(xm,1,npar);
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-   free_vector(xp,1,npar);
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
- }
+   for (age=bage; age<=fage; age ++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
- /************ Variance ******************/
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- 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 (stepm >= YEARM) hstepm=1;*/
- {
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     /* If stepm=6 months */
-   /* double **newm;*/
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   double **dnewm,**doldm;
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   double **dnewmp,**doldmp;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   int k, cptcode;
-   double *xp;
+     /* Computing  Variances of health expectancies */
-   double **gp, **gm;  /* for var eij */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-   double ***gradg, ***trgradg; /*for var eij */
+        decrease memory allocation */
-   double **gradgp, **trgradgp; /* for var p point j */
+     for(theta=1; theta <=npar; theta++){
-   double *gpp, *gmp; /* for var p point j */
+       for(i=1; i<=npar; i++){
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   double ***p3mat;
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-   double age,agelim, hf;
+       }
-   double ***mobaverage;
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   int theta;
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   char digit[4];
-   char digitp[25];
+       for(j=1; j<= nlstate; j++){
+         for(i=1; i<=nlstate; i++){
-   char fileresprobmorprev[FILENAMELENGTH];
+           for(h=0; h<=nhstepm-1; h++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   if(popbased==1){
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-     if(mobilav!=0)
+           }
-       strcpy(digitp,"-populbased-mobilav-");
+         }
-     else strcpy(digitp,"-populbased-nomobil-");
+       }
-   }
-   else
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-     strcpy(digitp,"-stablbased-");
+         for(h=0; h<=nhstepm-1; h++){
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   if (mobilav!=0) {
+         }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     }/* End theta */
-     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);
+     for(h=0; h<=nhstepm-1; h++)
-     }
+       for(j=1; j<=nlstate*nlstate;j++)
-   }
+         for(theta=1; theta <=npar; theta++)
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   strcpy(fileresprobmorprev,"prmorprev");
-   sprintf(digit,"%-d",ij);
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+         varhe[ij][ji][(int)age] =0.;
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+      printf("%d|",(int)age);fflush(stdout);
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+      for(h=0;h<=nhstepm-1;h++){
-   }
+       for(k=0;k<=nhstepm-1;k++){
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   pstamp(ficresprobmorprev);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   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);
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+       }
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+     }
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
+     /* Computing expectancies */
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   }
+     for(i=1; i<=nlstate;i++)
-   fprintf(ficresprobmorprev,"\n");
+       for(j=1; j<=nlstate;j++)
-   fprintf(ficgp,"\n# Routine varevsij");
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+           /* 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]);*/
- /*   } */
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+         }
-   pstamp(ficresvij);
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+     fprintf(ficresstdeij,"%3.0f",age );
-   if(popbased==1)
+     for(i=1; i<=nlstate;i++){
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+       eip=0.;
-   else
+       vip=0.;
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+       for(j=1; j<=nlstate;j++){
-   fprintf(ficresvij,"# Age");
+         eip += eij[i][j][(int)age];
-   for(i=1; i<=nlstate;i++)
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-     for(j=1; j<=nlstate;j++)
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-   fprintf(ficresvij,"\n");
+       }
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   xp=vector(1,npar);
+     }
-   dnewm=matrix(1,nlstate,1,npar);
+     fprintf(ficresstdeij,"\n");
-   doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+     fprintf(ficrescveij,"%3.0f",age );
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+         cptj= (j-1)*nlstate+i;
-   gpp=vector(nlstate+1,nlstate+ndeath);
+         for(i2=1; i2<=nlstate;i2++)
-   gmp=vector(nlstate+1,nlstate+ndeath);
+           for(j2=1; j2<=nlstate;j2++){
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+             cptj2= (j2-1)*nlstate+i2;
+             if(cptj2 <= cptj)
-   if(estepm < stepm){
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+           }
-   }
+       }
-   else  hstepm=estepm;
+     fprintf(ficrescveij,"\n");
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   }
-      nhstepm is the number of hstepm from age to agelim
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-      nstepm is the number of stepm from age to agelin.
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-      Look at hpijx to understand the reason of that which relies in memory size
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-      and note for a fixed period like k years */
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-      survival function given by stepm (the optimization length). Unfortunately it
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-      means that if the survival funtion is printed every two years of age and if
+   printf("\n");
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   fprintf(ficlog,"\n");
-      results. So we changed our mind and took the option of the best precision.
-   */
+   free_vector(xm,1,npar);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   free_vector(xp,1,npar);
-   agelim = AGESUP;
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ }
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+ /************ Variance ******************/
-     gp=matrix(0,nhstepm,1,nlstate);
+ 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[])
-     gm=matrix(0,nhstepm,1,nlstate);
+ {
+   /* Variance of health expectancies */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-     for(theta=1; theta <=npar; theta++){
+   /* double **newm;*/
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   double **dnewm,**doldm;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   double **dnewmp,**doldmp;
-       }
+   int i, j, nhstepm, hstepm, h, nstepm ;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   int k, cptcode;
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   double *xp;
+   double **gp, **gm;  /* for var eij */
-       if (popbased==1) {
+   double ***gradg, ***trgradg; /*for var eij */
-         if(mobilav ==0){
+   double **gradgp, **trgradgp; /* for var p point j */
-           for(i=1; i<=nlstate;i++)
+   double *gpp, *gmp; /* for var p point j */
-             prlim[i][i]=probs[(int)age][i][ij];
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-         }else{ /* mobilav */
+   double ***p3mat;
-           for(i=1; i<=nlstate;i++)
+   double age,agelim, hf;
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   double ***mobaverage;
-         }
+   int theta;
-       }
+   char digit[4];
+   char digitp[25];
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+   char fileresprobmorprev[FILENAMELENGTH];
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+   if(popbased==1){
-         }
+     if(mobilav!=0)
-       }
+       strcpy(digitp,"-populbased-mobilav-");
-       /* This for computing probability of death (h=1 means
+     else strcpy(digitp,"-populbased-nomobil-");
-          computed over hstepm matrices product = hstepm*stepm months)
+   }
-          as a weighted average of prlim.
+   else
-       */
+     strcpy(digitp,"-stablbased-");
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+   if (mobilav!=0) {
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       }
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       /* end probability of death */
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       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);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   strcpy(fileresprobmorprev,"prmorprev");
+   sprintf(digit,"%-d",ij);
-       if (popbased==1) {
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-         if(mobilav ==0){
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-           for(i=1; i<=nlstate;i++)
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-             prlim[i][i]=probs[(int)age][i][ij];
+   strcat(fileresprobmorprev,fileres);
-         }else{ /* mobilav */
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-           for(i=1; i<=nlstate;i++)
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-         }
+   }
-       }
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-       for(j=1; j<= nlstate; j++){
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-         for(h=0; h<=nhstepm; h++){
+   pstamp(ficresprobmorprev);
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-         }
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       }
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-       /* This for computing probability of death (h=1 means
+     for(i=1; i<=nlstate;i++)
-          computed over hstepm matrices product = hstepm*stepm months)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-          as a weighted average of prlim.
+   }
-       */
+   fprintf(ficresprobmorprev,"\n");
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   fprintf(ficgp,"\n# Routine varevsij");
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-       }
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-       /* end probability of death */
+ /*   } */
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       for(j=1; j<= nlstate; j++) /* vareij */
+   pstamp(ficresvij);
-         for(h=0; h<=nhstepm; h++){
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   if(popbased==1)
-         }
+     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
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   fprintf(ficresvij,"# Age");
-       }
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=nlstate;j++)
-     } /* End theta */
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+   fprintf(ficresvij,"\n");
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   xp=vector(1,npar);
-     for(h=0; h<=nhstepm; h++) /* veij */
+   dnewm=matrix(1,nlstate,1,npar);
-       for(j=1; j<=nlstate;j++)
+   doldm=matrix(1,nlstate,1,nlstate);
-         for(theta=1; theta <=npar; theta++)
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-       for(theta=1; theta <=npar; theta++)
+   gpp=vector(nlstate+1,nlstate+ndeath);
-         trgradgp[j][theta]=gradgp[theta][j];
+   gmp=vector(nlstate+1,nlstate+ndeath);
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   if(estepm < stepm){
-     for(i=1;i<=nlstate;i++)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-       for(j=1;j<=nlstate;j++)
+   }
-         vareij[i][j][(int)age] =0.;
+   else  hstepm=estepm;
+   /* For example we decided to compute the life expectancy with the smallest unit */
-     for(h=0;h<=nhstepm;h++){
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       for(k=0;k<=nhstepm;k++){
+      nhstepm is the number of hstepm from age to agelim
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+      nstepm is the number of stepm from age to agelin.
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-         for(i=1;i<=nlstate;i++)
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-           for(j=1;j<=nlstate;j++)
+      survival function given by stepm (the optimization length). Unfortunately it
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+      means that if the survival funtion is printed every two years of age and if
-       }
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     }
+      results. So we changed our mind and took the option of the best precision.
+   */
-     /* pptj */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+   agelim = AGESUP;
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         varppt[j][i]=doldmp[j][i];
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* end ppptj */
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     /*  x centered again */
+     gp=matrix(0,nhstepm,1,nlstate);
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+     gm=matrix(0,nhstepm,1,nlstate);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-     if (popbased==1) {
+     for(theta=1; theta <=npar; theta++){
-       if(mobilav ==0){
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-         for(i=1; i<=nlstate;i++)
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-           prlim[i][i]=probs[(int)age][i][ij];
+       }
-       }else{ /* mobilav */
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         for(i=1; i<=nlstate;i++)
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-           prlim[i][i]=mobaverage[(int)age][i][ij];
-       }
+       if (popbased==1) {
-     }
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-     /* This for computing probability of death (h=1 means
+             prlim[i][i]=probs[(int)age][i][ij];
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+         }else{ /* mobilav */
-        as a weighted average of prlim.
+           for(i=1; i<=nlstate;i++)
-     */
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         }
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+       }
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     }
+       for(j=1; j<= nlstate; j++){
-     /* end probability of death */
+         for(h=0; h<=nhstepm; h++){
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+         }
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       }
-       for(i=1; i<=nlstate;i++){
+       /* This for computing probability of death (h=1 means
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+          computed over hstepm matrices product = hstepm*stepm months)
-       }
+          as a weighted average of prlim.
-     }
+       */
-     fprintf(ficresprobmorprev,"\n");
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-     fprintf(ficresvij,"%.0f ",age );
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-     for(i=1; i<=nlstate;i++)
+       }
-       for(j=1; j<=nlstate;j++){
+       /* end probability of death */
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-       }
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-     fprintf(ficresvij,"\n");
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-     free_matrix(gp,0,nhstepm,1,nlstate);
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+       if (popbased==1) {
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         if(mobilav ==0){
-   } /* End age */
+           for(i=1; i<=nlstate;i++)
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+             prlim[i][i]=probs[(int)age][i][ij];
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+         }else{ /* mobilav */
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+           for(i=1; i<=nlstate;i++)
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+         }
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+       }
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+         for(h=0; h<=nhstepm; h++){
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+         }
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+       }
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+       /* This for computing probability of death (h=1 means
-   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);
+          computed over hstepm matrices product = hstepm*stepm months)
-   /*  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);
+          as a weighted average of prlim.
- */
+       */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-   free_vector(xp,1,npar);
+       }
-   free_matrix(doldm,1,nlstate,1,nlstate);
+       /* end probability of death */
-   free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       for(j=1; j<= nlstate; j++) /* vareij */
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+         for(h=0; h<=nhstepm; h++){
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         }
-   fclose(ficresprobmorprev);
-   fflush(ficgp);
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-   fflush(fichtm);
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
- }  /* end varevsij */
+       }
- /************ Variance of prevlim ******************/
+     } /* End theta */
- 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[])
- {
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   /* Variance of prevalence limit */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+     for(h=0; h<=nhstepm; h++) /* veij */
-   double **newm;
+       for(j=1; j<=nlstate;j++)
-   double **dnewm,**doldm;
+         for(theta=1; theta <=npar; theta++)
-   int i, j, nhstepm, hstepm;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   int k, cptcode;
-   double *xp;
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-   double *gp, *gm;
+       for(theta=1; theta <=npar; theta++)
-   double **gradg, **trgradg;
+         trgradgp[j][theta]=gradgp[theta][j];
-   double age,agelim;
-   int theta;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   pstamp(ficresvpl);
+     for(i=1;i<=nlstate;i++)
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+       for(j=1;j<=nlstate;j++)
-   fprintf(ficresvpl,"# Age");
+         vareij[i][j][(int)age] =0.;
-   for(i=1; i<=nlstate;i++)
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     for(h=0;h<=nhstepm;h++){
-   fprintf(ficresvpl,"\n");
+       for(k=0;k<=nhstepm;k++){
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-   xp=vector(1,npar);
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-   dnewm=matrix(1,nlstate,1,npar);
+         for(i=1;i<=nlstate;i++)
-   doldm=matrix(1,nlstate,1,nlstate);
+           for(j=1;j<=nlstate;j++)
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-   hstepm=1*YEARM; /* Every year of age */
+       }
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+     }
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+     /* pptj */
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-     if (stepm >= YEARM) hstepm=1;
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-     gradg=matrix(1,npar,1,nlstate);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-     gp=vector(1,nlstate);
+         varppt[j][i]=doldmp[j][i];
-     gm=vector(1,nlstate);
+     /* end ppptj */
+     /*  x centered again */
-     for(theta=1; theta <=npar; theta++){
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-       }
+     if (popbased==1) {
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if(mobilav ==0){
-       for(i=1;i<=nlstate;i++)
+         for(i=1; i<=nlstate;i++)
-         gp[i] = prlim[i][i];
+           prlim[i][i]=probs[(int)age][i][ij];
+       }else{ /* mobilav */
-       for(i=1; i<=npar; i++) /* Computes gradient */
+         for(i=1; i<=nlstate;i++)
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       }
-       for(i=1;i<=nlstate;i++)
+     }
-         gm[i] = prlim[i][i];
+     /* This for computing probability of death (h=1 means
-       for(i=1;i<=nlstate;i++)
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+        as a weighted average of prlim.
-     } /* End theta */
+     */
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     trgradg =matrix(1,nlstate,1,npar);
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     for(j=1; j<=nlstate;j++)
+     }
-       for(theta=1; theta <=npar; theta++)
+     /* end probability of death */
-         trgradg[j][theta]=gradg[theta][j];
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(i=1;i<=nlstate;i++)
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       varpl[i][(int)age] =0.;
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+       for(i=1; i<=nlstate;i++){
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-     for(i=1;i<=nlstate;i++)
+       }
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     }
+     fprintf(ficresprobmorprev,"\n");
-     fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+     fprintf(ficresvij,"%.0f ",age );
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+     for(i=1; i<=nlstate;i++)
-     fprintf(ficresvpl,"\n");
+       for(j=1; j<=nlstate;j++){
-     free_vector(gp,1,nlstate);
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-     free_vector(gm,1,nlstate);
+       }
-     free_matrix(gradg,1,npar,1,nlstate);
+     fprintf(ficresvij,"\n");
-     free_matrix(trgradg,1,nlstate,1,npar);
+     free_matrix(gp,0,nhstepm,1,nlstate);
-   } /* End age */
+     free_matrix(gm,0,nhstepm,1,nlstate);
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-   free_vector(xp,1,npar);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-   free_matrix(doldm,1,nlstate,1,npar);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   } /* End age */
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
- }
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
- /************ Variance of one-step probabilities  ******************/
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
- void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
- {
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   int i, j=0,  i1, k1, l1, t, tj;
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-   int k2, l2, j1,  z1;
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-   int k=0,l, cptcode;
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   int first=1, first1;
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
-   double **dnewm,**doldm;
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
-   double *xp;
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
-   double *gp, *gm;
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   double **gradg, **trgradg;
+   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);
-   double **mu;
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
-   double age,agelim, cov[NCOVMAX];
+ */
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   int theta;
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+   free_vector(xp,1,npar);
-   char fileresprobcor[FILENAMELENGTH];
+   free_matrix(doldm,1,nlstate,1,nlstate);
+   free_matrix(dnewm,1,nlstate,1,npar);
-   double ***varpij;
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   strcpy(fileresprob,"prob");
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   strcat(fileresprob,fileres);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   fclose(ficresprobmorprev);
-     printf("Problem with resultfile: %s\n", fileresprob);
+   fflush(ficgp);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   fflush(fichtm);
-   }
+ }  /* end varevsij */
-   strcpy(fileresprobcov,"probcov");
-   strcat(fileresprobcov,fileres);
+ /************ Variance of prevlim ******************/
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+ 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[])
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+ {
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   /* Variance of prevalence limit */
-   }
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   strcpy(fileresprobcor,"probcor");
+   double **newm;
-   strcat(fileresprobcor,fileres);
+   double **dnewm,**doldm;
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+   int i, j, nhstepm, hstepm;
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+   int k, cptcode;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+   double *xp;
-   }
+   double *gp, *gm;
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   double **gradg, **trgradg;
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   double age,agelim;
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   int theta;
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresvpl);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   pstamp(ficresprob);
+   fprintf(ficresvpl,"# Age");
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+   for(i=1; i<=nlstate;i++)
-   fprintf(ficresprob,"# Age");
+       fprintf(ficresvpl," %1d-%1d",i,i);
-   pstamp(ficresprobcov);
+   fprintf(ficresvpl,"\n");
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+   xp=vector(1,npar);
-   pstamp(ficresprobcor);
+   dnewm=matrix(1,nlstate,1,npar);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   doldm=matrix(1,nlstate,1,nlstate);
-   fprintf(ficresprobcor,"# Age");
+   hstepm=1*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   for(i=1; i<=nlstate;i++)
+   agelim = AGESUP;
-     for(j=1; j<=(nlstate+ndeath);j++){
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+     if (stepm >= YEARM) hstepm=1;
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     }
+     gradg=matrix(1,npar,1,nlstate);
-  /* fprintf(ficresprob,"\n");
+     gp=vector(1,nlstate);
-   fprintf(ficresprobcov,"\n");
+     gm=vector(1,nlstate);
-   fprintf(ficresprobcor,"\n");
-  */
+     for(theta=1; theta <=npar; theta++){
-  xp=vector(1,npar);
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+       }
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+       for(i=1;i<=nlstate;i++)
-   first=1;
+         gp[i] = prlim[i][i];
-   fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+       for(i=1; i<=npar; i++) /* Computes gradient */
-   fprintf(fichtm,"\n");
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+       for(i=1;i<=nlstate;i++)
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+         gm[i] = prlim[i][i];
-   file %s<br>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+       for(i=1;i<=nlstate;i++)
- and drawn. It helps understanding how is the covariance between two incidences.\
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+     } /* End theta */
-   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 \
+     trgradg =matrix(1,nlstate,1,npar);
- 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>\
+     for(j=1; j<=nlstate;j++)
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+       for(theta=1; theta <=npar; theta++)
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+         trgradg[j][theta]=gradg[theta][j];
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     for(i=1;i<=nlstate;i++)
-   cov[1]=1;
+       varpl[i][(int)age] =0.;
-   tj=cptcoveff;
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-   j1=0;
+     for(i=1;i<=nlstate;i++)
-   for(t=1; t<=tj;t++){
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-     for(i1=1; i1<=ncodemax[t];i1++){
-       j1++;
+     fprintf(ficresvpl,"%.0f ",age );
-       if  (cptcovn>0) {
+     for(i=1; i<=nlstate;i++)
-         fprintf(ficresprob, "\n#********** Variable ");
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     fprintf(ficresvpl,"\n");
-         fprintf(ficresprob, "**********\n#\n");
+     free_vector(gp,1,nlstate);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+     free_vector(gm,1,nlstate);
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     free_matrix(gradg,1,npar,1,nlstate);
-         fprintf(ficresprobcov, "**********\n#\n");
+     free_matrix(trgradg,1,nlstate,1,npar);
+   } /* End age */
-         fprintf(ficgp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   free_vector(xp,1,npar);
-         fprintf(ficgp, "**********\n#\n");
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+ }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+ /************ Variance of one-step probabilities  ******************/
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-         fprintf(ficresprobcor, "\n#********** Variable ");
+ {
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   int i, j=0,  i1, k1, l1, t, tj;
-         fprintf(ficresprobcor, "**********\n#");
+   int k2, l2, j1,  z1;
-       }
+   int k=0,l, cptcode;
+   int first=1, first1;
-       for (age=bage; age<=fage; age ++){
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-         cov[2]=age;
+   double **dnewm,**doldm;
-         for (k=1; k<=cptcovn;k++) {
+   double *xp;
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   double *gp, *gm;
-         }
+   double **gradg, **trgradg;
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   double **mu;
-         for (k=1; k<=cptcovprod;k++)
+   double age,agelim, cov[NCOVMAX];
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   int theta;
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   char fileresprob[FILENAMELENGTH];
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   char fileresprobcov[FILENAMELENGTH];
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+   char fileresprobcor[FILENAMELENGTH];
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   double ***varpij;
-         for(theta=1; theta <=npar; theta++){
-           for(i=1; i<=npar; i++)
+   strcpy(fileresprob,"prob");
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   strcat(fileresprob,fileres);
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     printf("Problem with resultfile: %s\n", fileresprob);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-           k=0;
+   }
-           for(i=1; i<= (nlstate); i++){
+   strcpy(fileresprobcov,"probcov");
-             for(j=1; j<=(nlstate+ndeath);j++){
+   strcat(fileresprobcov,fileres);
-               k=k+1;
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-               gp[k]=pmmij[i][j];
+     printf("Problem with resultfile: %s\n", fileresprobcov);
-             }
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-           }
+   }
+   strcpy(fileresprobcor,"probcor");
-           for(i=1; i<=npar; i++)
+   strcat(fileresprobcor,fileres);
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-           k=0;
+   }
-           for(i=1; i<=(nlstate); i++){
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-             for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-               k=k+1;
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-               gm[k]=pmmij[i][j];
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-             }
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-           }
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   pstamp(ficresprob);
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+   fprintf(ficresprob,"# Age");
-         }
+   pstamp(ficresprobcov);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+   fprintf(ficresprobcov,"# Age");
-           for(theta=1; theta <=npar; theta++)
+   pstamp(ficresprobcor);
-             trgradg[j][theta]=gradg[theta][j];
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   fprintf(ficresprobcor,"# Age");
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   for(i=1; i<=nlstate;i++)
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+     for(j=1; j<=(nlstate+ndeath);j++){
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+     }
+  /* fprintf(ficresprob,"\n");
-         k=0;
+   fprintf(ficresprobcov,"\n");
-         for(i=1; i<=(nlstate); i++){
+   fprintf(ficresprobcor,"\n");
-           for(j=1; j<=(nlstate+ndeath);j++){
+  */
-             k=k+1;
+   xp=vector(1,npar);
-             mu[k][(int) age]=pmmij[i][j];
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-           }
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-         }
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+   first=1;
-             varpij[i][j][(int)age] = doldm[i][j];
+   fprintf(ficgp,"\n# Routine varprob");
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-         /*printf("\n%d ",(int)age);
+   fprintf(fichtm,"\n");
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-           }*/
+   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-         fprintf(ficresprob,"\n%d ",(int)age);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+   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 \
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+ standard deviations wide on each axis. <br>\
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-         }
-         i=0;
+   cov[1]=1;
-         for (k=1; k<=(nlstate);k++){
+   tj=cptcoveff;
-           for (l=1; l<=(nlstate+ndeath);l++){
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-             i=i++;
+   j1=0;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+   for(t=1; t<=tj;t++){
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+     for(i1=1; i1<=ncodemax[t];i1++){
-             for (j=1; j<=i;j++){
+       j1++;
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+       if  (cptcovn>0) {
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+         fprintf(ficresprob, "\n#********** Variable ");
-             }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-           }
+         fprintf(ficresprob, "**********\n#\n");
-         }/* end of loop for state */
+         fprintf(ficresprobcov, "\n#********** Variable ");
-       } /* end of loop for age */
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprobcov, "**********\n#\n");
-       /* Confidence intervalle of pij  */
-       /*
+         fprintf(ficgp, "\n#********** Variable ");
-         fprintf(ficgp,"\nset noparametric;unset label");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+         fprintf(ficgp, "**********\n#\n");
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-       */
+         fprintf(ficresprobcor, "\n#********** Variable ");
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       first1=1;
+         fprintf(ficresprobcor, "**********\n#");
-       for (k2=1; k2<=(nlstate);k2++){
+       }
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
+       for (age=bage; age<=fage; age ++){
-           j=(k2-1)*(nlstate+ndeath)+l2;
+         cov[2]=age;
-           for (k1=1; k1<=(nlstate);k1++){
+         for (k=1; k<=cptcovn;k++) {
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
-               if(l1==k1) continue;
+         }
-               i=(k1-1)*(nlstate+ndeath)+l1;
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-               if(i<=j) continue;
+         for (k=1; k<=cptcovprod;k++)
-               for (age=bage; age<=fage; age ++){
+           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-                 if ((int)age %5==0){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
-                   mu2=mu[j][(int) age]/stepm*YEARM;
-                   c12=cv12/sqrt(v1*v2);
+         for(theta=1; theta <=npar; theta++){
-                   /* Computing eigen value of matrix of covariance */
+           for(i=1; i<=npar; i++)
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   /* Eigen vectors */
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+           k=0;
-                   v21=(lc1-v1)/cv12*v11;
+           for(i=1; i<= (nlstate); i++){
-                   v12=-v21;
+             for(j=1; j<=(nlstate+ndeath);j++){
-                   v22=v11;
+               k=k+1;
-                   tnalp=v21/v11;
+               gp[k]=pmmij[i][j];
-                   if(first1==1){
+             }
-                     first1=0;
+           }
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-                   }
+           for(i=1; i<=npar; i++)
-                   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);
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-                   /*printf(fignu*/
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+           k=0;
-                   if(first==1){
+           for(i=1; i<=(nlstate); i++){
-                     first=0;
+             for(j=1; j<=(nlstate+ndeath);j++){
-                     fprintf(ficgp,"\nset parametric;unset label");
+               k=k+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);
+               gm[k]=pmmij[i][j];
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+             }
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+           }
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-                             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);
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+           for(theta=1; theta <=npar; theta++)
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+             trgradg[j][theta]=gradg[theta][j];
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-                   }else{
+         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-                     first=0;
+         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+         k=0;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+         for(i=1; i<=(nlstate); i++){
-                   }/* if first */
+           for(j=1; j<=(nlstate+ndeath);j++){
-                 } /* age mod 5 */
+             k=k+1;
-               } /* end loop age */
+             mu[k][(int) age]=pmmij[i][j];
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+           }
-               first=1;
+         }
-             } /*l12 */
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           } /* k12 */
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-         } /*l1 */
+             varpij[i][j][(int)age] = doldm[i][j];
-       }/* k1 */
-     } /* loop covariates */
+         /*printf("\n%d ",(int)age);
-   }
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+           }*/
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_vector(xp,1,npar);
+         fprintf(ficresprob,"\n%d ",(int)age);
-   fclose(ficresprob);
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-   fclose(ficresprobcov);
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-   fclose(ficresprobcor);
-   fflush(ficgp);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-   fflush(fichtmcov);
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
- }
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
- /******************* Printing html file ***********/
+         }
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+         i=0;
-                   int lastpass, int stepm, int weightopt, char model[],\
+         for (k=1; k<=(nlstate);k++){
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+           for (l=1; l<=(nlstate+ndeath);l++){
-                   int popforecast, int estepm ,\
+             i=i++;
-                   double jprev1, double mprev1,double anprev1, \
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-                   double jprev2, double mprev2,double anprev2){
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   int jj1, k1, i1, cpt;
+             for (j=1; j<=i;j++){
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-    <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 \
+         }/* end of loop for state */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+       } /* end of loop for age */
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-    fprintf(fichtm,"\
+       /* Confidence intervalle of pij  */
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+       /*
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+         fprintf(ficgp,"\nunset parametric;unset label");
-    fprintf(fichtm,"\
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+         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,"\
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-  - (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,"\nset out \"pijgr%s.png\"",optionfilefiname);
-    <a href=\"%s\">%s</a> <br>\n",
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+       */
-    fprintf(fichtm,"\
-  - Population projections by age and states: \
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+       first1=1;
+       for (k2=1; k2<=(nlstate);k2++){
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
+           if(l2==k2) continue;
-  m=cptcoveff;
+           j=(k2-1)*(nlstate+ndeath)+l2;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+           for (k1=1; k1<=(nlstate);k1++){
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-  jj1=0;
+               if(l1==k1) continue;
-  for(k1=1; k1<=m;k1++){
+               i=(k1-1)*(nlstate+ndeath)+l1;
-    for(i1=1; i1<=ncodemax[k1];i1++){
+               if(i<=j) continue;
-      jj1++;
+               for (age=bage; age<=fage; age ++){
-      if (cptcovn > 0) {
+                 if ((int)age %5==0){
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-      }
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-      /* Pij */
+                   c12=cv12/sqrt(v1*v2);
-      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> \
+                   /* Computing eigen value of matrix of covariance */
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-      /* Quasi-incidences */
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+                   if ((lc2 <0) || (lc1 <0) ){
-  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> \
+                     printf("Error: 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. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+                     fprintf(ficlog,"Error: 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", lc1, lc2, v1, v2, cv12);fflush(ficlog);
-        /* Period (stable) prevalence in each health state */
+                     lc1=fabs(lc1);
-        for(cpt=1; cpt<nlstate;cpt++){
+                     lc2=fabs(lc2);
-          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);
-        }
+                   /* Eigen vectors */
-      for(cpt=1; cpt<=nlstate;cpt++) {
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-         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> \
+                   /*v21=sqrt(1.-v11*v11); *//* error */
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+                   v21=(lc1-v1)/cv12*v11;
-      }
+                   v12=-v21;
-    } /* end i1 */
+                   v22=v11;
-  }/* End k1 */
+                   tnalp=v21/v11;
-  fprintf(fichtm,"</ul>");
+                   if(first1==1){
+                     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);
-  fprintf(fichtm,"\
+                   }
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+                   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);
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+                   /*printf(fignu*/
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+                   if(first==1){
-  fprintf(fichtm,"\
+                     first=0;
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                     fprintf(ficgp,"\nset parametric;unset label");
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-  fprintf(fichtm,"\
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-  fprintf(fichtm,"\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-  - 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): \
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-  fprintf(fichtm,"\
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-  fprintf(fichtm,"\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-  - 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",
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+                   }else{
-  fprintf(fichtm,"\
+                     first=0;
-  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-  fprintf(fichtm,"\
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+                     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",\
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+                   }/* if first */
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+                 } /* age mod 5 */
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+               } /* end loop age */
- /*      <br>",fileres,fileres,fileres,fileres); */
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- /*  else  */
+               first=1;
- /*    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); */
+             } /*l12 */
-  fflush(fichtm);
+           } /* k12 */
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+         } /*l1 */
+       }/* k1 */
-  m=cptcoveff;
+     } /* loop covariates */
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+   }
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-  jj1=0;
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-  for(k1=1; k1<=m;k1++){
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-    for(i1=1; i1<=ncodemax[k1];i1++){
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-      jj1++;
+   free_vector(xp,1,npar);
-      if (cptcovn > 0) {
+   fclose(ficresprob);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+   fclose(ficresprobcov);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+   fclose(ficresprobcor);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   fflush(ficgp);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fflush(fichtmcov);
-      }
+ }
-      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+ /******************* Printing html file ***********/
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-      }
+                   int lastpass, int stepm, int weightopt, char model[],\
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
- health expectancies in states (1) and (2): %s%d.png<br>\
+                   int popforecast, int estepm ,\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+                   double jprev1, double mprev1,double anprev1, \
-    } /* end i1 */
+                   double jprev2, double mprev2,double anprev2){
-  }/* End k1 */
+   int jj1, k1, i1, cpt;
-  fprintf(fichtm,"</ul>");
-  fflush(fichtm);
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
- }
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+ </ul>");
- /******************* Gnuplot file **************/
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-   char dirfileres[132],optfileres[132];
+    fprintf(fichtm,"\
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-   int ng;
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+    fprintf(fichtm,"\
- /*     printf("Problem with file %s",optionfilegnuplot); */
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
- /*   } */
+    fprintf(fichtm,"\
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
-   /*#ifdef windows */
+    <a href=\"%s\">%s</a> <br>\n",
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-     /*#endif */
+    fprintf(fichtm,"\
-   m=pow(2,cptcoveff);
+  - Population projections by age and states: \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   strcpy(dirfileres,optionfilefiname);
-   strcpy(optfileres,"vpl");
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+  m=cptcoveff;
-    for (k1=1; k1<= m ; k1 ++) {
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-      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);
+  jj1=0;
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+  for(k1=1; k1<=m;k1++){
- set ylabel \"Probability\" \n\
+    for(i1=1; i1<=ncodemax[k1];i1++){
- set ter png small\n\
+      jj1++;
- set size 0.65,0.65\n\
+      if (cptcovn > 0) {
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-      for (i=1; i<= nlstate ; i ++) {
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-      }
+      /* Pij */
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      fprintf(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> \
-      for (i=1; i<= nlstate ; i ++) {
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+      /* Quasi-incidences */
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-      }
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-      for (i=1; i<= nlstate ; i ++) {
+        /* Period (stable) prevalence in each health state */
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        for(cpt=1; cpt<nlstate;cpt++){
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
-      }
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+        }
-    }
+      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> \
-   /*2 eme*/
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+      }
-   for (k1=1; k1<= m ; k1 ++) {
+    } /* end i1 */
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+  }/* End k1 */
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+  fprintf(fichtm,"</ul>");
-     for (i=1; i<= nlstate+1 ; i ++) {
-       k=2*i;
+  fprintf(fichtm,"\
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-       for (j=1; j<= nlstate+1 ; j ++) {
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       }
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+  fprintf(fichtm,"\
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-       for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  fprintf(fichtm,"\
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       }
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-       fprintf(ficgp,"\" t\"\" w l 0,");
+  fprintf(fichtm,"\
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+  - 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 (j=1; j<= nlstate+1 ; j ++) {
+    <a href=\"%s\">%s</a> <br>\n</li>",
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+  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): \
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+    <a href=\"%s\">%s</a> <br>\n</li>",
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-     }
+  fprintf(fichtm,"\
-   }
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-   /*3eme*/
+  fprintf(fichtm,"\
+  - 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",
-   for (k1=1; k1<= m ; k1 ++) {
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+  fprintf(fichtm,"\
-       /*       k=2+nlstate*(2*cpt-2); */
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-       k=2+(nlstate+1)*(cpt-1);
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
- set size 0.65,0.65\n\
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ /*      <br>",fileres,fileres,fileres,fileres); */
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ /*  else  */
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+  fflush(fichtm);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+  m=cptcoveff;
-       */
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-       for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+  jj1=0;
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+  for(k1=1; k1<=m;k1++){
+    for(i1=1; i1<=ncodemax[k1];i1++){
-       }
+      jj1++;
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+      if (cptcovn > 0) {
-     }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   }
+        for (cpt=1; cpt<=cptcoveff;cpt++)
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-   /* CV preval stable (period) */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   for (k1=1; k1<= m ; k1 ++) {
+      }
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-       k=3;
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
- set ter png small\nset size 0.65,0.65\n\
+      }
- unset log y\n\
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ true period expectancies (those weighted with period prevalences are also\
-       for (i=1; i< nlstate ; i ++)
+  drawn in addition to the population based expectancies computed using\
-         fprintf(ficgp,"+$%d",k+i+1);
+  observed and cahotic prevalences: %s%d.png<br>\
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+    } /* end i1 */
-       l=3+(nlstate+ndeath)*cpt;
+  }/* End k1 */
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+  fprintf(fichtm,"</ul>");
-       for (i=1; i< nlstate ; i ++) {
+  fflush(fichtm);
-         l=3+(nlstate+ndeath)*cpt;
+ }
-         fprintf(ficgp,"+$%d",l+i+1);
-       }
+ /******************* Gnuplot file **************/
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     }
-   }
+   char dirfileres[132],optfileres[132];
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-   /* proba elementaires */
+   int ng=0;
-   for(i=1,jk=1; i <=nlstate; i++){
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-     for(k=1; k <=(nlstate+ndeath); k++){
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       if (k != i) {
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-         for(j=1; j <=ncovmodel; j++){
+ /*   } */
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-           jk++;
+   /*#ifdef windows */
-           fprintf(ficgp,"\n");
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-         }
+     /*#endif */
-       }
+   m=pow(2,cptcoveff);
-     }
-    }
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+  /* 1eme*/
-      for(jk=1; jk <=m; jk++) {
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+    for (k1=1; k1<= m ; k1 ++) {
-        if (ng==2)
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
-        else
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+ set ylabel \"Probability\" \n\
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+ set ter png small\n\
-        i=1;
+ set size 0.65,0.65\n\
-        for(k2=1; k2<=nlstate; k2++) {
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-          k3=i;
-          for(k=1; k<=(nlstate+ndeath); k++) {
+      for (i=1; i<= nlstate ; i ++) {
-            if (k != k2){
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-              if(ng==2)
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+      }
-              else
+      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+      for (i=1; i<= nlstate ; i ++) {
-              ij=1;
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-              for(j=3; j <=ncovmodel; j++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+      }
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-                  ij++;
+      for (i=1; i<= nlstate ; i ++) {
-                }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-                else
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+      }
-              }
+      fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-              fprintf(ficgp,")/(1");
+    }
+   }
-              for(k1=1; k1 <=nlstate; k1++){
+   /*2 eme*/
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-                ij=1;
+   for (k1=1; k1<= m ; k1 ++) {
-                for(j=3; j <=ncovmodel; j++){
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-                    ij++;
+     for (i=1; i<= nlstate+1 ; i ++) {
-                  }
+       k=2*i;
-                  else
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       for (j=1; j<= nlstate+1 ; j ++) {
-                }
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                fprintf(ficgp,")");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-              }
+       }
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-              i=i+ncovmodel;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-            }
+       for (j=1; j<= nlstate+1 ; j ++) {
-          } /* end k */
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-        } /* end k2 */
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-      } /* end jk */
+       }
-    } /* end ng */
+       fprintf(ficgp,"\" t\"\" w l lt 1,");
-    fflush(ficgp);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- }  /* end gnuplot */
+       for (j=1; j<= nlstate+1 ; j ++) {
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
- /*************** Moving average **************/
+       }
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
+       else fprintf(ficgp,"\" t\"\" w l lt 1,");
-   int i, cpt, cptcod;
+     }
-   int modcovmax =1;
+   }
-   int mobilavrange, mob;
-   double age;
+   /*3eme*/
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+   for (k1=1; k1<= m ; k1 ++) {
-                            a covariate has 2 modalities */
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-     if(mobilav==1) mobilavrange=5; /* default */
+       fprintf(ficgp,"set ter png small\n\
-     else mobilavrange=mobilav;
+ set size 0.65,0.65\n\
-     for (age=bage; age<=fage; age++)
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-       for (i=1; i<=nlstate;i++)
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     /* We keep the original values on the extreme ages bage, fage and for
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-        we use a 5 terms etc. until the borders are no more concerned.
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-     */
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+       */
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+       for (i=1; i< nlstate ; i ++) {
-         for (i=1; i<=nlstate;i++){
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+         /*      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);*/
-             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];
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+     }
-               }
+   }
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-           }
+   /* CV preval stable (period) */
-         }
+   for (k1=1; k1<= m ; k1 ++) {
-       }/* end age */
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
-     }/* end mob */
+       k=3;
-   }else return -1;
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-   return 0;
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- }/* End movingaverage */
+ set ter png small\nset size 0.65,0.65\n\
+ unset log y\n\
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
- /************** Forecasting ******************/
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+       for (i=1; i< nlstate ; i ++)
-   /* proj1, year, month, day of starting projection
+         fprintf(ficgp,"+$%d",k+i+1);
-      agemin, agemax range of age
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-      dateprev1 dateprev2 range of dates during which prevalence is computed
-      anproj2 year of en of projection (same day and month as proj1).
+       l=3+(nlstate+ndeath)*cpt;
-   */
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+       for (i=1; i< nlstate ; i ++) {
-   int *popage;
+         l=3+(nlstate+ndeath)*cpt;
-   double agec; /* generic age */
+         fprintf(ficgp,"+$%d",l+i+1);
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+       }
-   double *popeffectif,*popcount;
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-   double ***p3mat;
+     }
-   double ***mobaverage;
+   }
-   char fileresf[FILENAMELENGTH];
+   /* proba elementaires */
-   agelim=AGESUP;
+   for(i=1,jk=1; i <=nlstate; i++){
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
-   strcpy(fileresf,"f");
+         for(j=1; j <=ncovmodel; j++){
-   strcat(fileresf,fileres);
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+           jk++;
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+           fprintf(ficgp,"\n");
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+         }
-   }
+       }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+     }
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+    }
-   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\nset size 0.65,0.65\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(estepm < stepm){
+            if (k != k2){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+              if(ng==2)
-   }
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-   else  hstepm=estepm;
+              else
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-   hstepm=hstepm/stepm;
+              ij=1;/* To be checked else nbcode[0][0] wrong */
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+              for(j=3; j <=ncovmodel; j++) {
-                                fractional in yp1 */
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
-   anprojmean=yp;
+                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-   yp2=modf((yp1*12),&yp);
+                  ij++;
-   mprojmean=yp;
+                }
-   yp1=modf((yp2*30.5),&yp);
+                else
-   jprojmean=yp;
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   if(jprojmean==0) jprojmean=1;
+              }
-   if(mprojmean==0) jprojmean=1;
+              fprintf(ficgp,")/(1");
-   i1=cptcoveff;
+              for(k1=1; k1 <=nlstate; k1++){
-   if (cptcovn < 1){i1=1;}
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                ij=1;
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+                for(j=3; j <=ncovmodel; j++){
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    ij++;
- /*            if (h==(int)(YEARM*yearp)){ */
+                  }
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+                  else
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-       k=k+1;
+                }
-       fprintf(ficresf,"\n#******");
+                fprintf(ficgp,")");
-       for(j=1;j<=cptcoveff;j++) {
+              }
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-       }
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-       fprintf(ficresf,"******\n");
+              i=i+ncovmodel;
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+            }
-       for(j=1; j<=nlstate+ndeath;j++){
+          } /* end k */
-         for(i=1; i<=nlstate;i++)
+        } /* end k2 */
-           fprintf(ficresf," p%d%d",i,j);
+      } /* end jk */
-         fprintf(ficresf," p.%d",j);
+    } /* end ng */
-       }
+    fflush(ficgp);
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+ }  /* end gnuplot */
-         fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+ /*************** Moving average **************/
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
+   int i, cpt, cptcod;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int modcovmax =1;
-           oldm=oldms;savm=savms;
+   int mobilavrange, mob;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+   double age;
-           for (h=0; h<=nhstepm; h++){
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-             if (h*hstepm/YEARM*stepm ==yearp) {
+                            a covariate has 2 modalities */
-               fprintf(ficresf,"\n");
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-               for(j=1;j<=cptcoveff;j++)
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+     if(mobilav==1) mobilavrange=5; /* default */
-             }
+     else mobilavrange=mobilav;
-             for(j=1; j<=nlstate+ndeath;j++) {
+     for (age=bage; age<=fage; age++)
-               ppij=0.;
+       for (i=1; i<=nlstate;i++)
-               for(i=1; i<=nlstate;i++) {
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-                 if (mobilav==1)
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
-                 else {
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+        we use a 5 terms etc. until the borders are no more concerned.
-                 }
+     */
-                 if (h*hstepm/YEARM*stepm== yearp) {
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-                 }
+         for (i=1; i<=nlstate;i++){
-               } /* end i */
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-               if (h*hstepm/YEARM*stepm==yearp) {
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-                 fprintf(ficresf," %.3f", ppij);
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-               }
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-             }/* end j */
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-           } /* end h */
+               }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-         } /* end agec */
+           }
-       } /* end yearp */
+         }
-     } /* end cptcod */
+       }/* end age */
-   } /* end  cptcov */
+     }/* end mob */
+   }else return -1;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   return 0;
+ }/* End movingaverage */
-   fclose(ficresf);
- }
+ /************** Forecasting ******************/
- /************** Forecasting *****not tested NB*************/
+ 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){
- 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){
+   /* proj1, year, month, day of starting projection
+      agemin, agemax range of age
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-   int *popage;
+      anproj2 year of en of projection (same day and month as proj1).
-   double calagedatem, agelim, kk1, kk2;
+   */
-   double *popeffectif,*popcount;
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-   double ***p3mat,***tabpop,***tabpopprev;
+   int *popage;
-   double ***mobaverage;
+   double agec; /* generic age */
-   char filerespop[FILENAMELENGTH];
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double ***p3mat;
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   double ***mobaverage;
-   agelim=AGESUP;
+   char fileresf[FILENAMELENGTH];
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   agelim=AGESUP;
    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   strcpy(fileresf,"f");
-   strcpy(filerespop,"pop");
+   strcat(fileresf,fileres);
-   strcat(filerespop,fileres);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
-   }
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav!=0) {
-   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
-     }
+   }
-   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
-   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   agelim=AGESUP;
+   }
+   else  hstepm=estepm;
-   hstepm=1;
    hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-   if (popforecast==1) {
+                                fractional in yp1 */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+   anprojmean=yp;
-       printf("Problem with population file : %s\n",popfile);exit(0);
+   yp2=modf((yp1*12),&yp);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+   mprojmean=yp;
-     }
+   yp1=modf((yp2*30.5),&yp);
-     popage=ivector(0,AGESUP);
+   jprojmean=yp;
-     popeffectif=vector(0,AGESUP);
+   if(jprojmean==0) jprojmean=1;
-     popcount=vector(0,AGESUP);
+   if(mprojmean==0) jprojmean=1;
-     i=1;
+   i1=cptcoveff;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+   if (cptcovn < 1){i1=1;}
-     imx=i;
+   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<imx;i++) popeffectif[popage[i]]=popcount[i];
-   }
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ /*            if (h==(int)(YEARM*yearp)){ */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-       k=k+1;
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       fprintf(ficrespop,"\n#******");
+       k=k+1;
-       for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficresf,"\n#******");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for(j=1;j<=cptcoveff;j++) {
-       }
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficrespop,"******\n");
+       }
-       fprintf(ficrespop,"# Age");
+       fprintf(ficresf,"******\n");
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
-       for (cpt=0; cpt<=0;cpt++) {
+           fprintf(ficresf," p%d%d",i,j);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+         fprintf(ficresf," p.%d",j);
+       }
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+         fprintf(ficresf,"\n");
-           nhstepm = nhstepm/hstepm;
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-           oldm=oldms;savm=savms;
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           for (h=0; h<=nhstepm; h++){
+           oldm=oldms;savm=savms;
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
+           for (h=0; h<=nhstepm; h++){
-             for(j=1; j<=nlstate+ndeath;j++) {
+             if (h*hstepm/YEARM*stepm ==yearp) {
-               kk1=0.;kk2=0;
+               fprintf(ficresf,"\n");
-               for(i=1; i<=nlstate;i++) {
+               for(j=1;j<=cptcoveff;j++)
-                 if (mobilav==1)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-                 else {
+             }
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+             for(j=1; j<=nlstate+ndeath;j++) {
-                 }
+               ppij=0.;
-               }
+               for(i=1; i<=nlstate;i++) {
-               if (h==(int)(calagedatem+12*cpt)){
+                 if (mobilav==1)
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-                   /*fprintf(ficrespop," %.3f", kk1);
+                 else {
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-               }
+                 }
-             }
+                 if (h*hstepm/YEARM*stepm== yearp) {
-             for(i=1; i<=nlstate;i++){
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-               kk1=0.;
+                 }
-                 for(j=1; j<=nlstate;j++){
+               } /* end i */
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+               if (h*hstepm/YEARM*stepm==yearp) {
-                 }
+                 fprintf(ficresf," %.3f", ppij);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+               }
-             }
+             }/* end j */
+           } /* end h */
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+         } /* end agec */
-           }
+       } /* end yearp */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     } /* end cptcod */
-         }
+   } /* end  cptcov */
-       }
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   /******/
+   fclose(ficresf);
-       for (cpt=1; cpt<=(anpyram1-anpyram);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--){
+ /************** Forecasting *****not tested NB*************/
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ 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){
-           nhstepm = nhstepm/hstepm;
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int *popage;
-           oldm=oldms;savm=savms;
+   double calagedatem, agelim, kk1, kk2;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   double *popeffectif,*popcount;
-           for (h=0; h<=nhstepm; h++){
+   double ***p3mat,***tabpop,***tabpopprev;
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   double ***mobaverage;
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   char filerespop[FILENAMELENGTH];
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               kk1=0.;kk2=0;
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               for(i=1; i<=nlstate;i++) {
+   agelim=AGESUP;
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-               }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   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(filerespop,"pop");
-         }
+   strcat(filerespop,fileres);
-       }
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-    }
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-   }
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
+   if (mobilav!=0) {
-   }
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   fclose(ficrespop);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
- } /* End of popforecast */
+     }
+   }
- int fileappend(FILE *fichier, char *optionfich)
- {
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+   if (stepm<=12) stepsize=1;
-     printf("Problem with file: %s\n", optionfich);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+   agelim=AGESUP;
-     return (0);
-   }
+   hstepm=1;
-   fflush(fichier);
+   hstepm=hstepm/stepm;
-   return (1);
- }
+   if (popforecast==1) {
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
- /**************** function prwizard **********************/
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+     }
- {
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
-   /* Wizard to print covariance matrix template */
+     popcount=vector(0,AGESUP);
-   char ca[32], cb[32], cc[32];
+     i=1;
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   int numlinepar;
+     imx=i;
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   }
-   for(i=1; i <=nlstate; i++){
-     jj=0;
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-     for(j=1; j <=nlstate+ndeath; j++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-       if(j==i) continue;
+       k=k+1;
-       jj++;
+       fprintf(ficrespop,"\n#******");
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+       for(j=1;j<=cptcoveff;j++) {
-       printf("%1d%1d",i,j);
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-       fprintf(ficparo,"%1d%1d",i,j);
+       }
-       for(k=1; k<=ncovmodel;k++){
+       fprintf(ficrespop,"******\n");
-         /*        printf(" %lf",param[i][j][k]); */
+       fprintf(ficrespop,"# Age");
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-         printf(" 0.");
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-         fprintf(ficparo," 0.");
-       }
+       for (cpt=0; cpt<=0;cpt++) {
-       printf("\n");
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-       fprintf(ficparo,"\n");
-     }
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   }
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   printf("# Scales (for hessian or gradient estimation)\n");
+           nhstepm = nhstepm/hstepm;
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   for(i=1; i <=nlstate; i++){
+           oldm=oldms;savm=savms;
-     jj=0;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     for(j=1; j <=nlstate+ndeath; j++){
-       if(j==i) continue;
+           for (h=0; h<=nhstepm; h++){
-       jj++;
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       fprintf(ficparo,"%1d%1d",i,j);
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       printf("%1d%1d",i,j);
+             }
-       fflush(stdout);
+             for(j=1; j<=nlstate+ndeath;j++) {
-       for(k=1; k<=ncovmodel;k++){
+               kk1=0.;kk2=0;
-         /*      printf(" %le",delti3[i][j][k]); */
+               for(i=1; i<=nlstate;i++) {
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+                 if (mobilav==1)
-         printf(" 0.");
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-         fprintf(ficparo," 0.");
+                 else {
-       }
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-       numlinepar++;
+                 }
-       printf("\n");
+               }
-       fprintf(ficparo,"\n");
+               if (h==(int)(calagedatem+12*cpt)){
-     }
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-   }
+                   /*fprintf(ficrespop," %.3f", kk1);
-   printf("# Covariance matrix\n");
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
- /* # 121 Var(a12)\n\ */
+               }
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+             }
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+             for(i=1; i<=nlstate;i++){
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+               kk1=0.;
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+                 for(j=1; j<=nlstate;j++){
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
- /* # 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" */
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-   fflush(stdout);
+             }
-   fprintf(ficparo,"# Covariance matrix\n");
-   /* # 121 Var(a12)\n\ */
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-   /* #   ...\n\ */
+           }
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   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 (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         for(k=1; k<=ncovmodel;k++){
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-           jj++;
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           ca[0]= k+'a'-1;ca[1]='\0';
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           if(itimes==1){
+           nhstepm = nhstepm/hstepm;
-             printf("#%1d%1d%d",i,j,k);
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           }else{
+           oldm=oldms;savm=savms;
-             printf("%1d%1d%d",i,j,k);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+           for (h=0; h<=nhstepm; h++){
-             /*  printf(" %.5le",matcov[i][j]); */
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-           }
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-           ll=0;
+             }
-           for(li=1;li <=nlstate; li++){
+             for(j=1; j<=nlstate+ndeath;j++) {
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+               kk1=0.;kk2=0;
-               if(lj==li) continue;
+               for(i=1; i<=nlstate;i++) {
-               for(lk=1;lk<=ncovmodel;lk++){
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-                 ll++;
+               }
-                 if(ll<=jj){
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+             }
-                   if(ll<jj){
+           }
-                     if(itimes==1){
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                       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);
+       }
-                     }else{
+    }
-                       printf(" 0.");
+   }
-                       fprintf(ficparo," 0.");
-                     }
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                   }else{
-                     if(itimes==1){
+   if (popforecast==1) {
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+     free_ivector(popage,0,AGESUP);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+     free_vector(popeffectif,0,AGESUP);
-                     }else{
+     free_vector(popcount,0,AGESUP);
-                       printf(" 0.");
+   }
-                       fprintf(ficparo," 0.");
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                     }
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                   }
+   fclose(ficrespop);
-                 }
+ } /* End of popforecast */
-               } /* end lk */
-             } /* end lj */
+ int fileappend(FILE *fichier, char *optionfich)
-           } /* end li */
+ {
-           printf("\n");
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-           fprintf(ficparo,"\n");
+     printf("Problem with file: %s\n", optionfich);
-           numlinepar++;
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-         } /* end k*/
+     return (0);
-       } /*end j */
+   }
-     } /* end i */
+   fflush(fichier);
-   } /* end itimes */
+   return (1);
+ }
- } /* end of prwizard */
- /******************* Gompertz Likelihood ******************************/
- double gompertz(double x[])
+ /**************** function prwizard **********************/
- {
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   double A,B,L=0.0,sump=0.,num=0.;
+ {
-   int i,n=0; /* n is the size of the sample */
+   /* Wizard to print covariance matrix template */
-   for (i=0;i<=imx-1 ; i++) {
-     sump=sump+weight[i];
+   char ca[32], cb[32], cc[32];
-     /*    sump=sump+1;*/
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-     num=num+1;
+   int numlinepar;
-   }
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-   /* for (i=0; i<=imx; i++)
+   for(i=1; i <=nlstate; 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]);*/
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-   for (i=1;i<=imx ; i++)
+       if(j==i) continue;
-     {
+       jj++;
-       if (cens[i] == 1 && wav[i]>1)
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+       printf("%1d%1d",i,j);
+       fprintf(ficparo,"%1d%1d",i,j);
-       if (cens[i] == 0 && wav[i]>1)
+       for(k=1; k<=ncovmodel;k++){
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+         /*        printf(" %lf",param[i][j][k]); */
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+         fprintf(ficparo," 0.");
-       if (wav[i] > 1 ) { /* ??? */
+       }
-         L=L+A*weight[i];
+       printf("\n");
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       fprintf(ficparo,"\n");
-       }
+     }
-     }
+   }
+   printf("# Scales (for hessian or gradient estimation)\n");
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-   return -2*L*num/sump;
+   for(i=1; i <=nlstate; i++){
- }
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
- /******************* Printing html file ***********/
+       if(j==i) continue;
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+       jj++;
-                   int lastpass, int stepm, int weightopt, char model[],\
+       fprintf(ficparo,"%1d%1d",i,j);
-                   int imx,  double p[],double **matcov,double agemortsup){
+       printf("%1d%1d",i,j);
-   int i,k;
+       fflush(stdout);
+       for(k=1; k<=ncovmodel;k++){
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+         /*      printf(" %le",delti3[i][j][k]); */
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-   for (i=1;i<=2;i++)
+         printf(" 0.");
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+         fprintf(ficparo," 0.");
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+       }
-   fprintf(fichtm,"</ul>");
+       numlinepar++;
+       printf("\n");
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+       fprintf(ficparo,"\n");
+     }
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+   }
+   printf("# Covariance matrix\n");
-  for (k=agegomp;k<(agemortsup-2);k++)
+ /* # 121 Var(a12)\n\ */
-    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]);
+ /* # 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\ */
-   fflush(fichtm);
+ /* # 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\ */
- /******************* Gnuplot file **************/
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\n");
-   char dirfileres[132],optfileres[132];
+   /* # 121 Var(a12)\n\ */
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   int ng;
+   /* #   ...\n\ */
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-   /*#ifdef windows */
+   for(itimes=1;itimes<=2;itimes++){
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+     jj=0;
-     /*#endif */
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j==i) continue;
-   strcpy(dirfileres,optionfilefiname);
+         for(k=1; k<=ncovmodel;k++){
-   strcpy(optfileres,"vpl");
+           jj++;
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+           ca[0]= k+'a'-1;ca[1]='\0';
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+           if(itimes==1){
-   fprintf(ficgp, "set ter png small\n set log y\n");
+             printf("#%1d%1d%d",i,j,k);
-   fprintf(ficgp, "set size 0.65,0.65\n");
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+           }else{
+             printf("%1d%1d%d",i,j,k);
- }
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
+           for(li=1;li <=nlstate; li++){
+             for(lj=1;lj <=nlstate+ndeath; lj++){
- /***********************************************/
+               if(lj==li) continue;
- /**************** Main Program *****************/
+               for(lk=1;lk<=ncovmodel;lk++){
- /***********************************************/
+                 ll++;
+                 if(ll<=jj){
- int main(int argc, char *argv[])
+                   cb[0]= lk +'a'-1;cb[1]='\0';
- {
+                   if(ll<jj){
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+                     if(itimes==1){
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-   int linei, month, year,iout;
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-   int jj, ll, li, lj, lk, imk;
+                     }else{
-   int numlinepar=0; /* Current linenumber of parameter file */
+                       printf(" 0.");
-   int itimes;
+                       fprintf(ficparo," 0.");
-   int NDIM=2;
+                     }
+                   }else{
-   char ca[32], cb[32], cc[32];
+                     if(itimes==1){
-   char dummy[]="                         ";
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-   /*  FILE *fichtm; *//* Html File */
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-   /* FILE *ficgp;*/ /*Gnuplot File */
+                     }else{
-   struct stat info;
+                       printf(" 0.");
-   double agedeb, agefin,hf;
+                       fprintf(ficparo," 0.");
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+                     }
+                   }
-   double fret;
+                 }
-   double **xi,tmp,delta;
+               } /* end lk */
+             } /* end lj */
-   double dum; /* Dummy variable */
+           } /* end li */
-   double ***p3mat;
+           printf("\n");
-   double ***mobaverage;
+           fprintf(ficparo,"\n");
-   int *indx;
+           numlinepar++;
-   char line[MAXLINE], linepar[MAXLINE];
+         } /* end k*/
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+       } /*end j */
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     } /* end i */
-   char **bp, *tok, *val; /* pathtot */
+   } /* end itimes */
-   int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+ } /* end of prwizard */
-   int c,  h , cpt,l;
+ /******************* Gompertz Likelihood ******************************/
-   int ju,jl, mi;
+ double gompertz(double x[])
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+ {
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+   double A,B,L=0.0,sump=0.,num=0.;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   int i,n=0; /* n is the size of the sample */
-   int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
+   for (i=0;i<=imx-1 ; i++) {
-   int agemortsup;
+     sump=sump+weight[i];
-   float  sumlpop=0.;
+     /*    sump=sump+1;*/
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+     num=num+1;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   }
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
+   /* for (i=0; i<=imx; i++)
-   double **prlim;
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   double *severity;
-   double ***param; /* Matrix of parameters */
+   for (i=1;i<=imx ; i++)
-   double  *p;
+     {
-   double **matcov; /* Matrix of covariance */
+       if (cens[i] == 1 && wav[i]>1)
-   double ***delti3; /* Scale */
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   double *delti; /* Scale */
-   double ***eij, ***vareij;
+       if (cens[i] == 0 && wav[i]>1)
-   double **varpl; /* Variances of prevalence limits by age */
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-   double *epj, vepp;
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   double **ximort;
+       if (wav[i] > 1 ) { /* ??? */
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+         L=L+A*weight[i];
-   int *dcwave;
+         /*      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]);*/
+       }
-   char z[1]="c", occ;
+     }
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   char  *strt, strtend[80];
-   char *stratrunc;
+   return -2*L*num/sump;
-   int lstra;
+ }
-   long total_usecs;
+ #ifdef GSL
+ /******************* Gompertz_f Likelihood ******************************/
- /*   setlocale (LC_ALL, ""); */
+ double gompertz_f(const gsl_vector *v, void *params)
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ {
- /*   textdomain (PACKAGE); */
+   double A,B,LL=0.0,sump=0.,num=0.;
- /*   setlocale (LC_CTYPE, ""); */
+   double *x= (double *) v->data;
- /*   setlocale (LC_MESSAGES, ""); */
+   int i,n=0; /* n is the size of the sample */
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   for (i=0;i<=imx-1 ; i++) {
-   (void) gettimeofday(&start_time,&tzp);
+     sump=sump+weight[i];
-   curr_time=start_time;
+     /*    sump=sump+1;*/
-   tm = *localtime(&start_time.tv_sec);
+     num=num+1;
-   tmg = *gmtime(&start_time.tv_sec);
+   }
-   strcpy(strstart,asctime(&tm));
- /*  printf("Localtime (at start)=%s",strstart); */
+   /* for (i=0; i<=imx; i++)
- /*  tp.tv_sec = tp.tv_sec +86400; */
+      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]);*/
- /*  tm = *localtime(&start_time.tv_sec); */
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+   for (i=1;i<=imx ; i++)
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+     {
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+       if (cens[i] == 1 && wav[i]>1)
- /*   tp.tv_sec = mktime(&tmg); */
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
- /*   strt=asctime(&tmg); */
- /*   printf("Time(after) =%s",strstart);  */
+       if (cens[i] == 0 && wav[i]>1)
- /*  (void) time (&time_value);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
- *  tm = *localtime(&time_value);
- *  strstart=asctime(&tm);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+       if (wav[i] > 1 ) { /* ??? */
- */
+         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]);*/
-   nberr=0; /* Number of errors and warnings */
+       }
-   nbwarn=0;
+     }
-   getcwd(pathcd, size);
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   printf("\n%s\n%s",version,fullversion);
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-   if(argc <=1){
-     printf("\nEnter the parameter file name: ");
+   return -2*LL*num/sump;
-     fgets(pathr,FILENAMELENGTH,stdin);
+ }
-     i=strlen(pathr);
+ #endif
-     if(pathr[i-1]=='\n')
-       pathr[i-1]='\0';
+ /******************* Printing html file ***********/
-    for (tok = pathr; tok != NULL; ){
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-       printf("Pathr |%s|\n",pathr);
+                   int lastpass, int stepm, int weightopt, char model[],\
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+                   int imx,  double p[],double **matcov,double agemortsup){
-       printf("val= |%s| pathr=%s\n",val,pathr);
+   int i,k;
-       strcpy (pathtot, val);
-       if(pathr[0] == '\0') break; /* Dirty */
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-     }
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   }
+   for (i=1;i<=2;i++)
-   else{
+     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-     strcpy(pathtot,argv[1]);
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   }
+   fprintf(fichtm,"</ul>");
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-   /*cygwin_split_path(pathtot,path,optionfile);
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
+  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>");
-   /* Split argv[0], imach program to get pathimach */
+  for (k=agegomp;k<(agemortsup-2);k++)
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+    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]);
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-  /*   strcpy(pathimach,argv[0]); */
+   fflush(fichtm);
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+ }
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ /******************* Gnuplot file **************/
-   chdir(path); /* Can be a relative path */
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-     printf("Current directory %s!\n",pathcd);
+   char dirfileres[132],optfileres[132];
-   strcpy(command,"mkdir ");
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   strcat(command,optionfilefiname);
+   int ng;
-   if((outcmd=system(command)) != 0){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+   /*#ifdef windows */
-     /* fclose(ficlog); */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
- /*     exit(1); */
+     /*#endif */
-   }
- /*   if((imk=mkdir(optionfilefiname))<0){ */
- /*     perror("mkdir"); */
+   strcpy(dirfileres,optionfilefiname);
- /*   } */
+   strcpy(optfileres,"vpl");
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   /*-------- arguments in the command line --------*/
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+   fprintf(ficgp, "set ter png small\n set log y\n");
-   /* Log file */
+   fprintf(ficgp, "set size 0.65,0.65\n");
-   strcat(filelog, optionfilefiname);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-   strcat(filelog,".log");    /* */
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+ }
-     printf("Problem with logfile %s\n",filelog);
-     goto end;
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
-   }
+ {
-   fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   /*-------- data file ----------*/
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+   FILE *fic;
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+   char dummy[]="                         ";
-  path=%s \n\
+   int i, j, n;
-  optionfile=%s\n\
+   int linei, month, year,iout;
-  optionfilext=%s\n\
+   char line[MAXLINE], linetmp[MAXLINE];
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   char stra[80], strb[80];
+   char *stratrunc;
-   printf("Local time (at start):%s",strstart);
+   int lstra;
-   fprintf(ficlog,"Local time (at start): %s",strstart);
-   fflush(ficlog);
- /*   (void) gettimeofday(&curr_time,&tzp); */
+   if((fic=fopen(datafile,"r"))==NULL)    {
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-   /* */
+   }
-   strcpy(fileres,"r");
-   strcat(fileres, optionfilefiname);
+   i=1;
-   strcat(fileres,".txt");    /* Other files have txt extension */
+   linei=0;
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-   /*---------arguments file --------*/
+     linei=linei+1;
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+       if(line[j] == '\t')
-     printf("Problem with optionfile %s\n",optionfile);
+         line[j] = ' ';
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     }
-     fflush(ficlog);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-     goto end;
+       ;
-   }
+     };
+     line[j+1]=0;  /* Trims blanks at end of line */
+     if(line[0]=='#'){
+       fprintf(ficlog,"Comment line\n%s\n",line);
-   strcpy(filereso,"o");
+       printf("Comment line\n%s\n",line);
-   strcat(filereso,fileres);
+       continue;
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+     }
-     printf("Problem with Output resultfile: %s\n", filereso);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     for (j=0; line[j]!='\0';j++){
-     fflush(ficlog);
+       line[j]=linetmp[j];
-     goto end;
+     }
-   }
-   /* Reads comments: lines beginning with '#' */
+     for (j=maxwav;j>=1;j--){
-   numlinepar=0;
+       cutv(stra, strb, line, ' ');
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       if(strb[0]=='.') { /* Missing status */
-     ungetc(c,ficpar);
+         lval=-1;
-     fgets(line, MAXLINE, ficpar);
+       }else{
-     numlinepar++;
+         errno=0;
-     puts(line);
+         lval=strtol(strb,&endptr,10);
-     fputs(line,ficparo);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     fputs(line,ficlog);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   }
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-   ungetc(c,ficpar);
+           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);
+           return 1;
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+         }
-   numlinepar++;
+       }
-   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);
+       s[j][i]=lval;
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       strcpy(line,stra);
-   fflush(ficlog);
+       cutv(stra, strb,line,' ');
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     ungetc(c,ficpar);
+       }
-     fgets(line, MAXLINE, ficpar);
+       else  if(iout=sscanf(strb,"%s.") != 0){
-     numlinepar++;
+         month=99;
-     puts(line);
+         year=9999;
-     fputs(line,ficparo);
+       }else{
-     fputs(line,ficlog);
+         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);
-   }
+         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);
-   ungetc(c,ficpar);
+         return 1;
+       }
+       anint[j][i]= (double) year;
-   covar=matrix(0,NCOVMAX,1,n);
+       mint[j][i]= (double)month;
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       strcpy(line,stra);
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+     } /* ENd Waves */
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+     cutv(stra, strb,line,' ');
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     }
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       month=99;
-   delti=delti3[1][1];
+       year=9999;
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+     }else{
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+       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);
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+         return 1;
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     }
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     andc[i]=(double) year;
-     fclose (ficparo);
+     moisdc[i]=(double) month;
-     fclose (ficlog);
+     strcpy(line,stra);
-     goto end;
-     exit(0);
+     cutv(stra, strb,line,' ');
-   }
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   else if(mle==-3) {
+     }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     else  if(iout=sscanf(strb,"%s.") != 0){
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       month=99;
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       year=9999;
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     }else{
-     matcov=matrix(1,npar,1,npar);
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-   }
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-   else{
+         return 1;
-     /* Read guess parameters */
+     }
-     /* Reads comments: lines beginning with '#' */
+     if (year==9999) {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       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);
-       ungetc(c,ficpar);
+       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);
-       fgets(line, MAXLINE, ficpar);
+         return 1;
-       numlinepar++;
-       puts(line);
+     }
-       fputs(line,ficparo);
+     annais[i]=(double)(year);
-       fputs(line,ficlog);
+     moisnais[i]=(double)(month);
-     }
+     strcpy(line,stra);
-     ungetc(c,ficpar);
+     cutv(stra, strb,line,' ');
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     errno=0;
-     for(i=1; i <=nlstate; i++){
+     dval=strtod(strb,&endptr);
-       j=0;
+     if( strb[0]=='\0' || (*endptr != '\0')){
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+       printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-         if(jj==i) continue;
+       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);
-         j++;
+       fflush(ficlog);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       return 1;
-         if ((i1 != i) && (j1 != j)){
+     }
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+     weight[i]=dval;
- It might be a problem of design; if ncovcol and the model are correct\n \
+     strcpy(line,stra);
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           exit(1);
+     for (j=ncovcol;j>=1;j--){
-         }
+       cutv(stra, strb,line,' ');
-         fprintf(ficparo,"%1d%1d",i1,j1);
+       if(strb[0]=='.') { /* Missing status */
-         if(mle==1)
+         lval=-1;
-           printf("%1d%1d",i,j);
+       }else{
-         fprintf(ficlog,"%1d%1d",i,j);
+         errno=0;
-         for(k=1; k<=ncovmodel;k++){
+         lval=strtol(strb,&endptr,10);
-           fscanf(ficpar," %lf",&param[i][j][k]);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-           if(mle==1){
+           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);
-             printf(" %lf",param[i][j][k]);
+           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);
-             fprintf(ficlog," %lf",param[i][j][k]);
+           return 1;
-           }
+         }
-           else
+       }
-             fprintf(ficlog," %lf",param[i][j][k]);
+       if(lval <-1 || lval >1){
-           fprintf(ficparo," %lf",param[i][j][k]);
+         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-         }
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-         fscanf(ficpar,"\n");
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-         numlinepar++;
+  For example, for multinomial values like 1, 2 and 3,\n \
-         if(mle==1)
+  build V1=0 V2=0 for the reference value (1),\n \
-           printf("\n");
+         V1=1 V2=0 for (2) \n \
-         fprintf(ficlog,"\n");
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-         fprintf(ficparo,"\n");
+  output of IMaCh is often meaningless.\n \
-       }
+  Exiting.\n",lval,linei, i,line,j);
-     }
+         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-     fflush(ficlog);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     p=param[1][1];
+  For example, for multinomial values like 1, 2 and 3,\n \
+  build V1=0 V2=0 for the reference value (1),\n \
-     /* Reads comments: lines beginning with '#' */
+         V1=1 V2=0 for (2) \n \
-     while((c=getc(ficpar))=='#' && c!= EOF){
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-       ungetc(c,ficpar);
+  output of IMaCh is often meaningless.\n \
-       fgets(line, MAXLINE, ficpar);
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-       numlinepar++;
+         return 1;
-       puts(line);
+       }
-       fputs(line,ficparo);
+       covar[j][i]=(double)(lval);
-       fputs(line,ficlog);
+       strcpy(line,stra);
      }
-     ungetc(c,ficpar);
+     lstra=strlen(stra);
-     for(i=1; i <=nlstate; i++){
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       stratrunc = &(stra[lstra-9]);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+       num[i]=atol(stratrunc);
-         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);
+     else
-           exit(1);
+       num[i]=atol(stra);
-         }
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-         printf("%1d%1d",i,j);
+       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;}*/
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+     i=i+1;
-         for(k=1; k<=ncovmodel;k++){
+   } /* End loop reading  data */
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
-           printf(" %le",delti3[i][j][k]);
+   *imax=i-1; /* Number of individuals */
-           fprintf(ficparo," %le",delti3[i][j][k]);
+   fclose(fic);
-           fprintf(ficlog," %le",delti3[i][j][k]);
-         }
+   return (0);
-         fscanf(ficpar,"\n");
+   endread:
-         numlinepar++;
+     printf("Exiting readdata: ");
-         printf("\n");
+     fclose(fic);
-         fprintf(ficparo,"\n");
+     return (1);
-         fprintf(ficlog,"\n");
-       }
-     }
-     fflush(ficlog);
+ }
-     delti=delti3[1][1];
+ int decodemodel ( char model[], int lastobs)
+ {
+   int i, j, k;
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+   int i1, j1, k1, k2;
+   char modelsav[80];
-     /* Reads comments: lines beginning with '#' */
+    char stra[80], strb[80], strc[80], strd[80],stre[80];
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-       fgets(line, MAXLINE, ficpar);
+     j=0, j1=0, k1=1, k2=1;
-       numlinepar++;
+     j=nbocc(model,'+'); /* j=Number of '+' */
-       puts(line);
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
-       fputs(line,ficparo);
+     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
-       fputs(line,ficlog);
+                   but the covariates which are product must be computed and stored. */
-     }
+     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
-     ungetc(c,ficpar);
+     strcpy(modelsav,model);
-     matcov=matrix(1,npar,1,npar);
+     if (strstr(model,"AGE") !=0){
-     for(i=1; i <=npar; i++){
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-       fscanf(ficpar,"%s",&str);
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-       if(mle==1)
+       return 1;
-         printf("%s",str);
+     }
-       fprintf(ficlog,"%s",str);
+     if (strstr(model,"v") !=0){
-       fprintf(ficparo,"%s",str);
+       printf("Error. 'v' must be in upper case 'V' model=%s ",model);
-       for(j=1; j <=i; j++){
+       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
-         fscanf(ficpar," %le",&matcov[i][j]);
+       return 1;
-         if(mle==1){
+     }
-           printf(" %.5le",matcov[i][j]);
-         }
+     /* This loop fills the array Tvar from the string 'model'.*/
-         fprintf(ficlog," %.5le",matcov[i][j]);
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-         fprintf(ficparo," %.5le",matcov[i][j]);
+     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
-       }
+     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
-       fscanf(ficpar,"\n");
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
-       numlinepar++;
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-       if(mle==1)
+     /*  k=1 Tvar[1]=2 (from V2) */
-         printf("\n");
+     /*  k=5 Tvar[5] */
-       fprintf(ficlog,"\n");
+     /* for (k=1; k<=cptcovn;k++) { */
-       fprintf(ficparo,"\n");
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-     }
+     /*  } */
-     for(i=1; i <=npar; i++)
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for(j=i+1;j<=npar;j++)
+     for(k=cptcovn; k>=1;k--){
-         matcov[i][j]=matcov[j][i];
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
-     if(mle==1)
+                                     */
-       printf("\n");
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-     fprintf(ficlog,"\n");
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       /*scanf("%d",i);*/
-     fflush(ficlog);
+       if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-     /*-------- Rewriting parameter file ----------*/
+         if (strcmp(strc,"age")==0) { /* Vn*age */
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+           cptcovprod--;
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+           cutv(strb,stre,strd,'V'); /* stre="V3" */
-     strcat(rfileres,".");    /* */
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+           /*printf("stre=%s ", stre);*/
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-     }
+           cptcovprod--;
-     fprintf(ficres,"#%s\n",version);
+           cutv(strb,stre,strc,'V');
-   }    /* End of mle != -3 */
+           Tvar[k]=atoi(stre);
+           cptcovage++;
-   /*-------- data file ----------*/
+           Tage[cptcovage]=k;
-   if((fic=fopen(datafile,"r"))==NULL)    {
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-   }
+           Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
+                                   because this model-covariate is a construction we invent a new column
-   n= lastobs;
+                                   ncovcol + k1
-   severity = vector(1,maxwav);
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-   outcome=imatrix(1,maxwav+1,1,n);
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-   num=lvector(1,n);
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-   moisnais=vector(1,n);
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-   annais=vector(1,n);
+           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
-   moisdc=vector(1,n);
+           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
-   andc=vector(1,n);
+           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
-   agedc=vector(1,n);
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
-   cod=ivector(1,n);
+           for (i=1; i<=lastobs;i++){
-   weight=vector(1,n);
+             /* Computes the new covariate which is a product of
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
-   mint=matrix(1,maxwav,1,n);
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-   anint=matrix(1,maxwav,1,n);
+           }
-   s=imatrix(1,maxwav+1,1,n);
+           k1++;
-   tab=ivector(1,NCOVMAX);
+           k2=k2+2;
-   ncodemax=ivector(1,8);
+         } /* End age is not in the model */
+       } /* End if model includes a product */
-   i=1;
+       else { /* no more sum */
-   linei=0;
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+        /*  scanf("%d",i);*/
-     linei=linei+1;
+         cutv(strd,strc,strb,'V');
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+         Tvar[k]=atoi(strc);
-       if(line[j] == '\t')
+       }
-         line[j] = ' ';
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-     }
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+         scanf("%d",i);*/
-       ;
+     } /* end of loop + */
-     };
+   } /* end model */
-     line[j+1]=0;  /* Trims blanks at end of line */
-     if(line[0]=='#'){
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-       fprintf(ficlog,"Comment line\n%s\n",line);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-       printf("Comment line\n%s\n",line);
-       continue;
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-     }
+   printf("cptcovprod=%d ", cptcovprod);
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-     for (j=maxwav;j>=1;j--){
-       cutv(stra, strb,line,' ');
+   scanf("%d ",i);*/
-       errno=0;
-       lval=strtol(strb,&endptr,10);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   endread:
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+     printf("Exiting decodemodel: ");
-         exit(1);
+     return (1);
-       }
+ }
-       s[j][i]=lval;
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-       strcpy(line,stra);
+ {
-       cutv(stra, strb,line,' ');
+   int i, m;
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-       }
+   for (i=1; i<=imx; i++) {
-       else  if(iout=sscanf(strb,"%s.") != 0){
+     for(m=2; (m<= maxwav); m++) {
-         month=99;
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-         year=9999;
+         anint[m][i]=9999;
-       }else{
+         s[m][i]=-1;
-         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);
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-       }
+         *nberr++;
-       anint[j][i]= (double) year;
+         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);
-       mint[j][i]= (double)month;
+         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);
-       strcpy(line,stra);
+         s[m][i]=-1;
-     } /* ENd Waves */
+       }
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-     cutv(stra, strb,line,' ');
+         *nberr++;
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         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]);
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       month=99;
+       }
-       year=9999;
+     }
-     }else{
+   }
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-       exit(1);
+   for (i=1; i<=imx; i++)  {
-     }
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     andc[i]=(double) year;
+     for(m=firstpass; (m<= lastpass); m++){
-     moisdc[i]=(double) month;
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-     strcpy(line,stra);
+         if (s[m][i] >= nlstate+1) {
+           if(agedc[i]>0)
-     cutv(stra, strb,line,' ');
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+               agev[m][i]=agedc[i];
-     }
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-     else  if(iout=sscanf(strb,"%s.") != 0){
+             else {
-       month=99;
+               if ((int)andc[i]!=9999){
-       year=9999;
+                 nbwarn++;
-     }else{
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-       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);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-       exit(1);
+                 agev[m][i]=-1;
-     }
+               }
-     annais[i]=(double)(year);
+             }
-     moisnais[i]=(double)(month);
+         }
-     strcpy(line,stra);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
+                                  years but with the precision of a month */
-     cutv(stra, strb,line,' ');
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-     errno=0;
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-     dval=strtod(strb,&endptr);
+             agev[m][i]=1;
-     if( strb[0]=='\0' || (*endptr != '\0')){
+           else if(agev[m][i] < *agemin){
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+             *agemin=agev[m][i];
-       exit(1);
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-     }
+           }
-     weight[i]=dval;
+           else if(agev[m][i] >*agemax){
-     strcpy(line,stra);
+             *agemax=agev[m][i];
+             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
-     for (j=ncovcol;j>=1;j--){
+           }
-       cutv(stra, strb,line,' ');
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-       errno=0;
+           /*     agev[m][i] = age[i]+2*m;*/
-       lval=strtol(strb,&endptr,10);
+         }
-       if( strb[0]=='\0' || (*endptr != '\0')){
+         else { /* =9 */
-         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);
+           agev[m][i]=1;
-         exit(1);
+           s[m][i]=-1;
-       }
+         }
-       if(lval <-1 || lval >1){
+       }
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+       else /*= 0 Unknown */
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+         agev[m][i]=1;
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+     }
-  For example, for multinomial values like 1, 2 and 3,\n \
-  build V1=0 V2=0 for the reference value (1),\n \
+   }
-         V1=1 V2=0 for (2) \n \
+   for (i=1; i<=imx; i++)  {
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+     for(m=firstpass; (m<=lastpass); m++){
-  output of IMaCh is often meaningless.\n \
+       if (s[m][i] > (nlstate+ndeath)) {
-  Exiting.\n",lval,linei, i,line,j);
+         *nberr++;
-         exit(1);
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-       }
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-       covar[j][i]=(double)(lval);
+         return 1;
-       strcpy(line,stra);
+       }
      }
-     lstra=strlen(stra);
+   }
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+   /*for (i=1; i<=imx; i++){
-       stratrunc = &(stra[lstra-9]);
+   for (m=firstpass; (m<lastpass); m++){
-       num[i]=atol(stratrunc);
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-     }
+ }
-     else
-       num[i]=atol(stra);
+ }*/
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-     i=i+1;
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-   } /* End loop reading  data */
-   fclose(fic);
+   return (0);
-   /* printf("ii=%d", ij);
+   endread:
-      scanf("%d",i);*/
+     printf("Exiting calandcheckages: ");
-   imx=i-1; /* Number of individuals */
+     return (1);
+ }
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+ /***********************************************/
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+ /**************** Main Program *****************/
-     }*/
+ /***********************************************/
-    /*  for (i=1; i<=imx; i++){
-      if (s[4][i]==9)  s[4][i]=-1;
+ int main(int argc, char *argv[])
-      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]));}*/
+ {
+ #ifdef GSL
-   /* for (i=1; i<=imx; i++) */
+   const gsl_multimin_fminimizer_type *T;
+   size_t iteri = 0, it;
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+   int rval = GSL_CONTINUE;
-      else weight[i]=1;*/
+   int status = GSL_SUCCESS;
+   double ssval;
-   /* Calculation of the number of parameters from char model */
+ #endif
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   Tprod=ivector(1,15);
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   Tvaraff=ivector(1,15);
+   int linei, month, year,iout;
-   Tvard=imatrix(1,15,1,2);
+   int jj, ll, li, lj, lk, imk;
-   Tage=ivector(1,15);
+   int numlinepar=0; /* Current linenumber of parameter file */
+   int itimes;
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+   int NDIM=2;
-     j=0, j1=0, k1=1, k2=1;
+   int vpopbased=0;
-     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+   char ca[32], cb[32], cc[32];
-     cptcovn=j+1;
+   /*  FILE *fichtm; *//* Html File */
-     cptcovprod=j1; /*Number of products */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
-     strcpy(modelsav,model);
+   double agedeb, agefin,hf;
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-       printf("Error. Non available option model=%s ",model);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+   double fret;
-       goto end;
+   double **xi,tmp,delta;
-     }
+   double dum; /* Dummy variable */
-     /* This loop fills the array Tvar from the string 'model'.*/
+   double ***p3mat;
+   double ***mobaverage;
-     for(i=(j+1); i>=1;i--){
+   int *indx;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+   char line[MAXLINE], linepar[MAXLINE];
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+   char pathr[MAXLINE], pathimach[MAXLINE];
-       /*scanf("%d",i);*/
+   char **bp, *tok, *val; /* pathtot */
-       if (strchr(strb,'*')) {  /* Model includes a product */
+   int firstobs=1, lastobs=10;
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+   int sdeb, sfin; /* Status at beginning and end */
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+   int c,  h , cpt,l;
-           cptcovprod--;
+   int ju,jl, mi;
-           cutv(strb,stre,strd,'V');
+   int i1,j1, jk,aa,bb, stepsize, ij;
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-           cptcovage++;
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-             Tage[cptcovage]=i;
+   int mobilav=0,popforecast=0;
-             /*printf("stre=%s ", stre);*/
+   int hstepm, nhstepm;
-         }
+   int agemortsup;
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+   float  sumlpop=0.;
-           cptcovprod--;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-           cutv(strb,stre,strc,'V');
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-           Tvar[i]=atoi(stre);
-           cptcovage++;
+   double bage, fage, age, agelim, agebase;
-           Tage[cptcovage]=i;
+   double ftolpl=FTOL;
-         }
+   double **prlim;
-         else {  /* Age is not in the model */
+   double ***param; /* Matrix of parameters */
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+   double  *p;
-           Tvar[i]=ncovcol+k1;
+   double **matcov; /* Matrix of covariance */
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+   double ***delti3; /* Scale */
-           Tprod[k1]=i;
+   double *delti; /* Scale */
-           Tvard[k1][1]=atoi(strc); /* m*/
+   double ***eij, ***vareij;
-           Tvard[k1][2]=atoi(stre); /* n */
+   double **varpl; /* Variances of prevalence limits by age */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+   double *epj, vepp;
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+   double kk1, kk2;
-           for (k=1; k<=lastobs;k++)
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   double **ximort;
-           k1++;
+   char *alph[]={"a","a","b","c","d","e"}, str[4];
-           k2=k2+2;
+   int *dcwave;
-         }
-       }
+   char z[1]="c", occ;
-       else { /* no more sum */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+   /*char  *strt;*/
-        /*  scanf("%d",i);*/
+   char strtend[80];
-       cutv(strd,strc,strb,'V');
-       Tvar[i]=atoi(strc);
+   long total_usecs;
-       }
-       strcpy(modelsav,stra);
+ /*   setlocale (LC_ALL, ""); */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-         scanf("%d",i);*/
+ /*   textdomain (PACKAGE); */
-     } /* end of loop + */
+ /*   setlocale (LC_CTYPE, ""); */
-   } /* end model */
+ /*   setlocale (LC_MESSAGES, ""); */
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   (void) gettimeofday(&start_time,&tzp);
+   curr_time=start_time;
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   tm = *localtime(&start_time.tv_sec);
-   printf("cptcovprod=%d ", cptcovprod);
+   tmg = *gmtime(&start_time.tv_sec);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   strcpy(strstart,asctime(&tm));
-   scanf("%d ",i);*/
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
-     /*  if(mle==1){*/
+ /*  tm = *localtime(&start_time.tv_sec); */
-   if (weightopt != 1) { /* Maximisation without weights*/
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-     for(i=1;i<=n;i++) weight[i]=1.0;
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-   }
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-     /*-calculation of age at interview from date of interview and age at death -*/
+ /*   tp.tv_sec = mktime(&tmg); */
-   agev=matrix(1,maxwav,1,imx);
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
-   for (i=1; i<=imx; i++) {
+ /*  (void) time (&time_value);
-     for(m=2; (m<= maxwav); m++) {
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+ *  tm = *localtime(&time_value);
-         anint[m][i]=9999;
+ *  strstart=asctime(&tm);
-         s[m][i]=-1;
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-       }
+ */
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         nberr++;
+   nberr=0; /* Number of errors and warnings */
-         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);
+   nbwarn=0;
-         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);
+   getcwd(pathcd, size);
-         s[m][i]=-1;
-       }
+   printf("\n%s\n%s",version,fullversion);
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+   if(argc <=1){
-         nberr++;
+     printf("\nEnter the parameter file name: ");
-         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]);
+     fgets(pathr,FILENAMELENGTH,stdin);
-         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]);
+     i=strlen(pathr);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+     if(pathr[i-1]=='\n')
-       }
+       pathr[i-1]='\0';
-     }
+    for (tok = pathr; tok != NULL; ){
-   }
+       printf("Pathr |%s|\n",pathr);
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-   for (i=1; i<=imx; i++)  {
+       printf("val= |%s| pathr=%s\n",val,pathr);
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+       strcpy (pathtot, val);
-     for(m=firstpass; (m<= lastpass); m++){
+       if(pathr[0] == '\0') break; /* Dirty */
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+     }
-         if (s[m][i] >= nlstate+1) {
+   }
-           if(agedc[i]>0)
+   else{
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     strcpy(pathtot,argv[1]);
-               agev[m][i]=agedc[i];
+   }
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-             else {
+   /*cygwin_split_path(pathtot,path,optionfile);
-               if ((int)andc[i]!=9999){
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-                 nbwarn++;
+   /* cutv(path,optionfile,pathtot,'\\');*/
-                 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);
+   /* Split argv[0], imach program to get pathimach */
-                 agev[m][i]=-1;
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-               }
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-             }
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-         }
+  /*   strcpy(pathimach,argv[0]); */
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-                                  years but with the precision of a month */
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+   chdir(path); /* Can be a relative path */
-             agev[m][i]=1;
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-           else if(agev[m][i] <agemin){
+     printf("Current directory %s!\n",pathcd);
-             agemin=agev[m][i];
+   strcpy(command,"mkdir ");
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+   strcat(command,optionfilefiname);
-           }
+   if((outcmd=system(command)) != 0){
-           else if(agev[m][i] >agemax){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-             agemax=agev[m][i];
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+     /* fclose(ficlog); */
-           }
+ /*     exit(1); */
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+   }
-           /*     agev[m][i] = age[i]+2*m;*/
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-         }
+ /*     perror("mkdir"); */
-         else { /* =9 */
+ /*   } */
-           agev[m][i]=1;
-           s[m][i]=-1;
+   /*-------- arguments in the command line --------*/
-         }
-       }
+   /* Log file */
-       else /*= 0 Unknown */
+   strcat(filelog, optionfilefiname);
-         agev[m][i]=1;
+   strcat(filelog,".log");    /* */
-     }
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
+     printf("Problem with logfile %s\n",filelog);
-   }
+     goto end;
-   for (i=1; i<=imx; i++)  {
+   }
-     for(m=firstpass; (m<=lastpass); m++){
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-       if (s[m][i] > (nlstate+ndeath)) {
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-         nberr++;
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+  path=%s \n\
-         goto end;
+  optionfile=%s\n\
-       }
+  optionfilext=%s\n\
-     }
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-   }
+   printf("Local time (at start):%s",strstart);
-   /*for (i=1; i<=imx; i++){
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-   for (m=firstpass; (m<lastpass); m++){
+   fflush(ficlog);
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+ /*   (void) gettimeofday(&curr_time,&tzp); */
- }
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
- }*/
+   /* */
+   strcpy(fileres,"r");
+   strcat(fileres, optionfilefiname);
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   strcat(fileres,".txt");    /* Other files have txt extension */
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+   /*---------arguments file --------*/
-   agegomp=(int)agemin;
-   free_vector(severity,1,maxwav);
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-   free_imatrix(outcome,1,maxwav+1,1,n);
+     printf("Problem with optionfile %s\n",optionfile);
-   free_vector(moisnais,1,n);
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-   free_vector(annais,1,n);
+     fflush(ficlog);
-   /* free_matrix(mint,1,maxwav,1,n);
+     goto end;
-      free_matrix(anint,1,maxwav,1,n);*/
+   }
-   free_vector(moisdc,1,n);
-   free_vector(andc,1,n);
+   strcpy(filereso,"o");
-   wav=ivector(1,imx);
+   strcat(filereso,fileres);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+     printf("Problem with Output resultfile: %s\n", filereso);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     fflush(ficlog);
-   /* Concatenates waves */
+     goto end;
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   }
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   /* Reads comments: lines beginning with '#' */
+   numlinepar=0;
-   Tcode=ivector(1,100);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+     ungetc(c,ficpar);
-   ncodemax[1]=1;
+     fgets(line, MAXLINE, ficpar);
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+     numlinepar++;
+     fputs(line,stdout);
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     fputs(line,ficparo);
-                                  the estimations*/
+     fputs(line,ficlog);
-   h=0;
+   }
-   m=pow(2,cptcoveff);
+   ungetc(c,ficpar);
-   for(k=1;k<=cptcoveff; k++){
+   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
-     for(i=1; i <=(m/pow(2,k));i++){
+   numlinepar++;
-       for(j=1; j <= ncodemax[k]; j++){
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+   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);
-           h++;
+   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);
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   fflush(ficlog);
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+   while((c=getc(ficpar))=='#' && c!= EOF){
-         }
+     ungetc(c,ficpar);
-       }
+     fgets(line, MAXLINE, ficpar);
-     }
+     numlinepar++;
-   }
+     fputs(line, stdout);
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+     //puts(line);
-      codtab[1][2]=1;codtab[2][2]=2; */
+     fputs(line,ficparo);
-   /* for(i=1; i <=m ;i++){
+     fputs(line,ficlog);
-      for(k=1; k <=cptcovn; k++){
+   }
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   ungetc(c,ficpar);
-      }
-      printf("\n");
-      }
+   covar=matrix(0,NCOVMAX,1,n);
-      scanf("%d",i);*/
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-   /*------------ gnuplot -------------*/
+      v1+v2*age+v2*v3 makes cptcovn = 3
-   strcpy(optionfilegnuplot,optionfilefiname);
+   */
-   if(mle==-3)
+   if (strlen(model)>1)
-     strcat(optionfilegnuplot,"-mort");
+     cptcovn=nbocc(model,'+')+1;
-   strcat(optionfilegnuplot,".gp");
+   /* ncovprod */
+   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-     printf("Problem with file %s",optionfilegnuplot);
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-   }
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-   else{
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-     fprintf(ficgp,"\n# %s\n", version);
+     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(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-     fprintf(ficgp,"set missing 'NaNq'\n");
+     fflush(stdout);
-   }
+     fclose (ficlog);
-   /*  fclose(ficgp);*/
+     goto end;
-   /*--------- index.htm --------*/
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   delti=delti3[1][1];
-   if(mle==-3)
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-     strcat(optionfilehtm,"-mort");
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-   strcat(optionfilehtm,".htm");
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-   }
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fclose (ficparo);
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+     fclose (ficlog);
-   strcat(optionfilehtmcov,"-cov.htm");
+     goto end;
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+     exit(0);
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+   }
-   }
+   else if(mle==-3) {
-   else{
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+     matcov=matrix(1,npar,1,npar);
    }
+   else{
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     /* Read guess parameters */
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     /* Reads comments: lines beginning with '#' */
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+     while((c=getc(ficpar))=='#' && c!= EOF){
- \n\
+       ungetc(c,ficpar);
- <hr  size=\"2\" color=\"#EC5E5E\">\
+       fgets(line, MAXLINE, ficpar);
-  <ul><li><h4>Parameter files</h4>\n\
+       numlinepar++;
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+       fputs(line,stdout);
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+       fputs(line,ficparo);
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+       fputs(line,ficlog);
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+     }
-  - Date and time at start: %s</ul>\n",\
+     ungetc(c,ficpar);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-           fileres,fileres,\
+     for(i=1; i <=nlstate; i++){
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+       j=0;
-   fflush(fichtm);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
-   strcpy(pathr,path);
+         j++;
-   strcat(pathr,optionfilefiname);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+         if ((i1 != i) && (j1 != j)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+ It might be a problem of design; if ncovcol and the model are correct\n \
-      and prints on file fileres'p'. */
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+           exit(1);
+         }
-   fprintf(fichtm,"\n");
+         fprintf(ficparo,"%1d%1d",i1,j1);
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         if(mle==1)
- Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+           printf("%1d%1d",i,j);
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+         fprintf(ficlog,"%1d%1d",i,j);
-           imx,agemin,agemax,jmin,jmax,jmean);
+         for(k=1; k<=ncovmodel;k++){
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           fscanf(ficpar," %lf",&param[i][j][k]);
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+           if(mle==1){
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+             printf(" %lf",param[i][j][k]);
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+             fprintf(ficlog," %lf",param[i][j][k]);
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+           }
+           else
+             fprintf(ficlog," %lf",param[i][j][k]);
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+           fprintf(ficparo," %lf",param[i][j][k]);
-      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) */
+         fscanf(ficpar,"\n");
+         numlinepar++;
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+         if(mle==1)
+           printf("\n");
-   if (mle==-3){
+         fprintf(ficlog,"\n");
-     ximort=matrix(1,NDIM,1,NDIM);
+         fprintf(ficparo,"\n");
-     cens=ivector(1,n);
+       }
-     ageexmed=vector(1,n);
+     }
-     agecens=vector(1,n);
+     fflush(ficlog);
-     dcwave=ivector(1,n);
+     p=param[1][1];
-     for (i=1; i<=imx; i++){
-       dcwave[i]=-1;
+     /* Reads comments: lines beginning with '#' */
-       for (m=firstpass; m<=lastpass; m++)
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         if (s[m][i]>nlstate) {
+       ungetc(c,ficpar);
-           dcwave[i]=m;
+       fgets(line, MAXLINE, ficpar);
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+       numlinepar++;
-           break;
+       fputs(line,stdout);
-         }
+       fputs(line,ficparo);
-     }
+       fputs(line,ficlog);
+     }
-     for (i=1; i<=imx; i++) {
+     ungetc(c,ficpar);
-       if (wav[i]>0){
-         ageexmed[i]=agev[mw[1][i]][i];
+     for(i=1; i <=nlstate; i++){
-         j=wav[i];
+       for(j=1; j <=nlstate+ndeath-1; j++){
-         agecens[i]=1.;
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1-i)*(j1-j)!=0){
-         if (ageexmed[i]> 1 && wav[i] > 0){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-           agecens[i]=agev[mw[j][i]][i];
+           exit(1);
-           cens[i]= 1;
+         }
-         }else if (ageexmed[i]< 1)
+         printf("%1d%1d",i,j);
-           cens[i]= -1;
+         fprintf(ficparo,"%1d%1d",i1,j1);
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+         fprintf(ficlog,"%1d%1d",i1,j1);
-           cens[i]=0 ;
+         for(k=1; k<=ncovmodel;k++){
-       }
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-       else cens[i]=-1;
+           printf(" %le",delti3[i][j][k]);
-     }
+           fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-     for (i=1;i<=NDIM;i++) {
+         }
-       for (j=1;j<=NDIM;j++)
+         fscanf(ficpar,"\n");
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+         numlinepar++;
-     }
+         printf("\n");
+         fprintf(ficparo,"\n");
-     p[1]=0.0268; p[NDIM]=0.083;
+         fprintf(ficlog,"\n");
-     /*printf("%lf %lf", p[1], p[2]);*/
+       }
+     }
+     fflush(ficlog);
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     strcpy(filerespow,"pow-mort");
+     delti=delti3[1][1];
-     strcat(filerespow,fileres);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-       printf("Problem with resultfile: %s\n", filerespow);
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     }
+     /* Reads comments: lines beginning with '#' */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     /*  for (i=1;i<=nlstate;i++)
+       ungetc(c,ficpar);
-         for(j=1;j<=nlstate+ndeath;j++)
+       fgets(line, MAXLINE, ficpar);
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+       numlinepar++;
-     */
+       fputs(line,stdout);
-     fprintf(ficrespow,"\n");
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     }
-     fclose(ficrespow);
+     ungetc(c,ficpar);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
-     for(i=1; i <=NDIM; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-       for(j=i+1;j<=NDIM;j++)
-         matcov[i][j]=matcov[j][i];
+     for(i=1; i <=npar; i++){
+       fscanf(ficpar,"%s",&str);
-     printf("\nCovariance matrix\n ");
+       if(mle==1)
-     for(i=1; i <=NDIM; i++) {
+         printf("%s",str);
-       for(j=1;j<=NDIM;j++){
+       fprintf(ficlog,"%s",str);
-         printf("%f ",matcov[i][j]);
+       fprintf(ficparo,"%s",str);
-       }
+       for(j=1; j <=i; j++){
-       printf("\n ");
+         fscanf(ficpar," %le",&matcov[i][j]);
-     }
+         if(mle==1){
+           printf(" %.5le",matcov[i][j]);
-     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++)
+         fprintf(ficlog," %.5le",matcov[i][j]);
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
-     lsurv=vector(1,AGESUP);
+       fscanf(ficpar,"\n");
-     lpop=vector(1,AGESUP);
+       numlinepar++;
-     tpop=vector(1,AGESUP);
+       if(mle==1)
-     lsurv[agegomp]=100000;
+         printf("\n");
+       fprintf(ficlog,"\n");
-     for (k=agegomp;k<=AGESUP;k++) {
+       fprintf(ficparo,"\n");
-       agemortsup=k;
+     }
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     for(i=1; i <=npar; i++)
-     }
+       for(j=i+1;j<=npar;j++)
+         matcov[i][j]=matcov[j][i];
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+     if(mle==1)
+       printf("\n");
-     for (k=agegomp;k<agemortsup;k++){
+     fprintf(ficlog,"\n");
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
-       sumlpop=sumlpop+lpop[k];
+     fflush(ficlog);
-     }
+     /*-------- Rewriting parameter file ----------*/
-     tpop[agegomp]=sumlpop;
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     for (k=agegomp;k<(agemortsup-3);k++){
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-       /*  tpop[k+1]=2;*/
+     strcat(rfileres,".");    /* */
-       tpop[k+1]=tpop[k]-lpop[k];
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     }
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+     }
-     for (k=agegomp;k<(agemortsup-2);k++)
+     fprintf(ficres,"#%s\n",version);
-       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]);
+   }    /* End of mle != -3 */
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+   n= lastobs;
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   num=lvector(1,n);
+   moisnais=vector(1,n);
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+   annais=vector(1,n);
-                      stepm, weightopt,\
+   moisdc=vector(1,n);
-                      model,imx,p,matcov,agemortsup);
+   andc=vector(1,n);
+   agedc=vector(1,n);
-     free_vector(lsurv,1,AGESUP);
+   cod=ivector(1,n);
-     free_vector(lpop,1,AGESUP);
+   weight=vector(1,n);
-     free_vector(tpop,1,AGESUP);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-   } /* Endof if mle==-3 */
+   mint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
-   else{ /* For mle >=1 */
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   tab=ivector(1,NCOVMAX);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   ncodemax=ivector(1,8); /* hard coded ? */
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     for (k=1; k<=npar;k++)
+   /* Reads data from file datafile */
-       printf(" %d %8.5f",k,p[k]);
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     printf("\n");
+     goto end;
-     globpr=1; /* to print the contributions */
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   /* Calculation of the number of parameters from char model */
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-     for (k=1; k<=npar;k++)
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-       printf(" %d %8.5f",k,p[k]);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
-     printf("\n");
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     if(mle>=1){ /* Could be 1 or 2 */
+         k=1 Tvar[1]=2 (from V2)
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     */
-     }
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
-     /*--------- results files --------------*/
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
-     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);
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
+   /* For model-covariate k tells which data-covariate to use but
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     because this model-covariate is a construction we invent a new column
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     ncovcol + k1
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     for(i=1,jk=1; i <=nlstate; i++){
+     Tvar[3=V1*V4]=4+1 etc */
-       for(k=1; k <=(nlstate+ndeath); k++){
+   Tprod=ivector(1,15); /* Gives the position of a product */
-         if (k != i) {
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-           printf("%d%d ",i,k);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-           fprintf(ficlog,"%d%d ",i,k);
+   */
-           fprintf(ficres,"%1d%1d ",i,k);
+   Tvaraff=ivector(1,15);
-           for(j=1; j <=ncovmodel; j++){
+   Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
-             printf("%lf ",p[jk]);
+                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
-             fprintf(ficlog,"%lf ",p[jk]);
+                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-             fprintf(ficres,"%lf ",p[jk]);
+   Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-             jk++;
+covariates (3 plus signs)
-           }
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-           printf("\n");
+                       */
-           fprintf(ficlog,"\n");
-           fprintf(ficres,"\n");
+   if(decodemodel(model, lastobs) == 1)
-         }
+     goto end;
-       }
-     }
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-     if(mle!=0){
+     nbwarn++;
-       /* Computing hessian and covariance matrix */
+     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);
-       ftolhess=ftol; /* Usually correct */
+     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);
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+   }
-     }
+     /*  if(mle==1){*/
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-     printf("# Scales (for hessian or gradient estimation)\n");
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   }
-     for(i=1,jk=1; i <=nlstate; i++){
-       for(j=1; j <=nlstate+ndeath; j++){
+     /*-calculation of age at interview from date of interview and age at death -*/
-         if (j!=i) {
+   agev=matrix(1,maxwav,1,imx);
-           fprintf(ficres,"%1d%1d",i,j);
-           printf("%1d%1d",i,j);
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-           fprintf(ficlog,"%1d%1d",i,j);
+     goto end;
-           for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
+   agegomp=(int)agemin;
-             fprintf(ficres," %.5e",delti[jk]);
+   free_vector(moisnais,1,n);
-             jk++;
+   free_vector(annais,1,n);
-           }
+   /* free_matrix(mint,1,maxwav,1,n);
-           printf("\n");
+      free_matrix(anint,1,maxwav,1,n);*/
-           fprintf(ficlog,"\n");
+   free_vector(moisdc,1,n);
-           fprintf(ficres,"\n");
+   free_vector(andc,1,n);
-         }
-       }
-     }
+   wav=ivector(1,imx);
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     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");
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-     if(mle>=1)
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-       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");
+   /* Concatenates waves */
-     /* # 121 Var(a12)\n\ */
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-     /* # 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\ */
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   ncodemax[1]=1;
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+                                  the estimations*/
-     /* Just to have a covariance matrix which will be more understandable
+   h=0;
-        even is we still don't want to manage dictionary of variables
+   m=pow(2,cptcoveff);
-     */
-     for(itimes=1;itimes<=2;itimes++){
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-       jj=0;
+     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       for(i=1; i <=nlstate; i++){
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-         for(j=1; j <=nlstate+ndeath; j++){
+         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-           if(j==i) continue;
+           h++;
-           for(k=1; k<=ncovmodel;k++){
+           if (h>m)
-             jj++;
+             h=1;
-             ca[0]= k+'a'-1;ca[1]='\0';
+           /**< codtab(h,k)  k
-             if(itimes==1){
+            *     h     1     2     3     4
-               if(mle>=1)
+            *______________________________
-                 printf("#%1d%1d%d",i,j,k);
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+            *     2     2     1     1     1
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+            *     3 i=2 1     2     1     1
-             }else{
+            *     4     2     2     1     1
-               if(mle>=1)
+            *     5 i=3 1 i=2 1     2     1
-                 printf("%1d%1d%d",i,j,k);
+            *     6     2     1     2     1
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+            *     7 i=4 1     2     2     1
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+            *     8     2     2     2     1
-             }
+            *     9 i=5 1 i=3 1 i=2 1     1
-             ll=0;
+            *    10     2     1     1     1
-             for(li=1;li <=nlstate; li++){
+            *    11 i=6 1     2     1     1
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+            *    12     2     2     1     1
-                 if(lj==li) continue;
+            *    13 i=7 1 i=4 1     2     1
-                 for(lk=1;lk<=ncovmodel;lk++){
+            *    14     2     1     2     1
-                   ll++;
+            *    15 i=8 1     2     2     1
-                   if(ll<=jj){
+            *    16     2     2     2     1
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+            */
-                     if(ll<jj){
+           codtab[h][k]=j;
-                       if(itimes==1){
+           codtab[h][Tvar[k]]=j;
-                         if(mle>=1)
+           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]]);
-                           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("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-                           printf(" %.5e",matcov[jj][ll]);
+      codtab[1][2]=1;codtab[2][2]=2; */
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   /* for(i=1; i <=m ;i++){
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+      for(k=1; k <=cptcovn; k++){
-                       }
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-                     }else{
+      }
-                       if(itimes==1){
+      printf("\n");
-                         if(mle>=1)
+      }
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+      scanf("%d",i);*/
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+   /*------------ gnuplot -------------*/
-                       }else{
+   strcpy(optionfilegnuplot,optionfilefiname);
-                         if(mle>=1)
+   if(mle==-3)
-                           printf(" %.5e",matcov[jj][ll]);
+     strcat(optionfilegnuplot,"-mort");
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   strcat(optionfilegnuplot,".gp");
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-                     }
+     printf("Problem with file %s",optionfilegnuplot);
-                   }
+   }
-                 } /* end lk */
+   else{
-               } /* end lj */
+     fprintf(ficgp,"\n# %s\n", version);
-             } /* end li */
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-             if(mle>=1)
+     //fprintf(ficgp,"set missing 'NaNq'\n");
-               printf("\n");
+     fprintf(ficgp,"set datafile missing 'NaNq'\n");
-             fprintf(ficlog,"\n");
+   }
-             fprintf(ficres,"\n");
+   /*  fclose(ficgp);*/
-             numlinepar++;
+   /*--------- index.htm --------*/
-           } /* end k*/
-         } /*end j */
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-       } /* end i */
+   if(mle==-3)
-     } /* end itimes */
+     strcat(optionfilehtm,"-mort");
+   strcat(optionfilehtm,".htm");
-     fflush(ficlog);
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-     fflush(ficres);
+     printf("Problem with %s \n",optionfilehtm);
+     exit(0);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   }
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-       puts(line);
+   strcat(optionfilehtmcov,"-cov.htm");
-       fputs(line,ficparo);
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-     }
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-     ungetc(c,ficpar);
+   }
+   else{
-     estepm=0;
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-     if (fage <= 2) {
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-       bage = ageminpar;
+   }
-       fage = agemaxpar;
-     }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+ \n\
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
+  <ul><li><h4>Parameter files</h4>\n\
-     while((c=getc(ficpar))=='#' && c!= EOF){
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-       ungetc(c,ficpar);
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-       fgets(line, MAXLINE, ficpar);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-       puts(line);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-       fputs(line,ficparo);
+  - Date and time at start: %s</ul>\n",\
-     }
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-     ungetc(c,ficpar);
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fileres,fileres,\
-     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);
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-     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);
+   fflush(fichtm);
-     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);
+   strcpy(pathr,path);
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+   strcat(pathr,optionfilefiname);
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   /* Calculates basic frequencies. Computes observed prevalence at single age
-       fgets(line, MAXLINE, ficpar);
+      and prints on file fileres'p'. */
-       puts(line);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-       fputs(line,ficparo);
-     }
+   fprintf(fichtm,"\n");
-     ungetc(c,ficpar);
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+           imx,agemin,agemax,jmin,jmax,jmean);
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     fprintf(ficres,"pop_based=%d\n",popbased);
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-       fgets(line, MAXLINE, ficpar);
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-       puts(line);
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-       fputs(line,ficparo);
-     }
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     ungetc(c,ficpar);
+   if (mle==-3){
-     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);
+     ximort=matrix(1,NDIM,1,NDIM);
-     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);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     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);
+     cens=ivector(1,n);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+     ageexmed=vector(1,n);
-     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);
+     agecens=vector(1,n);
-     /* day and month of proj2 are not used but only year anproj2.*/
+     dcwave=ivector(1,n);
+     for (i=1; i<=imx; i++){
+       dcwave[i]=-1;
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+       for (m=firstpass; m<=lastpass; m++)
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         if (s[m][i]>nlstate) {
+           dcwave[i]=m;
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+           break;
+         }
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     }
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     for (i=1; i<=imx; i++) {
+       if (wav[i]>0){
-    /*------------ free_vector  -------------*/
+         ageexmed[i]=agev[mw[1][i]][i];
-    /*  chdir(path); */
+         j=wav[i];
+         agecens[i]=1.;
-     free_ivector(wav,1,imx);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+         if (ageexmed[i]> 1 && wav[i] > 0){
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+           agecens[i]=agev[mw[j][i]][i];
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+           cens[i]= 1;
-     free_lvector(num,1,n);
+         }else if (ageexmed[i]< 1)
-     free_vector(agedc,1,n);
+           cens[i]= -1;
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+           cens[i]=0 ;
-     fclose(ficparo);
+       }
-     fclose(ficres);
+       else cens[i]=-1;
+     }
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     for (i=1;i<=NDIM;i++) {
+       for (j=1;j<=NDIM;j++)
-     strcpy(filerespl,"pl");
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-     strcat(filerespl,fileres);
+     }
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     p[1]=0.0268; p[NDIM]=0.083;
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     /*printf("%lf %lf", p[1], p[2]);*/
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ #ifdef GSL
-     pstamp(ficrespl);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+ #elsedef
-     fprintf(ficrespl,"#Age ");
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+ #endif
-     fprintf(ficrespl,"\n");
+     strcpy(filerespow,"pow-mort");
+     strcat(filerespow,fileres);
-     prlim=matrix(1,nlstate,1,nlstate);
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
-     agebase=ageminpar;
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     agelim=agemaxpar;
+     }
-     ftolpl=1.e-10;
+ #ifdef GSL
-     i1=cptcoveff;
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-     if (cptcovn < 1){i1=1;}
+ #elsedef
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ #endif
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     /*  for (i=1;i<=nlstate;i++)
-         k=k+1;
+         for(j=1;j<=nlstate+ndeath;j++)
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-         fprintf(ficrespl,"\n#******");
+     */
-         printf("\n#******");
+     fprintf(ficrespow,"\n");
-         fprintf(ficlog,"\n#******");
+ #ifdef GSL
-         for(j=1;j<=cptcoveff;j++) {
+     /* gsl starts here */
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     T = gsl_multimin_fminimizer_nmsimplex;
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     gsl_multimin_fminimizer *sfm = NULL;
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     gsl_vector *ss, *x;
-         }
+     gsl_multimin_function minex_func;
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
+     /* Initial vertex size vector */
-         fprintf(ficlog,"******\n");
+     ss = gsl_vector_alloc (NDIM);
-         for (age=agebase; age<=agelim; age++){
+     if (ss == NULL){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-           fprintf(ficrespl,"%.0f ",age );
+     }
-           for(j=1;j<=cptcoveff;j++)
+     /* Set all step sizes to 1 */
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     gsl_vector_set_all (ss, 0.001);
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+     /* Starting point */
-           fprintf(ficrespl,"\n");
-         }
+     x = gsl_vector_alloc (NDIM);
-       }
-     }
+     if (x == NULL){
-     fclose(ficrespl);
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-     /*------------- h Pij x at various ages ------------*/
+     }
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     /* Initialize method and iterate */
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+ /*     gsl_vector_set(x, 0, 0.0268); */
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+ /*     gsl_vector_set(x, 1, 0.083); */
-     }
+     gsl_vector_set(x, 0, p[1]);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     gsl_vector_set(x, 1, p[2]);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     minex_func.f = &gompertz_f;
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     minex_func.n = NDIM;
-     /*if (stepm<=24) stepsize=2;*/
+     minex_func.params = (void *)&p; /* ??? */
-     agelim=AGESUP;
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-     hstepm=stepsize*YEARM; /* Every year of age */
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     printf("Iterations beginning .....\n\n");
-     /* hstepm=1;   aff par mois*/
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-     pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     iteri=0;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     while (rval == GSL_CONTINUE){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       iteri++;
-         k=k+1;
+       status = gsl_multimin_fminimizer_iterate(sfm);
-         fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+       if (status) printf("error: %s\n", gsl_strerror (status));
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fflush(0);
-         fprintf(ficrespij,"******\n");
+       if (status)
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         break;
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+       if (rval == GSL_SUCCESS)
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         printf ("converged to a local maximum at\n");
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       printf("%5d ", iteri);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+       for (it = 0; it < NDIM; it++){
-           for(i=1; i<=nlstate;i++)
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
-             for(j=1; j<=nlstate+ndeath;j++)
+       }
-               fprintf(ficrespij," %1d-%1d",i,j);
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
-           fprintf(ficrespij,"\n");
+     }
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
+     gsl_vector_free(x); /* initial values */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+     gsl_vector_free(ss); /* inital step size */
-             fprintf(ficrespij,"\n");
+     for (it=0; it<NDIM; it++){
-           }
+       p[it+1]=gsl_vector_get(sfm->x,it);
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficrespow," %.12lf", p[it]);
-           fprintf(ficrespij,"\n");
+     }
-         }
+     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);
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+ #endif
+     fclose(ficrespow);
-     fclose(ficrespij);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for(i=1;i<=AGESUP;i++)
+     for(i=1; i <=NDIM; i++)
-       for(j=1;j<=NCOVMAX;j++)
+       for(j=i+1;j<=NDIM;j++)
-         for(k=1;k<=NCOVMAX;k++)
+         matcov[i][j]=matcov[j][i];
-           probs[i][j][k]=0.;
+     printf("\nCovariance matrix\n ");
-     /*---------- Forecasting ------------------*/
+     for(i=1; i <=NDIM; i++) {
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+       for(j=1;j<=NDIM;j++){
-     if(prevfcast==1){
+         printf("%f ",matcov[i][j]);
-       /*    if(stepm ==1){*/
+       }
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       printf("\n ");
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     }
-       /*      }  */
-       /*      else{ */
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-       /*        erreur=108; */
+     for (i=1;i<=NDIM;i++)
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-       /*        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); */
-       /*      } */
+     lsurv=vector(1,AGESUP);
-     }
+     lpop=vector(1,AGESUP);
+     tpop=vector(1,AGESUP);
+     lsurv[agegomp]=100000;
-     /*---------- Health expectancies and variances ------------*/
+     for (k=agegomp;k<=AGESUP;k++) {
-     strcpy(filerest,"t");
+       agemortsup=k;
-     strcat(filerest,fileres);
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     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;
+     for (k=agegomp;k<agemortsup;k++)
-     }
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-     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);
+     for (k=agegomp;k<agemortsup;k++){
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+       sumlpop=sumlpop+lpop[k];
-     strcpy(filerese,"e");
+     }
-     strcat(filerese,fileres);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+     tpop[agegomp]=sumlpop;
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     for (k=agegomp;k<(agemortsup-3);k++){
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       /*  tpop[k+1]=2;*/
-     }
+       tpop[k+1]=tpop[k]-lpop[k];
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     }
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-     strcpy(fileresstde,"stde");
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-     strcat(fileresstde,fileres);
+     for (k=agegomp;k<(agemortsup-2);k++)
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+       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("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);
-     }
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
-     strcpy(filerescve,"cve");
+                      stepm, weightopt,\
-     strcat(filerescve,fileres);
+                      model,imx,p,matcov,agemortsup);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     free_vector(lsurv,1,AGESUP);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+     free_vector(lpop,1,AGESUP);
-     }
+     free_vector(tpop,1,AGESUP);
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ #ifdef GSL
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
-     strcpy(fileresv,"v");
+     free_ivector(dcwave,1,n);
-     strcat(fileresv,fileres);
+     free_matrix(ximort,1,NDIM,1,NDIM);
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+ #endif
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+   } /* Endof if mle==-3 */
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
-     }
+   else{ /* For mle >=1 */
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     globpr=0;/* debug */
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     for (k=1; k<=npar;k++)
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+       printf(" %d %8.5f",k,p[k]);
-     /*  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",\
+     printf("\n");
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+     globpr=1; /* to print the contributions */
-     */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     if (mobilav!=0) {
+     for (k=1; k<=npar;k++)
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       printf(" %d %8.5f",k,p[k]);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+     printf("\n");
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+     if(mle>=1){ /* Could be 1 or 2 */
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-       }
+     }
-     }
+     /*--------- results files --------------*/
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     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);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficrest,"\n#****** ");
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-         for(j=1;j<=cptcoveff;j++)
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-         fprintf(ficrest,"******\n");
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
-         fprintf(ficreseij,"\n#****** ");
+         if (k != i) {
-         fprintf(ficresstdeij,"\n#****** ");
+           printf("%d%d ",i,k);
-         fprintf(ficrescveij,"\n#****** ");
+           fprintf(ficlog,"%d%d ",i,k);
-         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficres,"%1d%1d ",i,k);
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           for(j=1; j <=ncovmodel; j++){
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             printf("%lf ",p[jk]);
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             fprintf(ficlog,"%lf ",p[jk]);
-         }
+             fprintf(ficres,"%lf ",p[jk]);
-         fprintf(ficreseij,"******\n");
+             jk++;
-         fprintf(ficresstdeij,"******\n");
+           }
-         fprintf(ficrescveij,"******\n");
+           printf("\n");
+           fprintf(ficlog,"\n");
-         fprintf(ficresvij,"\n#****** ");
+           fprintf(ficres,"\n");
-         for(j=1;j<=cptcoveff;j++)
+         }
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-         fprintf(ficresvij,"******\n");
+     }
+     if(mle!=0){
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       /* Computing hessian and covariance matrix */
-         oldm=oldms;savm=savms;
+       ftolhess=ftol; /* Usually correct */
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+     }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     printf("# Scales (for hessian or gradient estimation)\n");
-         oldm=oldms;savm=savms;
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+     for(i=1,jk=1; i <=nlstate; i++){
-         if(popbased==1){
+       for(j=1; j <=nlstate+ndeath; j++){
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+         if (j!=i) {
-         }
+           fprintf(ficres,"%1d%1d",i,j);
+           printf("%1d%1d",i,j);
-         pstamp(ficrest);
+           fprintf(ficlog,"%1d%1d",i,j);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+           for(k=1; k<=ncovmodel;k++){
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+             printf(" %.5e",delti[jk]);
-         fprintf(ficrest,"\n");
+             fprintf(ficlog," %.5e",delti[jk]);
+             fprintf(ficres," %.5e",delti[jk]);
-         epj=vector(1,nlstate+1);
+             jk++;
-         for(age=bage; age <=fage ;age++){
+           }
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           printf("\n");
-           if (popbased==1) {
+           fprintf(ficlog,"\n");
-             if(mobilav ==0){
+           fprintf(ficres,"\n");
-               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(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");
-           fprintf(ficrest," %4.0f",age);
+     /* # 121 Var(a12)\n\ */
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+     /* # 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\ */
-             epj[nlstate+1] +=epj[j];
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-           }
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-           for(i=1, vepp=0.;i <=nlstate;i++)
-             for(j=1;j <=nlstate;j++)
+     /* Just to have a covariance matrix which will be more understandable
-               vepp += vareij[i][j][(int)age];
+        even is we still don't want to manage dictionary of variables
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+     */
-           for(j=1;j <=nlstate;j++){
+     for(itimes=1;itimes<=2;itimes++){
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+       jj=0;
-           }
+       for(i=1; i <=nlstate; i++){
-           fprintf(ficrest,"\n");
+         for(j=1; j <=nlstate+ndeath; j++){
-         }
+           if(j==i) continue;
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+           for(k=1; k<=ncovmodel;k++){
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+             jj++;
-         free_vector(epj,1,nlstate+1);
+             ca[0]= k+'a'-1;ca[1]='\0';
-       }
+             if(itimes==1){
-     }
+               if(mle>=1)
-     free_vector(weight,1,n);
+                 printf("#%1d%1d%d",i,j,k);
-     free_imatrix(Tvard,1,15,1,2);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-     free_imatrix(s,1,maxwav+1,1,n);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
-     free_matrix(anint,1,maxwav,1,n);
+             }else{
-     free_matrix(mint,1,maxwav,1,n);
+               if(mle>=1)
-     free_ivector(cod,1,n);
+                 printf("%1d%1d%d",i,j,k);
-     free_ivector(tab,1,NCOVMAX);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
-     fclose(ficreseij);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
-     fclose(ficresstdeij);
+             }
-     fclose(ficrescveij);
+             ll=0;
-     fclose(ficresvij);
+             for(li=1;li <=nlstate; li++){
-     fclose(ficrest);
+               for(lj=1;lj <=nlstate+ndeath; lj++){
-     fclose(ficpar);
+                 if(lj==li) continue;
+                 for(lk=1;lk<=ncovmodel;lk++){
-     /*------- Variance of period (stable) prevalence------*/
+                   ll++;
+                   if(ll<=jj){
-     strcpy(fileresvpl,"vpl");
+                     cb[0]= lk +'a'-1;cb[1]='\0';
-     strcat(fileresvpl,fileres);
+                     if(ll<jj){
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+                       if(itimes==1){
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+                         if(mle>=1)
-       exit(0);
+                           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);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       }else{
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+                         if(mle>=1)
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+                           printf(" %.5e",matcov[jj][ll]);
-         k=k+1;
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-         fprintf(ficresvpl,"\n#****** ");
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-         for(j=1;j<=cptcoveff;j++)
+                       }
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                     }else{
-         fprintf(ficresvpl,"******\n");
+                       if(itimes==1){
+                         if(mle>=1)
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+                           printf(" Var(%s%1d%1d)",ca,i,j);
-         oldm=oldms;savm=savms;
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+                       }else{
-       }
+                         if(mle>=1)
-     }
+                           printf(" %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-     fclose(ficresvpl);
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                       }
-     /*---------- End : free ----------------*/
+                     }
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                   }
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                 } /* end lk */
+               } /* end lj */
-   }  /* mle==-3 arrives here for freeing */
+             } /* end li */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+             if(mle>=1)
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+               printf("\n");
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+             fprintf(ficlog,"\n");
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+             fprintf(ficres,"\n");
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+             numlinepar++;
-     free_matrix(covar,0,NCOVMAX,1,n);
+           } /* end k*/
-     free_matrix(matcov,1,npar,1,npar);
+         } /*end j */
-     /*free_vector(delti,1,npar);*/
+       } /* end i */
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     } /* end itimes */
-     free_matrix(agev,1,maxwav,1,imx);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+     fflush(ficlog);
+     fflush(ficres);
-     free_ivector(ncodemax,1,8);
-     free_ivector(Tvar,1,15);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     free_ivector(Tprod,1,15);
+       ungetc(c,ficpar);
-     free_ivector(Tvaraff,1,15);
+       fgets(line, MAXLINE, ficpar);
-     free_ivector(Tage,1,15);
+       fputs(line,stdout);
-     free_ivector(Tcode,1,100);
+       fputs(line,ficparo);
+     }
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     ungetc(c,ficpar);
-     free_imatrix(codtab,1,100,1,10);
-   fflush(fichtm);
+     estepm=0;
-   fflush(ficgp);
+     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) {
-   if((nberr >0) || (nbwarn>0)){
+       bage = ageminpar;
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+       fage = agemaxpar;
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     }
-   }else{
-     printf("End of Imach\n");
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficlog,"End of Imach\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);
-   printf("See log file on %s\n",filelog);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   (void) gettimeofday(&end_time,&tzp);
+       ungetc(c,ficpar);
-   tm = *localtime(&end_time.tv_sec);
+       fgets(line, MAXLINE, ficpar);
-   tmg = *gmtime(&end_time.tv_sec);
+       fputs(line,stdout);
-   strcpy(strtend,asctime(&tm));
+       fputs(line,ficparo);
-   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);
+     ungetc(c,ficpar);
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     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);
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     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(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     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);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
+     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);
- /*   if(fileappend(fichtm,optionfilehtm)){ */
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   fclose(fichtm);
+       ungetc(c,ficpar);
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+       fgets(line, MAXLINE, ficpar);
-   fclose(fichtmcov);
+       fputs(line,stdout);
-   fclose(ficgp);
+       fputs(line,ficparo);
-   fclose(ficlog);
+     }
-   /*------ End -----------*/
+     ungetc(c,ficpar);
-    printf("Before Current directory %s!\n",pathcd);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-    if(chdir(pathcd) != 0)
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     printf("Can't move to directory %s!\n",path);
-   if(getcwd(pathcd,MAXLINE) > 0)
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     printf("Current directory %s!\n",pathcd);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     fprintf(ficres,"pop_based=%d\n",popbased);
-   sprintf(plotcmd,"gnuplot");
- #ifndef UNIX
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+       ungetc(c,ficpar);
- #endif
+       fgets(line, MAXLINE, ficpar);
-   if(!stat(plotcmd,&info)){
+       fputs(line,stdout);
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+       fputs(line,ficparo);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     }
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     ungetc(c,ficpar);
-     }else
-       strcpy(pplotcmd,plotcmd);
+     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);
- #ifdef UNIX
+     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);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     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(!stat(plotcmd,&info)){
+     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);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     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);
-     }else
+     /* day and month of proj2 are not used but only year anproj2.*/
-       strcpy(pplotcmd,plotcmd);
- #endif
-   }else
-     strcpy(pplotcmd,plotcmd);
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   if((outcmd=system(plotcmd)) != 0){
-     printf("\n Problem with gnuplot\n");
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-   }
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-   printf(" Wait...");
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-   while (z[0] != 'q') {
-     /* chdir(path); */
+    /*------------ free_vector  -------------*/
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+    /*  chdir(path); */
-     scanf("%s",z);
- /*     if (z[0] == 'c') system("./imach"); */
+     free_ivector(wav,1,imx);
-     if (z[0] == 'e') {
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-       system(optionfilehtm);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-     }
+     free_lvector(num,1,n);
-     else if (z[0] == 'g') system(plotcmd);
+     free_vector(agedc,1,n);
-     else if (z[0] == 'q') exit(0);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
-   }
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   end:
+     fclose(ficparo);
-   while (z[0] != 'q') {
+     fclose(ficres);
-     printf("\nType  q for exiting: ");
-     scanf("%s",z);
-   }
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
- }
+     strcpy(filerespl,"pl");
+     strcat(filerespl,fileres);
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     }
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     pstamp(ficrespl);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     fprintf(ficrespl,"#Age ");
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     fprintf(ficrespl,"\n");
+     prlim=matrix(1,nlstate,1,nlstate);
+     agebase=ageminpar;
+     agelim=agemaxpar;
+     ftolpl=1.e-10;
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         /* to clean */
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
+         fprintf(ficrespl,"\n#******");
+         printf("\n#******");
+         fprintf(ficlog,"\n#******");
+         for(j=1;j<=cptcoveff;j++) {
+           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]]);
+         }
+         fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         for (age=agebase; age<=agelim; age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           fprintf(ficrespl,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           for(i=1; i<=nlstate;i++)
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl,"\n");
+         } /* Age */
+         /* was end of cptcod */
+     } /* cptcov */
+     fclose(ficrespl);
+     /*------------- h Pij x at various ages ------------*/
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* 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++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         fprintf(ficrespij,"\n#****** ");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespij,"******\n");
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %1d-%1d",i,j);
+           fprintf(ficrespij,"\n");
+           for (h=0; h<=nhstepm; h++){
+             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+             for(i=1; i<=nlstate;i++)
+               for(j=1; j<=nlstate+ndeath;j++)
+                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespij,"\n");
+           }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           fprintf(ficrespij,"\n");
+         }
+       }
+     }
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     fclose(ficrespij);
+     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++){
+         k=k+1;
+         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++){
+         k=k+1;
+         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);
+         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;
+           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,1,15,1,2);
+     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++){
+         k=k+1;
+         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,1,8);
+     free_ivector(Tvar,1,15);
+     free_ivector(Tprod,1,15);
+     free_ivector(Tvaraff,1,15);
+     free_ivector(Tage,1,15);
+     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\n");
+   }
+   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') {
+       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+       system(optionfilehtm);
+     }
+     else if (z[0] == 'g') system(plotcmd);
+     else if (z[0] == 'q') exit(0);
+   }
+   end:
+   while (z[0] != 'q') {
+     printf("\nType  q for exiting: ");
+     scanf("%s",z);
+   }
+ }

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

Removed from v.1.125
changed lines
	Added in v.1.143