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Diff for /imach/src/imach.c between versions 1.125 and 1.139

-version 1.125, 2006/04/04 15:20:31
+version 1.139, 2010/06/14 07:50:17
  Line 1
  /* $Id$
    $State$
    $Log$
+   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> */
  #include <time.h>
  #include "timeval.h"
- /* #include <libintl.h> */
+ #ifdef GSL
- /* #define _(String) gettext (String) */
+ #include <gsl/gsl_errno.h>
+ #include <gsl/gsl_multimin.h>
- #define MAXLINE 256
+ #endif
- #define GNUPLOTPROGRAM "gnuplot"
+ /* #include <libintl.h> */
- /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+ /* #define _(String) gettext (String) */
- #define FILENAMELENGTH 132
+ #define MAXLINE 256
- #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
+ #define GNUPLOTPROGRAM "gnuplot"
+ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define MAXPARM 30 /* Maximum number of parameters for the optimization */
+ #define FILENAMELENGTH 132
- #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+ #define GLOCK_ERROR_NOPATH              -1      /* empty path */
- #define NINTERVMAX 8
+ #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+ #define MAXPARM 128 /* Maximum number of parameters for the optimization */
- #define NCOVMAX 8 /* Maximum number of covariates */
+ #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
- #define MAXN 20000
- #define YEARM 12. /* Number of months per year */
+ #define NINTERVMAX 8
- #define AGESUP 130
+ #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
- #define AGEBASE 40
+ #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
- #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
+ #define NCOVMAX 20 /* Maximum number of covariates */
- #ifdef UNIX
+ #define MAXN 20000
- #define DIRSEPARATOR '/'
+ #define YEARM 12. /* Number of months per year */
- #define CHARSEPARATOR "/"
+ #define AGESUP 130
- #define ODIRSEPARATOR '\\'
+ #define AGEBASE 40
- #else
+ #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
- #define DIRSEPARATOR '\\'
+ #ifdef UNIX
- #define CHARSEPARATOR "\\"
+ #define DIRSEPARATOR '/'
- #define ODIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
- #endif
+ #define ODIRSEPARATOR '\\'
+ #else
- /* $Id$ */
+ #define DIRSEPARATOR '\\'
- /* $State$ */
+ #define CHARSEPARATOR "\\"
+ #define ODIRSEPARATOR '/'
- char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
+ #endif
- char fullversion[]="$Revision$ $Date$";
- char strstart[80];
+ /* $Id$ */
- char optionfilext[10], optionfilefiname[FILENAMELENGTH];
+ /* $State$ */
- int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar;
+ char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+ char fullversion[]="$Revision$ $Date$";
- int npar=NPARMAX;
+ char strstart[80];
- int nlstate=2; /* Number of live states */
+ char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- int ndeath=1; /* Number of dead states */
+ int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+ int nvar=0, nforce=0; /* Number of variables, number of forces */
- int popbased=0;
+ int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
+ int npar=NPARMAX;
- int *wav; /* Number of waves for this individuual 0 is possible */
+ int nlstate=2; /* Number of live states */
- int maxwav; /* Maxim number of waves */
+ int ndeath=1; /* Number of dead states */
- int jmin, jmax; /* min, max spacing between 2 waves */
+ int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- int ijmin, ijmax; /* Individuals having jmin and jmax */
+ int popbased=0;
- int gipmx, gsw; /* Global variables on the number of contributions
-                    to the likelihood and the sum of weights (done by funcone)*/
+ int *wav; /* Number of waves for this individuual 0 is possible */
- int mle, weightopt;
+ int maxwav=0; /* Maxim number of waves */
- int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+ int jmin=0, jmax=0; /* min, max spacing between 2 waves */
- int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+ int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
- int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
+ int gipmx=0, gsw=0; /* Global variables on the number of contributions
-            * wave mi and wave mi+1 is not an exact multiple of stepm. */
+                    to the likelihood and the sum of weights (done by funcone)*/
- double jmean; /* Mean space between 2 waves */
+ int mle=1, weightopt=0;
- double **oldm, **newm, **savm; /* Working pointers to matrices */
+ int **mw; /* mw[mi][i] is number of the mi wave for this individual */
- double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
- FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- FILE *ficlog, *ficrespow;
+            * wave mi and wave mi+1 is not an exact multiple of stepm. */
- int globpr; /* Global variable for printing or not */
+ double jmean=1; /* Mean space between 2 waves */
- double fretone; /* Only one call to likelihood */
+ double **oldm, **newm, **savm; /* Working pointers to matrices */
- long ipmx; /* Number of contributions */
+ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
- double sw; /* Sum of weights */
+ /*FILE *fic ; */ /* Used in readdata only */
- char filerespow[FILENAMELENGTH];
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
- char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
+ FILE *ficlog, *ficrespow;
- FILE *ficresilk;
+ int globpr=0; /* Global variable for printing or not */
- FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+ double fretone; /* Only one call to likelihood */
- FILE *ficresprobmorprev;
+ long ipmx=0; /* Number of contributions */
- FILE *fichtm, *fichtmcov; /* Html File */
+ double sw; /* Sum of weights */
- FILE *ficreseij;
+ char filerespow[FILENAMELENGTH];
- char filerese[FILENAMELENGTH];
+ char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- FILE *ficresstdeij;
+ FILE *ficresilk;
- char fileresstde[FILENAMELENGTH];
+ FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
- FILE *ficrescveij;
+ FILE *ficresprobmorprev;
- char filerescve[FILENAMELENGTH];
+ FILE *fichtm, *fichtmcov; /* Html File */
- FILE  *ficresvij;
+ FILE *ficreseij;
- char fileresv[FILENAMELENGTH];
+ char filerese[FILENAMELENGTH];
- FILE  *ficresvpl;
+ FILE *ficresstdeij;
- char fileresvpl[FILENAMELENGTH];
+ char fileresstde[FILENAMELENGTH];
- char title[MAXLINE];
+ FILE *ficrescveij;
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char filerescve[FILENAMELENGTH];
- char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
+ FILE  *ficresvij;
- char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
+ char fileresv[FILENAMELENGTH];
- char command[FILENAMELENGTH];
+ FILE  *ficresvpl;
- int  outcmd=0;
+ char fileresvpl[FILENAMELENGTH];
+ char title[MAXLINE];
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
- char filelog[FILENAMELENGTH]; /* Log file */
+ char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- char filerest[FILENAMELENGTH];
+ char command[FILENAMELENGTH];
- char fileregp[FILENAMELENGTH];
+ int  outcmd=0;
- char popfile[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
- char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+ char filelog[FILENAMELENGTH]; /* Log file */
- struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ char filerest[FILENAMELENGTH];
- struct timezone tzp;
+ char fileregp[FILENAMELENGTH];
- extern int gettimeofday();
+ char popfile[FILENAMELENGTH];
- struct tm tmg, tm, tmf, *gmtime(), *localtime();
- long time_value;
+ char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
- extern long time();
- char strcurr[80], strfor[80];
+ struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+ struct timezone tzp;
- char *endptr;
+ extern int gettimeofday();
- long lval;
+ struct tm tmg, tm, tmf, *gmtime(), *localtime();
- double dval;
+ long time_value;
+ extern long time();
- #define NR_END 1
+ char strcurr[80], strfor[80];
- #define FREE_ARG char*
- #define FTOL 1.0e-10
+ char *endptr;
+ long lval;
- #define NRANSI
+ double dval;
- #define ITMAX 200
+ #define NR_END 1
- #define TOL 2.0e-4
+ #define FREE_ARG char*
+ #define FTOL 1.0e-10
- #define CGOLD 0.3819660
- #define ZEPS 1.0e-10
+ #define NRANSI
- #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+ #define ITMAX 200
- #define GOLD 1.618034
+ #define TOL 2.0e-4
- #define GLIMIT 100.0
- #define TINY 1.0e-20
+ #define CGOLD 0.3819660
+ #define ZEPS 1.0e-10
- static double maxarg1,maxarg2;
+ #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
- #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
- #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+ #define GOLD 1.618034
+ #define GLIMIT 100.0
- #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ #define TINY 1.0e-20
- #define rint(a) floor(a+0.5)
+ static double maxarg1,maxarg2;
- static double sqrarg;
+ #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
- #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- int agegomp= AGEGOMP;
+ #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+ #define rint(a) floor(a+0.5)
- int imx;
- int stepm=1;
+ static double sqrarg;
- /* Stepm, step in month: minimum step interpolation*/
+ #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+ #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- int estepm;
+ int agegomp= AGEGOMP;
- /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+ int imx;
- int m,nb;
+ int stepm=1;
- long *num;
+ /* Stepm, step in month: minimum step interpolation*/
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+ int estepm;
- double **pmmij, ***probs;
+ /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
- double *ageexmed,*agecens;
- double dateintmean=0;
+ int m,nb;
+ long *num;
- double *weight;
+ int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
- int **s; /* Status */
+ double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double *agedc, **covar, idx;
+ double **pmmij, ***probs;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double *ageexmed,*agecens;
- double *lsurv, *lpop, *tpop;
+ double dateintmean=0;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ double *weight;
- double ftolhess; /* Tolerance for computing hessian */
+ int **s; /* Status */
+ double *agedc, **covar, idx;
- /**************** split *************************/
+ int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
- static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ double *lsurv, *lpop, *tpop;
- {
-   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
+ double ftol=FTOL; /* Tolerance for computing Max Likelihood */
-      the name of the file (name), its extension only (ext) and its first part of the name (finame)
+ double ftolhess; /* Tolerance for computing hessian */
-   */
-   char  *ss;                            /* pointer */
+ /**************** split *************************/
-   int   l1, l2;                         /* length counters */
+ static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
+ {
-   l1 = strlen(path );                   /* length of path */
+   /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
-   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+      the name of the file (name), its extension only (ext) and its first part of the name (finame)
-   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
+   */
-   if ( ss == NULL ) {                   /* no directory, so determine current directory */
+   char  *ss;                            /* pointer */
-     strcpy( name, path );               /* we got the fullname name because no directory */
+   int   l1, l2;                         /* length counters */
-     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+   l1 = strlen(path );                   /* length of path */
-     /* get current working directory */
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
-     /*    extern  char* getcwd ( char *buf , int len);*/
+   ss= strrchr( path, DIRSEPARATOR );            /* find last / */
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+   if ( ss == NULL ) {                   /* no directory, so determine current directory */
-       return( GLOCK_ERROR_GETCWD );
+     strcpy( name, path );               /* we got the fullname name because no directory */
-     }
+     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
-     /* got dirc from getcwd*/
+       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
-     printf(" DIRC = %s \n",dirc);
+     /* get current working directory */
-   } else {                              /* strip direcotry from path */
+     /*    extern  char* getcwd ( char *buf , int len);*/
-     ss++;                               /* after this, the filename */
+     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
-     l2 = strlen( ss );                  /* length of filename */
+       return( GLOCK_ERROR_GETCWD );
-     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+     }
-     strcpy( name, ss );         /* save file name */
+     /* got dirc from getcwd*/
-     strncpy( dirc, path, l1 - l2 );     /* now the directory */
+     printf(" DIRC = %s \n",dirc);
-     dirc[l1-l2] = 0;                    /* add zero */
+   } else {                              /* strip direcotry from path */
-     printf(" DIRC2 = %s \n",dirc);
+     ss++;                               /* after this, the filename */
-   }
+     l2 = strlen( ss );                  /* length of filename */
-   /* We add a separator at the end of dirc if not exists */
+     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
-   l1 = strlen( dirc );                  /* length of directory */
+     strcpy( name, ss );         /* save file name */
-   if( dirc[l1-1] != DIRSEPARATOR ){
+     strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     dirc[l1] =  DIRSEPARATOR;
+     dirc[l1-l2] = 0;                    /* add zero */
-     dirc[l1+1] = 0;
+     printf(" DIRC2 = %s \n",dirc);
-     printf(" DIRC3 = %s \n",dirc);
+   }
-   }
+   /* We add a separator at the end of dirc if not exists */
-   ss = strrchr( name, '.' );            /* find last / */
+   l1 = strlen( dirc );                  /* length of directory */
-   if (ss >0){
+   if( dirc[l1-1] != DIRSEPARATOR ){
-     ss++;
+     dirc[l1] =  DIRSEPARATOR;
-     strcpy(ext,ss);                     /* save extension */
+     dirc[l1+1] = 0;
-     l1= strlen( name);
+     printf(" DIRC3 = %s \n",dirc);
-     l2= strlen(ss)+1;
+   }
-     strncpy( finame, name, l1-l2);
+   ss = strrchr( name, '.' );            /* find last / */
-     finame[l1-l2]= 0;
+   if (ss >0){
-   }
+     ss++;
+     strcpy(ext,ss);                     /* save extension */
-   return( 0 );                          /* we're done */
+     l1= strlen( name);
- }
+     l2= strlen(ss)+1;
+     strncpy( finame, name, l1-l2);
+     finame[l1-l2]= 0;
- /******************************************/
+   }
- void replace_back_to_slash(char *s, char*t)
+   return( 0 );                          /* we're done */
- {
+ }
-   int i;
-   int lg=0;
-   i=0;
+ /******************************************/
-   lg=strlen(t);
-   for(i=0; i<= lg; i++) {
+ void replace_back_to_slash(char *s, char*t)
-     (s[i] = t[i]);
+ {
-     if (t[i]== '\\') s[i]='/';
+   int i;
-   }
+   int lg=0;
- }
+   i=0;
+   lg=strlen(t);
- int nbocc(char *s, char occ)
+   for(i=0; i<= lg; i++) {
- {
+     (s[i] = t[i]);
-   int i,j=0;
+     if (t[i]== '\\') s[i]='/';
-   int lg=20;
+   }
-   i=0;
+ }
-   lg=strlen(s);
-   for(i=0; i<= lg; i++) {
+ char *trimbb(char *out, char *in)
-   if  (s[i] == occ ) j++;
+ { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
-   }
+   char *s;
-   return j;
+   s=out;
- }
+   while (*in != '\0'){
+     while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
- void cutv(char *u,char *v, char*t, char occ)
+       in++;
- {
+     }
-   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+     *out++ = *in++;
-      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
+   }
-      gives u="abcedf" and v="ghi2j" */
+   *out='\0';
-   int i,lg,j,p=0;
+   return s;
-   i=0;
+ }
-   for(j=0; j<=strlen(t)-1; j++) {
-     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ char *cutv(char *blocc, char *alocc, char *in, char occ)
-   }
+ {
+   /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
-   lg=strlen(t);
+      and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-   for(j=0; j<p; j++) {
+      gives blocc="abcdef2ghi" and alocc="j".
-     (u[j] = t[j]);
+      If occ is not found blocc is null and alocc is equal to in. Returns alocc
-   }
+   */
-      u[p]='\0';
+   char *s, *t;
+   t=in;s=in;
-    for(j=0; j<= lg; j++) {
+   while (*in != '\0'){
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+     while( *in == occ){
-   }
+       *blocc++ = *in++;
- }
+       s=in;
+     }
- /********************** nrerror ********************/
+     *blocc++ = *in++;
+   }
- void nrerror(char error_text[])
+   if (s == t) /* occ not found */
- {
+     *(blocc-(in-s))='\0';
-   fprintf(stderr,"ERREUR ...\n");
+   else
-   fprintf(stderr,"%s\n",error_text);
+     *(blocc-(in-s)-1)='\0';
-   exit(EXIT_FAILURE);
+   in=s;
- }
+   while ( *in != '\0'){
- /*********************** vector *******************/
+     *alocc++ = *in++;
- double *vector(int nl, int nh)
+   }
- {
-   double *v;
+   *alocc='\0';
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   return s;
-   if (!v) nrerror("allocation failure in vector");
+ }
-   return v-nl+NR_END;
- }
+ int nbocc(char *s, char occ)
+ {
- /************************ free vector ******************/
+   int i,j=0;
- void free_vector(double*v, int nl, int nh)
+   int lg=20;
- {
+   i=0;
-   free((FREE_ARG)(v+nl-NR_END));
+   lg=strlen(s);
- }
+   for(i=0; i<= lg; i++) {
+   if  (s[i] == occ ) j++;
- /************************ivector *******************************/
+   }
- int *ivector(long nl,long nh)
+   return j;
- {
+ }
-   int *v;
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ /* void cutv(char *u,char *v, char*t, char occ) */
-   if (!v) nrerror("allocation failure in ivector");
+ /* { */
-   return v-nl+NR_END;
+ /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
- }
+ /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
+ /*      gives u="abcdef2ghi" and v="j" *\/ */
- /******************free ivector **************************/
+ /*   int i,lg,j,p=0; */
- void free_ivector(int *v, long nl, long nh)
+ /*   i=0; */
- {
+ /*   lg=strlen(t); */
-   free((FREE_ARG)(v+nl-NR_END));
+ /*   for(j=0; j<=lg-1; j++) { */
- }
+ /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
+ /*   } */
- /************************lvector *******************************/
- long *lvector(long nl,long nh)
+ /*   for(j=0; j<p; j++) { */
- {
+ /*     (u[j] = t[j]); */
-   long *v;
+ /*   } */
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
+ /*      u[p]='\0'; */
-   if (!v) nrerror("allocation failure in ivector");
-   return v-nl+NR_END;
+ /*    for(j=0; j<= lg; j++) { */
- }
+ /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
+ /*   } */
- /******************free lvector **************************/
+ /* } */
- void free_lvector(long *v, long nl, long nh)
- {
+ /********************** nrerror ********************/
-   free((FREE_ARG)(v+nl-NR_END));
- }
+ void nrerror(char error_text[])
+ {
- /******************* imatrix *******************************/
+   fprintf(stderr,"ERREUR ...\n");
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+   fprintf(stderr,"%s\n",error_text);
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   exit(EXIT_FAILURE);
- {
+ }
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ /*********************** vector *******************/
-   int **m;
+ double *vector(int nl, int nh)
+ {
-   /* allocate pointers to rows */
+   double *v;
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   if (!v) nrerror("allocation failure in vector");
-   m += NR_END;
+   return v-nl+NR_END;
-   m -= nrl;
+ }
+ /************************ free vector ******************/
-   /* allocate rows and set pointers to them */
+ void free_vector(double*v, 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()");
+   free((FREE_ARG)(v+nl-NR_END));
-   m[nrl] += NR_END;
+ }
-   m[nrl] -= ncl;
+ /************************ivector *******************************/
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ int *ivector(long nl,long nh)
+ {
-   /* return pointer to array of pointers to rows */
+   int *v;
-   return m;
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- }
+   if (!v) nrerror("allocation failure in ivector");
+   return v-nl+NR_END;
- /****************** free_imatrix *************************/
+ }
- void free_imatrix(m,nrl,nrh,ncl,nch)
-       int **m;
+ /******************free ivector **************************/
-       long nch,ncl,nrh,nrl;
+ void free_ivector(int *v, long nl, long nh)
-      /* free an int matrix allocated by imatrix() */
+ {
- {
+   free((FREE_ARG)(v+nl-NR_END));
-   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ }
-   free((FREE_ARG) (m+nrl-NR_END));
- }
+ /************************lvector *******************************/
+ long *lvector(long nl,long nh)
- /******************* matrix *******************************/
+ {
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   long *v;
- {
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   if (!v) nrerror("allocation failure in ivector");
-   double **m;
+   return v-nl+NR_END;
+ }
-   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+ /******************free lvector **************************/
-   m += NR_END;
+ void free_lvector(long *v, long nl, long nh)
-   m -= nrl;
+ {
+   free((FREE_ARG)(v+nl-NR_END));
-   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ }
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   m[nrl] += NR_END;
+ /******************* imatrix *******************************/
-   m[nrl] -= ncl;
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ {
-   return m;
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+   int **m;
-    */
- }
+   /* allocate pointers to rows */
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- /*************************free matrix ************************/
+   if (!m) nrerror("allocation failure 1 in matrix()");
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   m += NR_END;
- {
+   m -= nrl;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+   /* allocate rows and set pointers to them */
+   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
- /******************* ma3x *******************************/
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+   m[nrl] += NR_END;
- {
+   m[nrl] -= ncl;
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
-   double ***m;
+   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+   /* return pointer to array of pointers to rows */
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   return m;
-   m += NR_END;
+ }
-   m -= nrl;
+ /****************** free_imatrix *************************/
-   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ void free_imatrix(m,nrl,nrh,ncl,nch)
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+       int **m;
-   m[nrl] += NR_END;
+       long nch,ncl,nrh,nrl;
-   m[nrl] -= ncl;
+      /* free an int matrix allocated by imatrix() */
+ {
-   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+   free((FREE_ARG) (m[nrl]+ncl-NR_END));
+   free((FREE_ARG) (m+nrl-NR_END));
-   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ }
-   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   m[nrl][ncl] += NR_END;
+ /******************* matrix *******************************/
-   m[nrl][ncl] -= nll;
+ double **matrix(long nrl, long nrh, long ncl, long nch)
-   for (j=ncl+1; j<=nch; j++)
+ {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+   double **m;
-   for (i=nrl+1; i<=nrh; i++) {
-     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-     for (j=ncl+1; j<=nch; j++)
+   if (!m) nrerror("allocation failure 1 in matrix()");
-       m[i][j]=m[i][j-1]+nlay;
+   m += NR_END;
-   }
+   m -= nrl;
-   return m;
-   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   */
+   m[nrl] += NR_END;
- }
+   m[nrl] -= ncl;
- /*************************free ma3x ************************/
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+   return m;
- {
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+    */
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ }
-   free((FREE_ARG)(m+nrl-NR_END));
- }
+ /*************************free matrix ************************/
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
- /*************** function subdirf ***********/
+ {
- char *subdirf(char fileres[])
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
- {
+   free((FREE_ARG)(m+nrl-NR_END));
-   /* Caution optionfilefiname is hidden */
+ }
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/"); /* Add to the right */
+ /******************* ma3x *******************************/
-   strcat(tmpout,fileres);
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-   return tmpout;
+ {
- }
+   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   double ***m;
- /*************** function subdirf2 ***********/
- char *subdirf2(char fileres[], char *preop)
+   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- {
+   if (!m) nrerror("allocation failure 1 in matrix()");
+   m += NR_END;
-   /* Caution optionfilefiname is hidden */
+   m -= nrl;
-   strcpy(tmpout,optionfilefiname);
-   strcat(tmpout,"/");
+   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   strcat(tmpout,preop);
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   strcat(tmpout,fileres);
+   m[nrl] += NR_END;
-   return tmpout;
+   m[nrl] -= ncl;
- }
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- /*************** function subdirf3 ***********/
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   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;
-   /* Caution optionfilefiname is hidden */
+   m[nrl][ncl] -= nll;
-   strcpy(tmpout,optionfilefiname);
+   for (j=ncl+1; j<=nch; j++)
-   strcat(tmpout,"/");
+     m[nrl][j]=m[nrl][j-1]+nlay;
-   strcat(tmpout,preop);
-   strcat(tmpout,preop2);
+   for (i=nrl+1; i<=nrh; i++) {
-   strcat(tmpout,fileres);
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   return tmpout;
+     for (j=ncl+1; j<=nch; j++)
- }
+       m[i][j]=m[i][j-1]+nlay;
+   }
- /***************** f1dim *************************/
+   return m;
- extern int ncom;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
- extern double *pcom,*xicom;
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
- extern double (*nrfunc)(double []);
+   */
+ }
- double f1dim(double x)
- {
+ /*************************free ma3x ************************/
-   int j;
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   double f;
+ {
-   double *xt;
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   xt=vector(1,ncom);
+   free((FREE_ARG)(m+nrl-NR_END));
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ }
-   f=(*nrfunc)(xt);
-   free_vector(xt,1,ncom);
+ /*************** function subdirf ***********/
-   return f;
+ char *subdirf(char fileres[])
- }
+ {
+   /* Caution optionfilefiname is hidden */
- /*****************brent *************************/
+   strcpy(tmpout,optionfilefiname);
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
+   strcat(tmpout,"/"); /* Add to the right */
- {
+   strcat(tmpout,fileres);
-   int iter;
+   return tmpout;
-   double a,b,d,etemp;
+ }
-   double fu,fv,fw,fx;
-   double ftemp;
+ /*************** function subdirf2 ***********/
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ char *subdirf2(char fileres[], char *preop)
-   double e=0.0;
+ {
-   a=(ax < cx ? ax : cx);
+   /* Caution optionfilefiname is hidden */
-   b=(ax > cx ? ax : cx);
+   strcpy(tmpout,optionfilefiname);
-   x=w=v=bx;
+   strcat(tmpout,"/");
-   fw=fv=fx=(*f)(x);
+   strcat(tmpout,preop);
-   for (iter=1;iter<=ITMAX;iter++) {
+   strcat(tmpout,fileres);
-     xm=0.5*(a+b);
+   return tmpout;
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ }
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-     printf(".");fflush(stdout);
+ /*************** function subdirf3 ***********/
-     fprintf(ficlog,".");fflush(ficlog);
+ char *subdirf3(char fileres[], char *preop, char *preop2)
- #ifdef DEBUG
+ {
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
-     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+   /* Caution optionfilefiname is hidden */
-     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+   strcpy(tmpout,optionfilefiname);
- #endif
+   strcat(tmpout,"/");
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   strcat(tmpout,preop);
-       *xmin=x;
+   strcat(tmpout,preop2);
-       return fx;
+   strcat(tmpout,fileres);
-     }
+   return tmpout;
-     ftemp=fu;
+ }
-     if (fabs(e) > tol1) {
-       r=(x-w)*(fx-fv);
+ /***************** f1dim *************************/
-       q=(x-v)*(fx-fw);
+ extern int ncom;
-       p=(x-v)*q-(x-w)*r;
+ extern double *pcom,*xicom;
-       q=2.0*(q-r);
+ extern double (*nrfunc)(double []);
-       if (q > 0.0) p = -p;
-       q=fabs(q);
+ double f1dim(double x)
-       etemp=e;
+ {
-       e=d;
+   int j;
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+   double f;
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+   double *xt;
-       else {
-         d=p/q;
+   xt=vector(1,ncom);
-         u=x+d;
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-         if (u-a < tol2 || b-u < tol2)
+   f=(*nrfunc)(xt);
-           d=SIGN(tol1,xm-x);
+   free_vector(xt,1,ncom);
-       }
+   return f;
-     } else {
+ }
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     }
+ /*****************brent *************************/
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-     fu=(*f)(u);
+ {
-     if (fu <= fx) {
+   int iter;
-       if (u >= x) a=x; else b=x;
+   double a,b,d,etemp;
-       SHFT(v,w,x,u)
+   double fu,fv,fw,fx;
-         SHFT(fv,fw,fx,fu)
+   double ftemp;
-         } else {
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-           if (u < x) a=u; else b=u;
+   double e=0.0;
-           if (fu <= fw || w == x) {
-             v=w;
+   a=(ax < cx ? ax : cx);
-             w=u;
+   b=(ax > cx ? ax : cx);
-             fv=fw;
+   x=w=v=bx;
-             fw=fu;
+   fw=fv=fx=(*f)(x);
-           } else if (fu <= fv || v == x || v == w) {
+   for (iter=1;iter<=ITMAX;iter++) {
-             v=u;
+     xm=0.5*(a+b);
-             fv=fu;
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-           }
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-         }
+     printf(".");fflush(stdout);
-   }
+     fprintf(ficlog,".");fflush(ficlog);
-   nrerror("Too many iterations in brent");
+ #ifdef DEBUG
-   *xmin=x;
+     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);
-   return fx;
+     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)))) { */
+ #endif
- /****************** mnbrak ***********************/
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+       *xmin=x;
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+       return fx;
-             double (*func)(double))
+     }
- {
+     ftemp=fu;
-   double ulim,u,r,q, dum;
+     if (fabs(e) > tol1) {
-   double fu;
+       r=(x-w)*(fx-fv);
+       q=(x-v)*(fx-fw);
-   *fa=(*func)(*ax);
+       p=(x-v)*q-(x-w)*r;
-   *fb=(*func)(*bx);
+       q=2.0*(q-r);
-   if (*fb > *fa) {
+       if (q > 0.0) p = -p;
-     SHFT(dum,*ax,*bx,dum)
+       q=fabs(q);
-       SHFT(dum,*fb,*fa,dum)
+       etemp=e;
-       }
+       e=d;
-   *cx=(*bx)+GOLD*(*bx-*ax);
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-   *fc=(*func)(*cx);
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-   while (*fb > *fc) {
+       else {
-     r=(*bx-*ax)*(*fb-*fc);
+         d=p/q;
-     q=(*bx-*cx)*(*fb-*fa);
+         u=x+d;
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+         if (u-a < tol2 || b-u < tol2)
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+           d=SIGN(tol1,xm-x);
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+       }
-     if ((*bx-u)*(u-*cx) > 0.0) {
+     } else {
-       fu=(*func)(u);
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+     }
-       fu=(*func)(u);
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-       if (fu < *fc) {
+     fu=(*f)(u);
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+     if (fu <= fx) {
-           SHFT(*fb,*fc,fu,(*func)(u))
+       if (u >= x) a=x; else b=x;
-           }
+       SHFT(v,w,x,u)
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+         SHFT(fv,fw,fx,fu)
-       u=ulim;
+         } else {
-       fu=(*func)(u);
+           if (u < x) a=u; else b=u;
-     } else {
+           if (fu <= fw || w == x) {
-       u=(*cx)+GOLD*(*cx-*bx);
+             v=w;
-       fu=(*func)(u);
+             w=u;
-     }
+             fv=fw;
-     SHFT(*ax,*bx,*cx,u)
+             fw=fu;
-       SHFT(*fa,*fb,*fc,fu)
+           } else if (fu <= fv || v == x || v == w) {
-       }
+             v=u;
- }
+             fv=fu;
+           }
- /*************** linmin ************************/
+         }
+   }
- int ncom;
+   nrerror("Too many iterations in brent");
- double *pcom,*xicom;
+   *xmin=x;
- double (*nrfunc)(double []);
+   return fx;
+ }
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
- {
+ /****************** mnbrak ***********************/
-   double brent(double ax, double bx, double cx,
-                double (*f)(double), double tol, double *xmin);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-   double f1dim(double x);
+             double (*func)(double))
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ {
-               double *fc, double (*func)(double));
+   double ulim,u,r,q, dum;
-   int j;
+   double fu;
-   double xx,xmin,bx,ax;
-   double fx,fb,fa;
+   *fa=(*func)(*ax);
+   *fb=(*func)(*bx);
-   ncom=n;
+   if (*fb > *fa) {
-   pcom=vector(1,n);
+     SHFT(dum,*ax,*bx,dum)
-   xicom=vector(1,n);
+       SHFT(dum,*fb,*fa,dum)
-   nrfunc=func;
+       }
-   for (j=1;j<=n;j++) {
+   *cx=(*bx)+GOLD*(*bx-*ax);
-     pcom[j]=p[j];
+   *fc=(*func)(*cx);
-     xicom[j]=xi[j];
+   while (*fb > *fc) {
-   }
+     r=(*bx-*ax)*(*fb-*fc);
-   ax=0.0;
+     q=(*bx-*cx)*(*fb-*fa);
-   xx=1.0;
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
- #ifdef DEBUG
+     if ((*bx-u)*(u-*cx) > 0.0) {
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+       fu=(*func)(u);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
- #endif
+       fu=(*func)(u);
-   for (j=1;j<=n;j++) {
+       if (fu < *fc) {
-     xi[j] *= xmin;
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-     p[j] += xi[j];
+           SHFT(*fb,*fc,fu,(*func)(u))
-   }
+           }
-   free_vector(xicom,1,n);
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-   free_vector(pcom,1,n);
+       u=ulim;
- }
+       fu=(*func)(u);
+     } else {
- char *asc_diff_time(long time_sec, char ascdiff[])
+       u=(*cx)+GOLD*(*cx-*bx);
- {
+       fu=(*func)(u);
-   long sec_left, days, hours, minutes;
+     }
-   days = (time_sec) / (60*60*24);
+     SHFT(*ax,*bx,*cx,u)
-   sec_left = (time_sec) % (60*60*24);
+       SHFT(*fa,*fb,*fc,fu)
-   hours = (sec_left) / (60*60) ;
+       }
-   sec_left = (sec_left) %(60*60);
+ }
-   minutes = (sec_left) /60;
-   sec_left = (sec_left) % (60);
+ /*************** linmin ************************/
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
-   return ascdiff;
+ int ncom;
- }
+ double *pcom,*xicom;
+ double (*nrfunc)(double []);
- /*************** powell ************************/
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-             double (*func)(double []))
+ {
- {
+   double brent(double ax, double bx, double cx,
-   void linmin(double p[], double xi[], int n, double *fret,
+                double (*f)(double), double tol, double *xmin);
-               double (*func)(double []));
+   double f1dim(double x);
-   int i,ibig,j;
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
-   double del,t,*pt,*ptt,*xit;
+               double *fc, double (*func)(double));
-   double fp,fptt;
+   int j;
-   double *xits;
+   double xx,xmin,bx,ax;
-   int niterf, itmp;
+   double fx,fb,fa;
-   pt=vector(1,n);
+   ncom=n;
-   ptt=vector(1,n);
+   pcom=vector(1,n);
-   xit=vector(1,n);
+   xicom=vector(1,n);
-   xits=vector(1,n);
+   nrfunc=func;
-   *fret=(*func)(p);
+   for (j=1;j<=n;j++) {
-   for (j=1;j<=n;j++) pt[j]=p[j];
+     pcom[j]=p[j];
-   for (*iter=1;;++(*iter)) {
+     xicom[j]=xi[j];
-     fp=(*fret);
+   }
-     ibig=0;
+   ax=0.0;
-     del=0.0;
+   xx=1.0;
-     last_time=curr_time;
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-     (void) gettimeofday(&curr_time,&tzp);
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-     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);
+ #ifdef DEBUG
-     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);
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-    for (i=1;i<=n;i++) {
+ #endif
-       printf(" %d %.12f",i, p[i]);
+   for (j=1;j<=n;j++) {
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+     xi[j] *= xmin;
-       fprintf(ficrespow," %.12lf", p[i]);
+     p[j] += xi[j];
-     }
+   }
-     printf("\n");
+   free_vector(xicom,1,n);
-     fprintf(ficlog,"\n");
+   free_vector(pcom,1,n);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+ }
-     if(*iter <=3){
-       tm = *localtime(&curr_time.tv_sec);
+ char *asc_diff_time(long time_sec, char ascdiff[])
-       strcpy(strcurr,asctime(&tm));
+ {
- /*       asctime_r(&tm,strcurr); */
+   long sec_left, days, hours, minutes;
-       forecast_time=curr_time;
+   days = (time_sec) / (60*60*24);
-       itmp = strlen(strcurr);
+   sec_left = (time_sec) % (60*60*24);
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+   hours = (sec_left) / (60*60) ;
-         strcurr[itmp-1]='\0';
+   sec_left = (sec_left) %(60*60);
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   minutes = (sec_left) /60;
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+   sec_left = (sec_left) % (60);
-       for(niterf=10;niterf<=30;niterf+=10){
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+   return ascdiff;
-         tmf = *localtime(&forecast_time.tv_sec);
+ }
- /*      asctime_r(&tmf,strfor); */
-         strcpy(strfor,asctime(&tmf));
+ /*************** powell ************************/
-         itmp = strlen(strfor);
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-         if(strfor[itmp-1]=='\n')
+             double (*func)(double []))
-         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);
+   void linmin(double p[], double xi[], int n, double *fret,
-         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);
+               double (*func)(double []));
-       }
+   int i,ibig,j;
-     }
+   double del,t,*pt,*ptt,*xit;
-     for (i=1;i<=n;i++) {
+   double fp,fptt;
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+   double *xits;
-       fptt=(*fret);
+   int niterf, itmp;
- #ifdef DEBUG
-       printf("fret=%lf \n",*fret);
+   pt=vector(1,n);
-       fprintf(ficlog,"fret=%lf \n",*fret);
+   ptt=vector(1,n);
- #endif
+   xit=vector(1,n);
-       printf("%d",i);fflush(stdout);
+   xits=vector(1,n);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+   *fret=(*func)(p);
-       linmin(p,xit,n,fret,func);
+   for (j=1;j<=n;j++) pt[j]=p[j];
-       if (fabs(fptt-(*fret)) > del) {
+   for (*iter=1;;++(*iter)) {
-         del=fabs(fptt-(*fret));
+     fp=(*fret);
-         ibig=i;
+     ibig=0;
-       }
+     del=0.0;
- #ifdef DEBUG
+     last_time=curr_time;
-       printf("%d %.12e",i,(*fret));
+     (void) gettimeofday(&curr_time,&tzp);
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+     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);
-       for (j=1;j<=n;j++) {
+     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);
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-         printf(" x(%d)=%.12e",j,xit[j]);
+    for (i=1;i<=n;i++) {
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+       printf(" %d %.12f",i, p[i]);
-       }
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-       for(j=1;j<=n;j++) {
+       fprintf(ficrespow," %.12lf", p[i]);
-         printf(" p=%.12e",p[j]);
+     }
-         fprintf(ficlog," p=%.12e",p[j]);
+     printf("\n");
-       }
+     fprintf(ficlog,"\n");
-       printf("\n");
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-       fprintf(ficlog,"\n");
+     if(*iter <=3){
- #endif
+       tm = *localtime(&curr_time.tv_sec);
-     }
+       strcpy(strcurr,asctime(&tm));
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+ /*       asctime_r(&tm,strcurr); */
- #ifdef DEBUG
+       forecast_time=curr_time;
-       int k[2],l;
+       itmp = strlen(strcurr);
-       k[0]=1;
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       k[1]=-1;
+         strcurr[itmp-1]='\0';
-       printf("Max: %.12e",(*func)(p));
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       for (j=1;j<=n;j++) {
+       for(niterf=10;niterf<=30;niterf+=10){
-         printf(" %.12e",p[j]);
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
-         fprintf(ficlog," %.12e",p[j]);
+         tmf = *localtime(&forecast_time.tv_sec);
-       }
+ /*      asctime_r(&tmf,strfor); */
-       printf("\n");
+         strcpy(strfor,asctime(&tmf));
-       fprintf(ficlog,"\n");
+         itmp = strlen(strfor);
-       for(l=0;l<=1;l++) {
+         if(strfor[itmp-1]=='\n')
-         for (j=1;j<=n;j++) {
+         strfor[itmp-1]='\0';
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+         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);
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       }
-         }
+     }
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     for (i=1;i<=n;i++) {
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       }
+       fptt=(*fret);
- #endif
+ #ifdef DEBUG
+       printf("fret=%lf \n",*fret);
+       fprintf(ficlog,"fret=%lf \n",*fret);
-       free_vector(xit,1,n);
+ #endif
-       free_vector(xits,1,n);
+       printf("%d",i);fflush(stdout);
-       free_vector(ptt,1,n);
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-       free_vector(pt,1,n);
+       linmin(p,xit,n,fret,func);
-       return;
+       if (fabs(fptt-(*fret)) > del) {
-     }
+         del=fabs(fptt-(*fret));
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+         ibig=i;
-     for (j=1;j<=n;j++) {
+       }
-       ptt[j]=2.0*p[j]-pt[j];
+ #ifdef DEBUG
-       xit[j]=p[j]-pt[j];
+       printf("%d %.12e",i,(*fret));
-       pt[j]=p[j];
+       fprintf(ficlog,"%d %.12e",i,(*fret));
-     }
+       for (j=1;j<=n;j++) {
-     fptt=(*func)(ptt);
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-     if (fptt < fp) {
+         printf(" x(%d)=%.12e",j,xit[j]);
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       if (t < 0.0) {
+       }
-         linmin(p,xit,n,fret,func);
+       for(j=1;j<=n;j++) {
-         for (j=1;j<=n;j++) {
+         printf(" p=%.12e",p[j]);
-           xi[j][ibig]=xi[j][n];
+         fprintf(ficlog," p=%.12e",p[j]);
-           xi[j][n]=xit[j];
+       }
-         }
+       printf("\n");
- #ifdef DEBUG
+       fprintf(ficlog,"\n");
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ #endif
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+     }
-         for(j=1;j<=n;j++){
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-           printf(" %.12e",xit[j]);
+ #ifdef DEBUG
-           fprintf(ficlog," %.12e",xit[j]);
+       int k[2],l;
-         }
+       k[0]=1;
-         printf("\n");
+       k[1]=-1;
-         fprintf(ficlog,"\n");
+       printf("Max: %.12e",(*func)(p));
- #endif
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-       }
+       for (j=1;j<=n;j++) {
-     }
+         printf(" %.12e",p[j]);
-   }
+         fprintf(ficlog," %.12e",p[j]);
- }
+       }
+       printf("\n");
- /**** Prevalence limit (stable or period prevalence)  ****************/
+       fprintf(ficlog,"\n");
+       for(l=0;l<=1;l++) {
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+         for (j=1;j<=n;j++) {
- {
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-      matrix by transitions matrix until convergence is reached */
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+         }
-   int i, ii,j,k;
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   double min, max, maxmin, maxmax,sumnew=0.;
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-   double **matprod2();
+       }
-   double **out, cov[NCOVMAX], **pmij();
+ #endif
-   double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+       free_vector(xit,1,n);
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+       free_vector(xits,1,n);
-     for (j=1;j<=nlstate+ndeath;j++){
+       free_vector(ptt,1,n);
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+       free_vector(pt,1,n);
-     }
+       return;
+     }
-    cov[1]=1.;
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     for (j=1;j<=n;j++) {
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+       ptt[j]=2.0*p[j]-pt[j];
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+       xit[j]=p[j]-pt[j];
-     newm=savm;
+       pt[j]=p[j];
-     /* Covariates have to be included here again */
+     }
-      cov[2]=agefin;
+     fptt=(*func)(ptt);
+     if (fptt < fp) {
-       for (k=1; k<=cptcovn;k++) {
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       if (t < 0.0) {
-         /*      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]]);*/
+         linmin(p,xit,n,fret,func);
-       }
+         for (j=1;j<=n;j++) {
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+           xi[j][ibig]=xi[j][n];
-       for (k=1; k<=cptcovprod;k++)
+           xi[j][n]=xit[j];
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         }
+ #ifdef DEBUG
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+         for(j=1;j<=n;j++){
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+           printf(" %.12e",xit[j]);
+           fprintf(ficlog," %.12e",xit[j]);
-     savm=oldm;
+         }
-     oldm=newm;
+         printf("\n");
-     maxmax=0.;
+         fprintf(ficlog,"\n");
-     for(j=1;j<=nlstate;j++){
+ #endif
-       min=1.;
+       }
-       max=0.;
+     }
-       for(i=1; i<=nlstate; i++) {
+   }
-         sumnew=0;
+ }
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-         max=FMAX(max,prlim[i][j]);
-         min=FMIN(min,prlim[i][j]);
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-       }
+ {
-       maxmin=max-min;
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-       maxmax=FMAX(maxmax,maxmin);
+      matrix by transitions matrix until convergence is reached */
-     }
-     if(maxmax < ftolpl){
+   int i, ii,j,k;
-       return prlim;
+   double min, max, maxmin, maxmax,sumnew=0.;
-     }
+   double **matprod2();
-   }
+   double **out, cov[NCOVMAX+1], **pmij();
- }
+   double **newm;
+   double agefin, delaymax=50 ; /* Max number of years to converge */
- /*************** transition probabilities ***************/
+   for (ii=1;ii<=nlstate+ndeath;ii++)
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+     for (j=1;j<=nlstate+ndeath;j++){
- {
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   double s1, s2;
+     }
-   /*double t34;*/
-   int i,j,j1, nc, ii, jj;
+    cov[1]=1.;
-     for(i=1; i<= nlstate; i++){
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-       for(j=1; j<i;j++){
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     newm=savm;
-           /*s2 += param[i][j][nc]*cov[nc];*/
+     /* Covariates have to be included here again */
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+     cov[2]=agefin;
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-         }
+     for (k=1; k<=cptcovn;k++) {
-         ps[i][j]=s2;
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+       /*        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=i+1; j<=nlstate+ndeath;j++){
+     for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+     for (k=1; k<=cptcovprod;k++)
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
-         }
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-         ps[i][j]=s2;
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       }
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     }
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-     /*ps[3][2]=1;*/
+     savm=oldm;
-     for(i=1; i<= nlstate; i++){
+     oldm=newm;
-       s1=0;
+     maxmax=0.;
-       for(j=1; j<i; j++)
+     for(j=1;j<=nlstate;j++){
-         s1+=exp(ps[i][j]);
+       min=1.;
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       max=0.;
-         s1+=exp(ps[i][j]);
+       for(i=1; i<=nlstate; i++) {
-       ps[i][i]=1./(s1+1.);
+         sumnew=0;
-       for(j=1; j<i; j++)
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-       for(j=i+1; j<=nlstate+ndeath; j++)
+         max=FMAX(max,prlim[i][j]);
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+         min=FMIN(min,prlim[i][j]);
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+       }
-     } /* end i */
+       maxmin=max-min;
+       maxmax=FMAX(maxmax,maxmin);
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+     if(maxmax < ftolpl){
-         ps[ii][jj]=0;
+       return prlim;
-         ps[ii][ii]=1;
+     }
-       }
+   }
-     }
+ }
+ /*************** transition probabilities ***************/
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
- /*         printf("ddd %lf ",ps[ii][jj]); */
+ {
- /*       } */
+   /* According to parameters values stored in x and the covariate's values stored in cov,
- /*       printf("\n "); */
+      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).
- /*        printf("\n ");printf("%lf ",cov[2]); */
+      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
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+      ncth covariate in the global vector x is given by the formula:
-       goto end;*/
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
-     return ps;
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
- }
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
- /**************** Product of 2 matrices ******************/
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+   */
- {
+   double s1, lnpijopii;
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+   /*double t34;*/
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+   int i,j,j1, nc, ii, jj;
-   /* in, b, out are matrice of pointers which should have been initialized
-      before: only the contents of out is modified. The function returns
+     for(i=1; i<= nlstate; i++){
-      a pointer to pointers identical to out */
+       for(j=1; j<i;j++){
-   long i, j, k;
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-   for(i=nrl; i<= nrh; i++)
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
-     for(k=ncolol; k<=ncoloh; k++)
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-         out[i][k] +=in[i][j]*b[j][k];
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-   return out;
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
- }
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- /************* Higher Matrix Product ***************/
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
- 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 %lx %lx\n",s1,lnpijopii,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
+       }
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+     }
-      nhstepm*hstepm matrices.
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+     for(i=1; i<= nlstate; i++){
-      (typically every 2 years instead of every month which is too big
+       s1=0;
-      for the memory).
+       for(j=1; j<i; j++){
-      Model is determined by parameters x and covariates have to be
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-      included manually here.
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
-      */
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-   int i, j, d, h, k;
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-   double **out, cov[NCOVMAX];
+       }
-   double **newm;
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+       ps[i][i]=1./(s1+1.);
-   /* Hstepm could be zero and should return the unit matrix */
+       /* Computing other pijs */
-   for (i=1;i<=nlstate+ndeath;i++)
+       for(j=1; j<i; j++)
-     for (j=1;j<=nlstate+ndeath;j++){
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       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);
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
-     }
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+     } /* end i */
-   for(h=1; h <=nhstepm; h++){
-     for(d=1; d <=hstepm; d++){
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       newm=savm;
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-       /* Covariates have to be included here again */
+         ps[ii][jj]=0;
-       cov[1]=1.;
+         ps[ii][ii]=1;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       }
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+     }
-       for (k=1; k<=cptcovage;k++)
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+ /*         printf("ddd %lf ",ps[ii][jj]); */
+ /*       } */
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+ /*       printf("\n "); */
-       /*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,
+ /*        printf("\n ");printf("%lf ",cov[2]); */
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+        /*
-       savm=oldm;
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
-       oldm=newm;
+       goto end;*/
-     }
+     return ps;
-     for(i=1; i<=nlstate+ndeath; i++)
+ }
-       for(j=1;j<=nlstate+ndeath;j++) {
-         po[i][j][h]=newm[i][j];
+ /**************** Product of 2 matrices ******************/
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
-          */
+ double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
-       }
+ {
-   } /* end h */
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-   return po;
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
- }
+   /* in, b, out are matrice of pointers which should have been initialized
+      before: only the contents of out is modified. The function returns
+      a pointer to pointers identical to out */
- /*************** log-likelihood *************/
+   long i, j, k;
- double func( double *x)
+   for(i=nrl; i<= nrh; i++)
- {
+     for(k=ncolol; k<=ncoloh; k++)
-   int i, ii, j, k, mi, d, kk;
+       for(j=ncl,out[i][k]=0.; j<=nch; j++)
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+         out[i][k] +=in[i][j]*b[j][k];
-   double **out;
-   double sw; /* Sum of weights */
+   return out;
-   double lli; /* Individual log likelihood */
+ }
-   int s1, s2;
-   double bbh, survp;
-   long ipmx;
+ /************* Higher Matrix Product ***************/
-   /*extern weight */
-   /* We are differentiating ll according to initial status */
+ 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;i<=npar;i++) printf("%f ", x[i]);*/
+ {
-   /*for(i=1;i<imx;i++)
+   /* Computes the transition matrix starting at age 'age' over
-     printf(" %d\n",s[4][i]);
+      'nhstepm*hstepm*stepm' months (i.e. until
-   */
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-   cov[1]=1.;
+      nhstepm*hstepm matrices.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+      (typically every 2 years instead of every month which is too big
+      for the memory).
-   if(mle==1){
+      Model is determined by parameters x and covariates have to be
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+      included manually here.
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       for(mi=1; mi<= wav[i]-1; mi++){
+      */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
-           for (j=1;j<=nlstate+ndeath;j++){
+   int i, j, d, h, k;
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+   double **out, cov[NCOVMAX+1];
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+   double **newm;
-           }
-         for(d=0; d<dh[mi][i]; d++){
+   /* Hstepm could be zero and should return the unit matrix */
-           newm=savm;
+   for (i=1;i<=nlstate+ndeath;i++)
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+     for (j=1;j<=nlstate+ndeath;j++){
-           for (kk=1; kk<=cptcovage;kk++) {
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-           }
+     }
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   for(h=1; h <=nhstepm; h++){
-           savm=oldm;
+     for(d=1; d <=hstepm; d++){
-           oldm=newm;
+       newm=savm;
-         } /* end mult */
+       /* Covariates have to be included here again */
+       cov[1]=1.;
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+       for (k=1; k<=cptcovn;k++)
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+       for (k=1; k<=cptcovage;k++)
-          * the nearest (and in case of equal distance, to the lowest) interval but now
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+       for (k=1; k<=cptcovprod;k++)
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-          * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-          * For stepm=1 the results are the same as for previous versions of Imach.
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-          * For stepm > 1 the results are less biased than in previous versions.
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,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;
-         bbh=(double)bh[mi][i]/(double)stepm;
+     }
-         /* bias bh is positive if real duration
+     for(i=1; i<=nlstate+ndeath; i++)
-          * is higher than the multiple of stepm and negative otherwise.
+       for(j=1;j<=nlstate+ndeath;j++) {
-          */
+         po[i][j][h]=newm[i][j];
-         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
-         if( s2 > nlstate){
+       }
-           /* i.e. if s2 is a death state and if the date of death is known
+     /*printf("h=%d ",h);*/
-              then the contribution to the likelihood is the probability to
+   } /* end h */
-              die between last step unit time and current  step unit time,
+ /*     printf("\n H=%d \n",h); */
-              which is also equal to probability to die before dh
+   return po;
-              minus probability to die before dh-stepm .
+ }
-              In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
-         health state: the date of the interview describes the actual state
+ /*************** log-likelihood *************/
-         and not the date of a change in health state. The former idea was
+ double func( double *x)
-         to consider that at each interview the state was recorded
+ {
-         (healthy, disable or death) and IMaCh was corrected; but when we
+   int i, ii, j, k, mi, d, kk;
-         introduced the exact date of death then we should have modified
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-         the contribution of an exact death to the likelihood. This new
+   double **out;
-         contribution is smaller and very dependent of the step unit
+   double sw; /* Sum of weights */
-         stepm. It is no more the probability to die between last interview
+   double lli; /* Individual log likelihood */
-         and month of death but the probability to survive from last
+   int s1, s2;
-         interview up to one month before death multiplied by the
+   double bbh, survp;
-         probability to die within a month. Thanks to Chris
+   long ipmx;
-         Jackson for correcting this bug.  Former versions increased
+   /*extern weight */
-         mortality artificially. The bad side is that we add another loop
+   /* We are differentiating ll according to initial status */
-         which slows down the processing. The difference can be up to 10%
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         lower mortality.
+   /*for(i=1;i<imx;i++)
-           */
+     printf(" %d\n",s[4][i]);
-           lli=log(out[s1][s2] - savm[s1][s2]);
+   */
+   cov[1]=1.;
-         } else if  (s2==-2) {
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-           for (j=1,survp=0. ; j<=nlstate; j++)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+   if(mle==1){
-           /*survp += out[s1][j]; */
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-           lli= log(survp);
+       /* Computes the values of the ncovmodel covariates of the model
-         }
+          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
-         else if  (s2==-4) {
+          to be observed in j being in i according to the model.
-           for (j=3,survp=0. ; j<=nlstate; j++)
+        */
-             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);
+       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-         }
+          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          has been calculated etc */
-         else if  (s2==-5) {
+       for(mi=1; mi<= wav[i]-1; mi++){
-           for (j=1,survp=0. ; j<=2; j++)
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           for (j=1;j<=nlstate+ndeath;j++){
-           lli= log(survp);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-         else{
+         for(d=0; d<dh[mi][i]; d++){
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           newm=savm;
-           /*  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 */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         }
+           for (kk=1; kk<=cptcovage;kk++) {
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
-         /*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); */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         ipmx +=1;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         sw += weight[i];
+           savm=oldm;
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           oldm=newm;
-       } /* end of wave */
+         } /* end mult */
-     } /* end of individual */
-   }  else if(mle==2){
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-       for(mi=1; mi<= wav[i]-1; mi++){
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-           for (j=1;j<=nlstate+ndeath;j++){
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+          * probability in order to take into account the bias as a fraction of the way
-           }
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         for(d=0; d<=dh[mi][i]; d++){
+          * -stepm/2 to stepm/2 .
-           newm=savm;
+          * For stepm=1 the results are the same as for previous versions of Imach.
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+          * For stepm > 1 the results are less biased than in previous versions.
-           for (kk=1; kk<=cptcovage;kk++) {
+          */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         s1=s[mw[mi][i]][i];
-           }
+         s2=s[mw[mi+1][i]][i];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         bbh=(double)bh[mi][i]/(double)stepm;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* bias bh is positive if real duration
-           savm=oldm;
+          * is higher than the multiple of stepm and negative otherwise.
-           oldm=newm;
+          */
-         } /* end mult */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         if( s2 > nlstate){
-         s1=s[mw[mi][i]][i];
+           /* i.e. if s2 is a death state and if the date of death is known
-         s2=s[mw[mi+1][i]][i];
+              then the contribution to the likelihood is the probability to
-         bbh=(double)bh[mi][i]/(double)stepm;
+              die between last step unit time and current  step unit time,
-         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 */
+              which is also equal to probability to die before dh
-         ipmx +=1;
+              minus probability to die before dh-stepm .
-         sw += weight[i];
+              In version up to 0.92 likelihood was computed
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         as if date of death was unknown. Death was treated as any other
-       } /* end of wave */
+         health state: the date of the interview describes the actual state
-     } /* end of individual */
+         and not the date of a change in health state. The former idea was
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+         to consider that at each interview the state was recorded
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+         (healthy, disable or death) and IMaCh was corrected; but when we
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         introduced the exact date of death then we should have modified
-       for(mi=1; mi<= wav[i]-1; mi++){
+         the contribution of an exact death to the likelihood. This new
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         contribution is smaller and very dependent of the step unit
-           for (j=1;j<=nlstate+ndeath;j++){
+         stepm. It is no more the probability to die between last interview
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         and month of death but the probability to survive from last
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         interview up to one month before death multiplied by the
-           }
+         probability to die within a month. Thanks to Chris
-         for(d=0; d<dh[mi][i]; d++){
+         Jackson for correcting this bug.  Former versions increased
-           newm=savm;
+         mortality artificially. The bad side is that we add another loop
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         which slows down the processing. The difference can be up to 10%
-           for (kk=1; kk<=cptcovage;kk++) {
+         lower mortality.
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           */
-           }
+           lli=log(out[s1][s2] - savm[s1][s2]);
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
+         } else if  (s2==-2) {
-           oldm=newm;
+           for (j=1,survp=0. ; j<=nlstate; j++)
-         } /* end mult */
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           /*survp += out[s1][j]; */
-         s1=s[mw[mi][i]][i];
+           lli= log(survp);
-         s2=s[mw[mi+1][i]][i];
+         }
-         bbh=(double)bh[mi][i]/(double)stepm;
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+         else if  (s2==-4) {
-         ipmx +=1;
+           for (j=3,survp=0. ; j<=nlstate; j++)
-         sw += weight[i];
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           lli= log(survp);
-       } /* end of wave */
+         }
-     } /* end of individual */
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+         else if  (s2==-5) {
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           for (j=1,survp=0. ; j<=2; j++)
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       for(mi=1; mi<= wav[i]-1; mi++){
+           lli= log(survp);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         }
-           for (j=1;j<=nlstate+ndeath;j++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         else{
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-           }
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-         for(d=0; d<dh[mi][i]; d++){
+         }
-           newm=savm;
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         /*if(lli ==000.0)*/
-           for (kk=1; kk<=cptcovage;kk++) {
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         ipmx +=1;
-           }
+         sw += weight[i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       } /* end of wave */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+     } /* end of individual */
-           savm=oldm;
+   }  else if(mle==2){
-           oldm=newm;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         } /* end mult */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for(mi=1; mi<= wav[i]-1; mi++){
-         s1=s[mw[mi][i]][i];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         s2=s[mw[mi+1][i]][i];
+           for (j=1;j<=nlstate+ndeath;j++){
-         if( s2 > nlstate){
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           lli=log(out[s1][s2] - savm[s1][s2]);
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }else{
+           }
-           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+         for(d=0; d<=dh[mi][i]; d++){
-         }
+           newm=savm;
-         ipmx +=1;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         sw += weight[i];
+           for (kk=1; kk<=cptcovage;kk++) {
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- /*      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 */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     } /* end of individual */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+           savm=oldm;
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           oldm=newm;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         } /* end mult */
-       for(mi=1; mi<= wav[i]-1; mi++){
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+         s1=s[mw[mi][i]][i];
-           for (j=1;j<=nlstate+ndeath;j++){
+         s2=s[mw[mi+1][i]][i];
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+         bbh=(double)bh[mi][i]/(double)stepm;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-           }
+         ipmx +=1;
-         for(d=0; d<dh[mi][i]; d++){
+         sw += weight[i];
-           newm=savm;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+       } /* end of wave */
-           for (kk=1; kk<=cptcovage;kk++) {
+     } /* end of individual */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-           }
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+       for(mi=1; mi<= wav[i]-1; mi++){
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-           savm=oldm;
+           for (j=1;j<=nlstate+ndeath;j++){
-           oldm=newm;
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         } /* end mult */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           }
-         s1=s[mw[mi][i]][i];
+         for(d=0; d<dh[mi][i]; d++){
-         s2=s[mw[mi+1][i]][i];
+           newm=savm;
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         ipmx +=1;
+           for (kk=1; kk<=cptcovage;kk++) {
-         sw += weight[i];
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           }
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       } /* end of wave */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     } /* end of individual */
+           savm=oldm;
-   } /* End of if */
+           oldm=newm;
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+         } /* end mult */
-   /* 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 */
+         s1=s[mw[mi][i]][i];
-   return -l;
+         s2=s[mw[mi+1][i]][i];
- }
+         bbh=(double)bh[mi][i]/(double)stepm;
+         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
- /*************** log-likelihood *************/
+         ipmx +=1;
- double funcone( double *x)
+         sw += weight[i];
- {
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   /* Same as likeli but slower because of a lot of printf and if */
+       } /* end of wave */
-   int i, ii, j, k, mi, d, kk;
+     } /* end of individual */
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-   double **out;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   double lli; /* Individual log likelihood */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-   double llt;
+       for(mi=1; mi<= wav[i]-1; mi++){
-   int s1, s2;
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   double bbh, survp;
+           for (j=1;j<=nlstate+ndeath;j++){
-   /*extern weight */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /* We are differentiating ll according to initial status */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+           }
-   /*for(i=1;i<imx;i++)
+         for(d=0; d<dh[mi][i]; d++){
-     printf(" %d\n",s[4][i]);
+           newm=savm;
-   */
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-   cov[1]=1.;
+           for (kk=1; kk<=cptcovage;kk++) {
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+           }
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-     for(mi=1; mi<= wav[i]-1; mi++){
+           savm=oldm;
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+           oldm=newm;
-         for (j=1;j<=nlstate+ndeath;j++){
+         } /* end mult */
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+         s1=s[mw[mi][i]][i];
-         }
+         s2=s[mw[mi+1][i]][i];
-       for(d=0; d<dh[mi][i]; d++){
+         if( s2 > nlstate){
-         newm=savm;
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         }else{
-         for (kk=1; kk<=cptcovage;kk++) {
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         }
-         }
+         ipmx +=1;
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         sw += weight[i];
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         savm=oldm;
+ /*      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=newm;
+       } /* end of wave */
-       } /* end mult */
+     } /* end of individual */
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-       s1=s[mw[mi][i]][i];
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       s2=s[mw[mi+1][i]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       bbh=(double)bh[mi][i]/(double)stepm;
+       for(mi=1; mi<= wav[i]-1; mi++){
-       /* bias is positive if real duration
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-        * is higher than the multiple of stepm and negative otherwise.
+           for (j=1;j<=nlstate+ndeath;j++){
-        */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli=log(out[s1][s2] - savm[s1][s2]);
+           }
-       } else if  (s2==-2) {
+         for(d=0; d<dh[mi][i]; d++){
-         for (j=1,survp=0. ; j<=nlstate; j++)
+           newm=savm;
-           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         lli= log(survp);
+           for (kk=1; kk<=cptcovage;kk++) {
-       }else if (mle==1){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+           }
-       } else if(mle==2){
-         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-       } else if(mle==3){  /* exponential inter-extrapolation */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         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 */
+           savm=oldm;
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+           oldm=newm;
-         lli=log(out[s1][s2]); /* Original formula */
+         } /* end mult */
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
-         lli=log(out[s1][s2]); /* Original formula */
+         s1=s[mw[mi][i]][i];
-       } /* End of if */
+         s2=s[mw[mi+1][i]][i];
-       ipmx +=1;
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-       sw += weight[i];
+         ipmx +=1;
-       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         sw += weight[i];
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-       if(globpr){
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+       } /* end of wave */
-  %11.6f %11.6f %11.6f ", \
+     } /* end of individual */
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+   } /* End of if */
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-           llt +=ll[k]*gipmx/gsw;
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+   return -l;
-         }
+ }
-         fprintf(ficresilk," %10.6f\n", -llt);
-       }
+ /*************** log-likelihood *************/
-     } /* end of wave */
+ double funcone( double *x)
-   } /* end of individual */
+ {
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+   /* Same as likeli but slower because of a lot of printf and if */
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+   int i, ii, j, k, mi, d, kk;
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-   if(globpr==0){ /* First time we count the contributions and weights */
+   double **out;
-     gipmx=ipmx;
+   double lli; /* Individual log likelihood */
-     gsw=sw;
+   double llt;
-   }
+   int s1, s2;
-   return -l;
+   double bbh, survp;
- }
+   /*extern weight */
+   /* We are differentiating ll according to initial status */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- /*************** function likelione ***********/
+   /*for(i=1;i<imx;i++)
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+     printf(" %d\n",s[4][i]);
- {
+   */
-   /* This routine should help understanding what is done with
+   cov[1]=1.;
-      the selection of individuals/waves and
-      to check the exact contribution to the likelihood.
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-      Plotting could be done.
-    */
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-   int k;
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for(mi=1; mi<= wav[i]-1; mi++){
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+       for (ii=1;ii<=nlstate+ndeath;ii++)
-     strcpy(fileresilk,"ilk");
+         for (j=1;j<=nlstate+ndeath;j++){
-     strcat(fileresilk,fileres);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-       printf("Problem with resultfile: %s\n", fileresilk);
+         }
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+       for(d=0; d<dh[mi][i]; d++){
-     }
+         newm=savm;
-     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");
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+         for (kk=1; kk<=cptcovage;kk++) {
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-     for(k=1; k<=nlstate; k++)
+         }
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   }
+         savm=oldm;
+         oldm=newm;
-   *fretone=(*funcone)(p);
+       } /* end mult */
-   if(*globpri !=0){
-     fclose(ficresilk);
+       s1=s[mw[mi][i]][i];
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+       s2=s[mw[mi+1][i]][i];
-     fflush(fichtm);
+       bbh=(double)bh[mi][i]/(double)stepm;
-   }
+       /* bias is positive if real duration
-   return;
+        * is higher than the multiple of stepm and negative otherwise.
- }
+        */
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+         lli=log(out[s1][s2] - savm[s1][s2]);
- /*********** Maximum Likelihood Estimation ***************/
+       } else if  (s2==-2) {
+         for (j=1,survp=0. ; j<=nlstate; j++)
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- {
+         lli= log(survp);
-   int i,j, iter;
+       }else if (mle==1){
-   double **xi;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   double fret;
+       } else if(mle==2){
-   double fretone; /* Only one call to likelihood */
+         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 */
-   /*  char filerespow[FILENAMELENGTH];*/
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   xi=matrix(1,npar,1,npar);
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
-   for (i=1;i<=npar;i++)
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     for (j=1;j<=npar;j++)
+         lli=log(out[s1][s2]); /* Original formula */
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+       } else{  /* mle=0 back to 1 */
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   strcpy(filerespow,"pow");
+         /*lli=log(out[s1][s2]); */ /* Original formula */
-   strcat(filerespow,fileres);
+       } /* End of if */
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       ipmx +=1;
-     printf("Problem with resultfile: %s\n", filerespow);
+       sw += weight[i];
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+       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]); */
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+       if(globpr){
-   for (i=1;i<=nlstate;i++)
+         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-     for(j=1;j<=nlstate+ndeath;j++)
+  %11.6f %11.6f %11.6f ", \
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-   fprintf(ficrespow,"\n");
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+           llt +=ll[k]*gipmx/gsw;
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-   free_matrix(xi,1,npar,1,npar);
+         }
-   fclose(ficrespow);
+         fprintf(ficresilk," %10.6f\n", -llt);
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+       }
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+     } /* end of wave */
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   } /* end of individual */
+   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 */
- /**** Computes Hessian and covariance matrix ***/
+   if(globpr==0){ /* First time we count the contributions and weights */
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+     gipmx=ipmx;
- {
+     gsw=sw;
-   double  **a,**y,*x,pd;
+   }
-   double **hess;
+   return -l;
-   int i, j,jk;
+ }
-   int *indx;
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+ /*************** function likelione ***********/
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+ {
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+   /* This routine should help understanding what is done with
-   double gompertz(double p[]);
+      the selection of individuals/waves and
-   hess=matrix(1,npar,1,npar);
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+    */
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+   int k;
-   for (i=1;i<=npar;i++){
-     printf("%d",i);fflush(stdout);
+   if(*globpri !=0){ /* Just counts and sums, no printings */
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+     strcpy(fileresilk,"ilk");
+     strcat(fileresilk,fileres);
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", fileresilk);
-     /*  printf(" %f ",p[i]);
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[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");
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-   for (i=1;i<=npar;i++) {
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-     for (j=1;j<=npar;j++)  {
+     for(k=1; k<=nlstate; k++)
-       if (j>i) {
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-         printf(".%d%d",i,j);fflush(stdout);
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+   }
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+   *fretone=(*funcone)(p);
-         hess[j][i]=hess[i][j];
+   if(*globpri !=0){
-         /*printf(" %lf ",hess[i][j]);*/
+     fclose(ficresilk);
-       }
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-     }
+     fflush(fichtm);
    }
-   printf("\n");
+   return;
-   fprintf(ficlog,"\n");
+ }
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+ /*********** Maximum Likelihood Estimation ***************/
-   a=matrix(1,npar,1,npar);
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   y=matrix(1,npar,1,npar);
+ {
-   x=vector(1,npar);
+   int i,j, iter;
-   indx=ivector(1,npar);
+   double **xi;
-   for (i=1;i<=npar;i++)
+   double fret;
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+   double fretone; /* Only one call to likelihood */
-   ludcmp(a,npar,indx,&pd);
+   /*  char filerespow[FILENAMELENGTH];*/
+   xi=matrix(1,npar,1,npar);
-   for (j=1;j<=npar;j++) {
+   for (i=1;i<=npar;i++)
-     for (i=1;i<=npar;i++) x[i]=0;
+     for (j=1;j<=npar;j++)
-     x[j]=1;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-     lubksb(a,npar,indx,x);
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-     for (i=1;i<=npar;i++){
+   strcpy(filerespow,"pow");
-       matcov[i][j]=x[i];
+   strcat(filerespow,fileres);
-     }
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   }
+     printf("Problem with resultfile: %s\n", filerespow);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   printf("\n#Hessian matrix#\n");
+   }
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   for (i=1;i<=npar;i++) {
+   for (i=1;i<=nlstate;i++)
-     for (j=1;j<=npar;j++) {
+     for(j=1;j<=nlstate+ndeath;j++)
-       printf("%.3e ",hess[i][j]);
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   fprintf(ficrespow,"\n");
-     }
-     printf("\n");
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-     fprintf(ficlog,"\n");
-   }
+   free_matrix(xi,1,npar,1,npar);
+   fclose(ficrespow);
-   /* Recompute Inverse */
+   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
-   for (i=1;i<=npar;i++)
+   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-   ludcmp(a,npar,indx,&pd);
+ }
-   /*  printf("\n#Hessian matrix recomputed#\n");
+ /**** Computes Hessian and covariance matrix ***/
-   for (j=1;j<=npar;j++) {
+ void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-     for (i=1;i<=npar;i++) x[i]=0;
+ {
-     x[j]=1;
+   double  **a,**y,*x,pd;
-     lubksb(a,npar,indx,x);
+   double **hess;
-     for (i=1;i<=npar;i++){
+   int i, j,jk;
-       y[i][j]=x[i];
+   int *indx;
-       printf("%.3e ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
-     }
+   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
-     printf("\n");
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-     fprintf(ficlog,"\n");
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   }
+   double gompertz(double p[]);
-   */
+   hess=matrix(1,npar,1,npar);
-   free_matrix(a,1,npar,1,npar);
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-   free_matrix(y,1,npar,1,npar);
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-   free_vector(x,1,npar);
+   for (i=1;i<=npar;i++){
-   free_ivector(indx,1,npar);
+     printf("%d",i);fflush(stdout);
-   free_matrix(hess,1,npar,1,npar);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- }
+     /*  printf(" %f ",p[i]);
- /*************** hessian matrix ****************/
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
+   }
- {
-   int i;
+   for (i=1;i<=npar;i++) {
-   int l=1, lmax=20;
+     for (j=1;j<=npar;j++)  {
-   double k1,k2;
+       if (j>i) {
-   double p2[NPARMAX+1];
+         printf(".%d%d",i,j);fflush(stdout);
-   double res;
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   double fx;
-   int k=0,kmax=10;
+         hess[j][i]=hess[i][j];
-   double l1;
+         /*printf(" %lf ",hess[i][j]);*/
+       }
-   fx=func(x);
+     }
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+   }
-   for(l=0 ; l <=lmax; l++){
+   printf("\n");
-     l1=pow(10,l);
+   fprintf(ficlog,"\n");
-     delts=delt;
-     for(k=1 ; k <kmax; k=k+1){
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-       delt = delta*(l1*k);
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-       p2[theta]=x[theta] +delt;
-       k1=func(p2)-fx;
+   a=matrix(1,npar,1,npar);
-       p2[theta]=x[theta]-delt;
+   y=matrix(1,npar,1,npar);
-       k2=func(p2)-fx;
+   x=vector(1,npar);
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
+   indx=ivector(1,npar);
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+   for (i=1;i<=npar;i++)
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
- #ifdef DEBUG
+   ludcmp(a,npar,indx,&pd);
-       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+   for (j=1;j<=npar;j++) {
- #endif
+     for (i=1;i<=npar;i++) x[i]=0;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+     x[j]=1;
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+     lubksb(a,npar,indx,x);
-         k=kmax;
+     for (i=1;i<=npar;i++){
-       }
+       matcov[i][j]=x[i];
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+     }
-         k=kmax; l=lmax*10.;
+   }
-       }
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   printf("\n#Hessian matrix#\n");
-         delts=delt;
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-       }
+   for (i=1;i<=npar;i++) {
-     }
+     for (j=1;j<=npar;j++) {
-   }
+       printf("%.3e ",hess[i][j]);
-   delti[theta]=delts;
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-   return res;
+     }
+     printf("\n");
- }
+     fprintf(ficlog,"\n");
+   }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
- {
+   /* Recompute Inverse */
-   int i;
+   for (i=1;i<=npar;i++)
-   int l=1, l1, lmax=20;
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
-   double k1,k2,k3,k4,res,fx;
+   ludcmp(a,npar,indx,&pd);
-   double p2[NPARMAX+1];
-   int k;
+   /*  printf("\n#Hessian matrix recomputed#\n");
-   fx=func(x);
+   for (j=1;j<=npar;j++) {
-   for (k=1; k<=2; k++) {
+     for (i=1;i<=npar;i++) x[i]=0;
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+     x[j]=1;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     lubksb(a,npar,indx,x);
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     for (i=1;i<=npar;i++){
-     k1=func(p2)-fx;
+       y[i][j]=x[i];
+       printf("%.3e ",y[i][j]);
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       fprintf(ficlog,"%.3e ",y[i][j]);
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     }
-     k2=func(p2)-fx;
+     printf("\n");
+     fprintf(ficlog,"\n");
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   }
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+   */
-     k3=func(p2)-fx;
+   free_matrix(a,1,npar,1,npar);
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   free_matrix(y,1,npar,1,npar);
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+   free_vector(x,1,npar);
-     k4=func(p2)-fx;
+   free_ivector(indx,1,npar);
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+   free_matrix(hess,1,npar,1,npar);
- #ifdef DEBUG
-     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
-   }
+ /*************** hessian matrix ****************/
-   return res;
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- }
+ {
+   int i;
- /************** Inverse of matrix **************/
+   int l=1, lmax=20;
- void ludcmp(double **a, int n, int *indx, double *d)
+   double k1,k2;
- {
+   double p2[MAXPARM+1]; /* identical to x */
-   int i,imax,j,k;
+   double res;
-   double big,dum,sum,temp;
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double *vv;
+   double fx;
+   int k=0,kmax=10;
-   vv=vector(1,n);
+   double l1;
-   *d=1.0;
-   for (i=1;i<=n;i++) {
+   fx=func(x);
-     big=0.0;
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-     for (j=1;j<=n;j++)
+   for(l=0 ; l <=lmax; l++){
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+     l1=pow(10,l);
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     delts=delt;
-     vv[i]=1.0/big;
+     for(k=1 ; k <kmax; k=k+1){
-   }
+       delt = delta*(l1*k);
-   for (j=1;j<=n;j++) {
+       p2[theta]=x[theta] +delt;
-     for (i=1;i<j;i++) {
+       k1=func(p2)-fx;
-       sum=a[i][j];
+       p2[theta]=x[theta]-delt;
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+       k2=func(p2)-fx;
-       a[i][j]=sum;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-     }
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-     big=0.0;
-     for (i=j;i<=n;i++) {
+ #ifdef DEBUGHESS
-       sum=a[i][j];
+       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<j;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);
-         sum -= a[i][k]*a[k][j];
+ #endif
-       a[i][j]=sum;
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-         big=dum;
+         k=kmax;
-         imax=i;
+       }
-       }
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-     }
+         k=kmax; l=lmax*10.;
-     if (j != imax) {
+       }
-       for (k=1;k<=n;k++) {
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
-         dum=a[imax][k];
+         delts=delt;
-         a[imax][k]=a[j][k];
+       }
-         a[j][k]=dum;
+     }
-       }
+   }
-       *d = -(*d);
+   delti[theta]=delts;
-       vv[imax]=vv[j];
+   return res;
-     }
-     indx[j]=imax;
+ }
-     if (a[j][j] == 0.0) a[j][j]=TINY;
-     if (j != n) {
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-       dum=1.0/(a[j][j]);
+ {
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+   int i;
-     }
+   int l=1, l1, lmax=20;
-   }
+   double k1,k2,k3,k4,res,fx;
-   free_vector(vv,1,n);  /* Doesn't work */
+   double p2[MAXPARM+1];
- ;
+   int k;
- }
+   fx=func(x);
- void lubksb(double **a, int n, int *indx, double b[])
+   for (k=1; k<=2; k++) {
- {
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-   int i,ii=0,ip,j;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   double sum;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     k1=func(p2)-fx;
-   for (i=1;i<=n;i++) {
-     ip=indx[i];
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-     sum=b[ip];
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     b[ip]=b[i];
+     k2=func(p2)-fx;
-     if (ii)
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-     else if (sum) ii=i;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-     b[i]=sum;
+     k3=func(p2)-fx;
-   }
-   for (i=n;i>=1;i--) {
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-     sum=b[i];
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     k4=func(p2)-fx;
-     b[i]=sum/a[i][i];
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-   }
+ #ifdef DEBUG
- }
+     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);
- void pstamp(FILE *fichier)
+ #endif
- {
+   }
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   return res;
  }
- /************ Frequencies ********************/
+ /************** Inverse of matrix **************/
- 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[])
+ void ludcmp(double **a, int n, int *indx, double *d)
- {  /* Some frequencies */
+ {
+   int i,imax,j,k;
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   double big,dum,sum,temp;
-   int first;
+   double *vv;
-   double ***freq; /* Frequencies */
-   double *pp, **prop;
+   vv=vector(1,n);
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   *d=1.0;
-   char fileresp[FILENAMELENGTH];
+   for (i=1;i<=n;i++) {
+     big=0.0;
-   pp=vector(1,nlstate);
+     for (j=1;j<=n;j++)
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-   strcpy(fileresp,"p");
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-   strcat(fileresp,fileres);
+     vv[i]=1.0/big;
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   }
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+   for (j=1;j<=n;j++) {
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+     for (i=1;i<j;i++) {
-     exit(0);
+       sum=a[i][j];
-   }
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+       a[i][j]=sum;
-   j1=0;
+     }
+     big=0.0;
-   j=cptcoveff;
+     for (i=j;i<=n;i++) {
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+       sum=a[i][j];
+       for (k=1;k<j;k++)
-   first=1;
+         sum -= a[i][k]*a[k][j];
+       a[i][j]=sum;
-   for(k1=1; k1<=j;k1++){
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-     for(i1=1; i1<=ncodemax[k1];i1++){
+         big=dum;
-       j1++;
+         imax=i;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+       }
-         scanf("%d", i);*/
+     }
-       for (i=-5; i<=nlstate+ndeath; i++)
+     if (j != imax) {
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+       for (k=1;k<=n;k++) {
-           for(m=iagemin; m <= iagemax+3; m++)
+         dum=a[imax][k];
-             freq[i][jk][m]=0;
+         a[imax][k]=a[j][k];
+         a[j][k]=dum;
-     for (i=1; i<=nlstate; i++)
+       }
-       for(m=iagemin; m <= iagemax+3; m++)
+       *d = -(*d);
-         prop[i][m]=0;
+       vv[imax]=vv[j];
+     }
-       dateintsum=0;
+     indx[j]=imax;
-       k2cpt=0;
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-       for (i=1; i<=imx; i++) {
+     if (j != n) {
-         bool=1;
+       dum=1.0/(a[j][j]);
-         if  (cptcovn>0) {
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
-           for (z1=1; z1<=cptcoveff; z1++)
+     }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   }
-               bool=0;
+   free_vector(vv,1,n);  /* Doesn't work */
-         }
+ ;
-         if (bool==1){
+ }
-           for(m=firstpass; m<=lastpass; m++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+ void lubksb(double **a, int n, int *indx, double b[])
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+ {
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   int i,ii=0,ip,j;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   double sum;
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               if (m<lastpass) {
+   for (i=1;i<=n;i++) {
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+     ip=indx[i];
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+     sum=b[ip];
-               }
+     b[ip]=b[i];
+     if (ii)
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-                 dateintsum=dateintsum+k2;
+     else if (sum) ii=i;
-                 k2cpt++;
+     b[i]=sum;
-               }
+   }
-               /*}*/
+   for (i=n;i>=1;i--) {
-           }
+     sum=b[i];
-         }
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-       }
+     b[i]=sum/a[i][i];
+   }
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+ }
-       pstamp(ficresp);
-       if  (cptcovn>0) {
+ void pstamp(FILE *fichier)
-         fprintf(ficresp, "\n#********** Variable ");
+ {
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-         fprintf(ficresp, "**********\n#");
+ }
-       }
-       for(i=1; i<=nlstate;i++)
+ /************ Frequencies ********************/
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-       fprintf(ficresp, "\n");
+ {  /* Some frequencies */
-       for(i=iagemin; i <= iagemax+3; i++){
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-         if(i==iagemax+3){
+   int first;
-           fprintf(ficlog,"Total");
+   double ***freq; /* Frequencies */
-         }else{
+   double *pp, **prop;
-           if(first==1){
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-             first=0;
+   char fileresp[FILENAMELENGTH];
-             printf("See log file for details...\n");
-           }
+   pp=vector(1,nlstate);
-           fprintf(ficlog,"Age %d", i);
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-         }
+   strcpy(fileresp,"p");
-         for(jk=1; jk <=nlstate ; jk++){
+   strcat(fileresp,fileres);
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-             pp[jk] += freq[jk][m][i];
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-         }
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-         for(jk=1; jk <=nlstate ; jk++){
+     exit(0);
-           for(m=-1, pos=0; m <=0 ; m++)
+   }
-             pos += freq[jk][m][i];
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-           if(pp[jk]>=1.e-10){
+   j1=0;
-             if(first==1){
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+   j=cptcoveff;
-             }
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           }else{
+   first=1;
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+   for(k1=1; k1<=j;k1++){
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+     for(i1=1; i1<=ncodemax[k1];i1++){
-           }
+       j1++;
-         }
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+         scanf("%d", i);*/
-         for(jk=1; jk <=nlstate ; jk++){
+       for (i=-5; i<=nlstate+ndeath; i++)
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
-             pp[jk] += freq[jk][m][i];
+           for(m=iagemin; m <= iagemax+3; m++)
-         }
+             freq[i][jk][m]=0;
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-           pos += pp[jk];
+     for (i=1; i<=nlstate; i++)
-           posprop += prop[jk][i];
+       for(m=iagemin; m <= iagemax+3; m++)
-         }
+         prop[i][m]=0;
-         for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
+       dateintsum=0;
-             if(first==1)
+       k2cpt=0;
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+       for (i=1; i<=imx; i++) {
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         bool=1;
-           }else{
+         if  (cptcovn>0) {
-             if(first==1)
+           for (z1=1; z1<=cptcoveff; z1++)
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+               bool=0;
-           }
+         }
-           if( i <= iagemax){
+         if (bool==1){
-             if(pos>=1.e-5){
+           for(m=firstpass; m<=lastpass; m++){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+             k2=anint[m][i]+(mint[m][i]/12.);
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               /*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(agev[m][i]==0) agev[m][i]=iagemax+1;
-             }
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-             else
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+               if (m<lastpass) {
-           }
+                 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];
+               }
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
-           for(m=-1; m <=nlstate+ndeath; m++)
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-             if(freq[jk][m][i] !=0 ) {
+                 dateintsum=dateintsum+k2;
-             if(first==1)
+                 k2cpt++;
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+               }
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+               /*}*/
-             }
+           }
-         if(i <= iagemax)
+         }
-           fprintf(ficresp,"\n");
+       }
-         if(first==1)
-           printf("Others in log...\n");
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-         fprintf(ficlog,"\n");
+       pstamp(ficresp);
-       }
+       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]]);
-   dateintmean=dateintsum/k2cpt;
+         fprintf(ficresp, "**********\n#");
+       }
-   fclose(ficresp);
+       for(i=1; i<=nlstate;i++)
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-   free_vector(pp,1,nlstate);
+       fprintf(ficresp, "\n");
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
-   /* End of Freq */
+       for(i=iagemin; i <= iagemax+3; i++){
- }
+         if(i==iagemax+3){
+           fprintf(ficlog,"Total");
- /************ Prevalence ********************/
+         }else{
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+           if(first==1){
- {
+             first=0;
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+             printf("See log file for details...\n");
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+           }
-      We still use firstpass and lastpass as another selection.
+           fprintf(ficlog,"Age %d", i);
-   */
+         }
+         for(jk=1; jk <=nlstate ; jk++){
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+           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;
+         for(jk=1; jk <=nlstate ; jk++){
-   double  y2; /* in fractional years */
+           for(m=-1, pos=0; m <=0 ; m++)
-   int iagemin, iagemax;
+             pos += freq[jk][m][i];
+           if(pp[jk]>=1.e-10){
-   iagemin= (int) agemin;
+             if(first==1){
-   iagemax= (int) agemax;
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   /*pp=vector(1,nlstate);*/
+             }
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+           }else{
-   j1=0;
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-   j=cptcoveff;
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+           }
+         }
-   for(k1=1; k1<=j;k1++){
-     for(i1=1; i1<=ncodemax[k1];i1++){
+         for(jk=1; jk <=nlstate ; jk++){
-       j1++;
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+             pp[jk] += freq[jk][m][i];
-       for (i=1; i<=nlstate; i++)
+         }
-         for(m=iagemin; m <= iagemax+3; m++)
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-           prop[i][m]=0.0;
+           pos += pp[jk];
+           posprop += prop[jk][i];
-       for (i=1; i<=imx; i++) { /* Each individual */
+         }
-         bool=1;
+         for(jk=1; jk <=nlstate ; jk++){
-         if  (cptcovn>0) {
+           if(pos>=1.e-5){
-           for (z1=1; z1<=cptcoveff; z1++)
+             if(first==1)
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-               bool=0;
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-         }
+           }else{
-         if (bool==1) {
+             if(first==1)
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+           }
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+           if( i <= iagemax){
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+             if(pos>=1.e-5){
-               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);
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-                 /*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]]);*/
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+             }
-                 prop[s[m][i]][iagemax+3] += weight[i];
+             else
-               }
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
-             }
+           }
-           } /* end selection of waves */
+         }
-         }
-       }
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-       for(i=iagemin; i <= iagemax+3; i++){
+           for(m=-1; m <=nlstate+ndeath; m++)
+             if(freq[jk][m][i] !=0 ) {
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+             if(first==1)
-           posprop += prop[jk][i];
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-         }
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+             }
-         for(jk=1; jk <=nlstate ; jk++){
+         if(i <= iagemax)
-           if( i <=  iagemax){
+           fprintf(ficresp,"\n");
-             if(posprop>=1.e-5){
+         if(first==1)
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+           printf("Others in log...\n");
-             }
+         fprintf(ficlog,"\n");
-           }
+       }
-         }/* end jk */
+     }
-       }/* end i */
+   }
-     } /* end i1 */
+   dateintmean=dateintsum/k2cpt;
-   } /* end k1 */
+   fclose(ficresp);
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   /*free_vector(pp,1,nlstate);*/
+   free_vector(pp,1,nlstate);
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
- }  /* End of prevalence */
+   /* End of Freq */
+ }
- /************* Waves Concatenation ***************/
+ /************ Prevalence ********************/
- 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)
+ 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)
  {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-      Death is a valid wave (if date is known).
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
+      We still use firstpass and lastpass as another selection.
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+   */
-      and mw[mi+1][i]. dh depends on stepm.
-      */
+   int i, m, jk, k1, i1, j1, bool, z1,j;
+   double ***freq; /* Frequencies */
-   int i, mi, m;
+   double *pp, **prop;
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+   double pos,posprop;
-      double sum=0., jmean=0.;*/
+   double  y2; /* in fractional years */
-   int first;
+   int iagemin, iagemax;
-   int j, k=0,jk, ju, jl;
-   double sum=0.;
+   iagemin= (int) agemin;
-   first=0;
+   iagemax= (int) agemax;
-   jmin=1e+5;
+   /*pp=vector(1,nlstate);*/
-   jmax=-1;
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-   jmean=0.;
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   for(i=1; i<=imx; i++){
+   j1=0;
-     mi=0;
-     m=firstpass;
+   j=cptcoveff;
-     while(s[m][i] <= nlstate){
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-         mw[++mi][i]=m;
+   for(k1=1; k1<=j;k1++){
-       if(m >=lastpass)
+     for(i1=1; i1<=ncodemax[k1];i1++){
-         break;
+       j1++;
-       else
-         m++;
+       for (i=1; i<=nlstate; i++)
-     }/* end while */
+         for(m=iagemin; m <= iagemax+3; m++)
-     if (s[m][i] > nlstate){
+           prop[i][m]=0.0;
-       mi++;     /* Death is another wave */
-       /* if(mi==0)  never been interviewed correctly before death */
+       for (i=1; i<=imx; i++) { /* Each individual */
-          /* Only death is a correct wave */
+         bool=1;
-       mw[mi][i]=m;
+         if  (cptcovn>0) {
-     }
+           for (z1=1; z1<=cptcoveff; z1++)
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-     wav[i]=mi;
+               bool=0;
-     if(mi==0){
+         }
-       nbwarn++;
+         if (bool==1) {
-       if(first==0){
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-         first=1;
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-       }
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-       if(first==1){
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
-       }
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-     } /* end mi==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]]);*/
-   } /* End individuals */
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[i];
-   for(i=1; i<=imx; i++){
+               }
-     for(mi=1; mi<wav[i];mi++){
+             }
-       if (stepm <=0)
+           } /* end selection of waves */
-         dh[mi][i]=1;
+         }
-       else{
+       }
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+       for(i=iagemin; i <= iagemax+3; i++){
-           if (agedc[i] < 2*AGESUP) {
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-             if(j==0) j=1;  /* Survives at least one month after exam */
+           posprop += prop[jk][i];
-             else if(j<0){
+         }
-               nberr++;
-               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+         for(jk=1; jk <=nlstate ; jk++){
-               j=1; /* Temporary Dangerous patch */
+           if( i <=  iagemax){
-               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);
+             if(posprop>=1.e-5){
-               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]);
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-               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);
+             } else
-             }
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
-             k=k+1;
+           }
-             if (j >= jmax){
+         }/* end jk */
-               jmax=j;
+       }/* end i */
-               ijmax=i;
+     } /* end i1 */
-             }
+   } /* end k1 */
-             if (j <= jmin){
-               jmin=j;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-               ijmin=i;
+   /*free_vector(pp,1,nlstate);*/
-             }
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-             sum=sum+j;
+ }  /* End of prevalence */
-             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+ /************* Waves Concatenation ***************/
-           }
-         }
+ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
-         else{
+ {
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
- /*        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]); */
+      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
-           k=k+1;
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-           if (j >= jmax) {
+      and mw[mi+1][i]. dh depends on stepm.
-             jmax=j;
+      */
-             ijmax=i;
-           }
+   int i, mi, m;
-           else if (j <= jmin){
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-             jmin=j;
+      double sum=0., jmean=0.;*/
-             ijmin=i;
+   int first;
-           }
+   int j, k=0,jk, ju, jl;
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+   double sum=0.;
-           /*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]);*/
+   first=0;
-           if(j<0){
+   jmin=1e+5;
-             nberr++;
+   jmax=-1;
-             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]);
+   jmean=0.;
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+   for(i=1; i<=imx; i++){
-           }
+     mi=0;
-           sum=sum+j;
+     m=firstpass;
-         }
+     while(s[m][i] <= nlstate){
-         jk= j/stepm;
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-         jl= j -jk*stepm;
+         mw[++mi][i]=m;
-         ju= j -(jk+1)*stepm;
+       if(m >=lastpass)
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+         break;
-           if(jl==0){
+       else
-             dh[mi][i]=jk;
+         m++;
-             bh[mi][i]=0;
+     }/* end while */
-           }else{ /* We want a negative bias in order to only have interpolation ie
+     if (s[m][i] > nlstate){
-                   * at the price of an extra matrix product in likelihood */
+       mi++;     /* Death is another wave */
-             dh[mi][i]=jk+1;
+       /* if(mi==0)  never been interviewed correctly before death */
-             bh[mi][i]=ju;
+          /* Only death is a correct wave */
-           }
+       mw[mi][i]=m;
-         }else{
+     }
-           if(jl <= -ju){
-             dh[mi][i]=jk;
+     wav[i]=mi;
-             bh[mi][i]=jl;       /* bias is positive if real duration
+     if(mi==0){
-                                  * is higher than the multiple of stepm and negative otherwise.
+       nbwarn++;
-                                  */
+       if(first==0){
-           }
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-           else{
+         first=1;
-             dh[mi][i]=jk+1;
+       }
-             bh[mi][i]=ju;
+       if(first==1){
-           }
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-           if(dh[mi][i]==0){
+       }
-             dh[mi][i]=1; /* At least one step */
+     } /* end mi==0 */
-             bh[mi][i]=ju; /* At least one step */
+   } /* End individuals */
-             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-           }
+   for(i=1; i<=imx; i++){
-         } /* end if mle */
+     for(mi=1; mi<wav[i];mi++){
-       }
+       if (stepm <=0)
-     } /* end wave */
+         dh[mi][i]=1;
-   }
+       else{
-   jmean=sum/k;
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-   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 (agedc[i] < 2*AGESUP) {
-   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);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-  }
+             if(j==0) j=1;  /* Survives at least one month after exam */
+             else if(j<0){
- /*********** Tricode ****************************/
+               nberr++;
- void tricode(int *Tvar, int **nbcode, int imx)
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
- {
+               j=1; /* Temporary Dangerous patch */
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+               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]);
-   int cptcode=0;
+               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);
-   cptcoveff=0;
+             }
+             k=k+1;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+             if (j >= jmax){
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+               jmax=j;
+               ijmax=i;
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+             }
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+             if (j <= jmin){
-                                modality*/
+               jmin=j;
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+               ijmin=i;
-       Ndum[ij]++; /*store the modality */
+             }
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+             sum=sum+j;
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-                                        Tvar[j]. If V=sex and male is 0 and
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-                                        female is 1, then  cptcode=1.*/
+           }
-     }
+         }
+         else{
-     for (i=0; i<=cptcode; i++) {
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-       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<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;
-     ij=1;
+           if (j >= jmax) {
-     for (i=1; i<=ncodemax[j]; i++) {
+             jmax=j;
-       for (k=0; k<= maxncov; k++) {
+             ijmax=i;
-         if (Ndum[k] != 0) {
+           }
-           nbcode[Tvar[j]][ij]=k;
+           else if (j <= jmin){
-           /* 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; */
+             jmin=j;
+             ijmin=i;
-           ij++;
+           }
-         }
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-         if (ij > ncodemax[j]) break;
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-       }
+           if(j<0){
-     }
+             nberr++;
-   }
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+           }
+           sum=sum+j;
-  for (i=1; i<=ncovmodel-2; i++) {
+         }
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+         jk= j/stepm;
-    ij=Tvar[i];
+         jl= j -jk*stepm;
-    Ndum[ij]++;
+         ju= j -(jk+1)*stepm;
-  }
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+           if(jl==0){
-  ij=1;
+             dh[mi][i]=jk;
-  for (i=1; i<= maxncov; i++) {
+             bh[mi][i]=0;
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+           }else{ /* We want a negative bias in order to only have interpolation ie
-      Tvaraff[ij]=i; /*For printing */
+                   * to avoid the price of an extra matrix product in likelihood */
-      ij++;
+             dh[mi][i]=jk+1;
-    }
+             bh[mi][i]=ju;
-  }
+           }
+         }else{
-  cptcoveff=ij-1; /*Number of simple covariates*/
+           if(jl <= -ju){
- }
+             dh[mi][i]=jk;
+             bh[mi][i]=jl;       /* bias is positive if real duration
- /*********** Health Expectancies ****************/
+                                  * is higher than the multiple of stepm and negative otherwise.
+                                  */
- void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+           }
+           else{
- {
+             dh[mi][i]=jk+1;
-   /* Health expectancies, no variances */
+             bh[mi][i]=ju;
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+           }
-   double age, agelim, hf;
+           if(dh[mi][i]==0){
-   double ***p3mat;
+             dh[mi][i]=1; /* At least one step */
-   double eip;
+             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);*/
-   pstamp(ficreseij);
+           }
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+         } /* end if mle */
-   fprintf(ficreseij,"# Age");
+       }
-   for(i=1; i<=nlstate;i++){
+     } /* end wave */
-     for(j=1; j<=nlstate;j++){
+   }
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   jmean=sum/k;
-     }
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-     fprintf(ficreseij," e%1d. ",i);
+   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(ficreseij,"\n");
+ /*********** Tricode ****************************/
+ void tricode(int *Tvar, int **nbcode, int imx)
-   if(estepm < stepm){
+ {
-     printf ("Problem %d lower than %d\n",estepm, 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 */
-   else  hstepm=estepm;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-    * This is mainly to measure the difference between two models: for example
+   int modmaxcovj=0; /* Modality max of covariates j */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   cptcoveff=0;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
-    * progression in between and thus overestimating or underestimating according
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
-    * to the curvature of the survival function. If, for the same date, we
+   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-    * to compare the new estimate of Life expectancy with the same linear
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
-    * hypothesis. A more precise result, taking into account a more precise
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
-    * curvature will be obtained if estepm is as small as stepm. */
+                                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
-   /* For example we decided to compute the life expectancy with the smallest unit */
+                                       modality of the nth covariate of individual i. */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-      nhstepm is the number of hstepm from age to agelim
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-      nstepm is the number of stepm from age to agelin.
+       if (ij > modmaxcovj) modmaxcovj=ij;
-      Look at hpijx to understand the reason of that which relies in memory size
+       /* getting the maximum value of the modality of the covariate
-      and note for a fixed period like estepm months */
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+          female is 1, then modmaxcovj=1.*/
-      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
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
-      results. So we changed our mind and took the option of the best precision.
+       if( Ndum[i] != 0 )
-   */
+         ncodemax[j]++;
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+       /* Number of modalities of the j th covariate. In fact
+          ncodemax[j]=2 (dichotom. variables only) but it could be more for
-   agelim=AGESUP;
+          historical reasons */
-   /* If stepm=6 months */
+     } /* Ndum[-1] number of undefined modalities */
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     ij=1;
- /* nhstepm age range expressed in number of stepm */
+     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-   /* if (stepm >= YEARM) hstepm=1;*/
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+                                      k is a modality. If we have model=V1+V1*sex
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+           ij++;
-   for (age=bage; age<=fage; age ++){
+         }
+         if (ij > ncodemax[j]) break;
+       }  /* end of loop on */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     } /* 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*/
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   for (k=0; k< maxncov; k++) Ndum[k]=0;
-     printf("%d|",(int)age);fflush(stdout);
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
+    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-     /* Computing expectancies */
+    Ndum[ij]++;
-     for(i=1; i<=nlstate;i++)
+  }
-       for(j=1; j<=nlstate;j++)
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+  ij=1;
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-           /*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]);*/
+      Tvaraff[ij]=i; /*For printing */
+      ij++;
-         }
+    }
+  }
-     fprintf(ficreseij,"%3.0f",age );
+  ij--;
-     for(i=1; i<=nlstate;i++){
+  cptcoveff=ij; /*Number of simple covariates*/
-       eip=0;
+ }
-       for(j=1; j<=nlstate;j++){
-         eip +=eij[i][j][(int)age];
+ /*********** Health Expectancies ****************/
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
-       }
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-       fprintf(ficreseij,"%9.4f", eip );
-     }
+ {
-     fprintf(ficreseij,"\n");
+   /* Health expectancies, no variances */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-   }
+   int nhstepma, nstepma; /* Decreasing with age */
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   double age, agelim, hf;
-   printf("\n");
+   double ***p3mat;
-   fprintf(ficlog,"\n");
+   double eip;
- }
+   pstamp(ficreseij);
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
- 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[] )
+   fprintf(ficreseij,"# Age");
+   for(i=1; i<=nlstate;i++){
- {
+     for(j=1; j<=nlstate;j++){
-   /* Covariances of health expectancies eij and of total life expectancies according
+       fprintf(ficreseij," e%1d%1d ",i,j);
-    to initial status i, ei. .
+     }
-   */
+     fprintf(ficreseij," e%1d. ",i);
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+   }
-   double age, agelim, hf;
+   fprintf(ficreseij,"\n");
-   double ***p3matp, ***p3matm, ***varhe;
-   double **dnewm,**doldm;
-   double *xp, *xm;
+   if(estepm < stepm){
-   double **gp, **gm;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-   double ***gradg, ***trgradg;
+   }
-   int theta;
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-   double eip, vip;
+    * This is mainly to measure the difference between two models: for example
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-   xp=vector(1,npar);
+    * progression in between and thus overestimating or underestimating according
-   xm=vector(1,npar);
+    * to the curvature of the survival function. If, for the same date, we
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+    * to compare the new estimate of Life expectancy with the same linear
+    * hypothesis. A more precise result, taking into account a more precise
-   pstamp(ficresstdeij);
+    * curvature will be obtained if estepm is as small as stepm. */
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-   fprintf(ficresstdeij,"# Age");
+   /* For example we decided to compute the life expectancy with the smallest unit */
-   for(i=1; i<=nlstate;i++){
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     for(j=1; j<=nlstate;j++)
+      nhstepm is the number of hstepm from age to agelim
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+      nstepm is the number of stepm from age to agelin.
-     fprintf(ficresstdeij," e%1d. ",i);
+      Look at hpijx to understand the reason of that which relies in memory size
-   }
+      and note for a fixed period like estepm months */
-   fprintf(ficresstdeij,"\n");
+   /* 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
-   pstamp(ficrescveij);
+      means that if the survival funtion is printed only each two years of age and if
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-   fprintf(ficrescveij,"# Age");
+      results. So we changed our mind and took the option of the best precision.
-   for(i=1; i<=nlstate;i++)
+   */
-     for(j=1; j<=nlstate;j++){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-       cptj= (j-1)*nlstate+i;
-       for(i2=1; i2<=nlstate;i2++)
+   agelim=AGESUP;
-         for(j2=1; j2<=nlstate;j2++){
+   /* If stepm=6 months */
-           cptj2= (j2-1)*nlstate+i2;
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-           if(cptj2 <= cptj)
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-         }
+ /* nhstepm age range expressed in number of stepm */
-     }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   fprintf(ficrescveij,"\n");
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   /* if (stepm >= YEARM) hstepm=1;*/
-   if(estepm < stepm){
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
-   else  hstepm=estepm;
+   for (age=bage; age<=fage; age ++){
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-    * This is mainly to measure the difference between two models: for example
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+     /* if (stepm >= YEARM) hstepm=1;*/
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-    * progression in between and thus overestimating or underestimating according
-    * to the curvature of the survival function. If, for the same date, we
+     /* If stepm=6 months */
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-    * to compare the new estimate of Life expectancy with the same linear
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-    * hypothesis. A more precise result, taking into account a more precise
-    * curvature will be obtained if estepm is as small as stepm. */
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year 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
+     printf("%d|",(int)age);fflush(stdout);
-      nstepm is the number of stepm from age to agelin.
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like estepm months */
+     /* Computing expectancies */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     for(i=1; i<=nlstate;i++)
-      survival function given by stepm (the optimization length). Unfortunately it
+       for(j=1; j<=nlstate;j++)
-      means that if the survival funtion is printed only each two years of age and if
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-      results. So we changed our mind and took the option of the best precision.
-   */
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+         }
-   /* If stepm=6 months */
-   /* nhstepm age range expressed in number of stepm */
+     fprintf(ficreseij,"%3.0f",age );
-   agelim=AGESUP;
+     for(i=1; i<=nlstate;i++){
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+       eip=0;
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+       for(j=1; j<=nlstate;j++){
-   /* if (stepm >= YEARM) hstepm=1;*/
+         eip +=eij[i][j][(int)age];
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficreseij,"%9.4f", eip );
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     }
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+     fprintf(ficreseij,"\n");
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
-   for (age=bage; age<=fage; age ++){
+   fprintf(ficlog,"\n");
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+ }
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+ 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[] )
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+ {
-     /* Computing  Variances of health expectancies */
+   /* Covariances of health expectancies eij and of total life expectancies according
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+    to initial status i, ei. .
-        decrease memory allocation */
+   */
-     for(theta=1; theta <=npar; theta++){
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-       for(i=1; i<=npar; i++){
+   int nhstepma, nstepma; /* Decreasing with age */
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   double age, agelim, hf;
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+   double ***p3matp, ***p3matm, ***varhe;
-       }
+   double **dnewm,**doldm;
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+   double *xp, *xm;
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+   double **gp, **gm;
+   double ***gradg, ***trgradg;
-       for(j=1; j<= nlstate; j++){
+   int theta;
-         for(i=1; i<=nlstate; i++){
-           for(h=0; h<=nhstepm-1; h++){
+   double eip, vip;
-             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.;
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-           }
+   xp=vector(1,npar);
-         }
+   xm=vector(1,npar);
-       }
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-       for(ij=1; ij<= nlstate*nlstate; ij++)
-         for(h=0; h<=nhstepm-1; h++){
+   pstamp(ficresstdeij);
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-         }
+   fprintf(ficresstdeij,"# Age");
-     }/* End theta */
+   for(i=1; i<=nlstate;i++){
+     for(j=1; j<=nlstate;j++)
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-     for(h=0; h<=nhstepm-1; h++)
+     fprintf(ficresstdeij," e%1d. ",i);
-       for(j=1; j<=nlstate*nlstate;j++)
+   }
-         for(theta=1; theta <=npar; theta++)
+   fprintf(ficresstdeij,"\n");
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   pstamp(ficrescveij);
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   fprintf(ficrescveij,"# Age");
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+   for(i=1; i<=nlstate;i++)
-         varhe[ij][ji][(int)age] =0.;
+     for(j=1; j<=nlstate;j++){
+       cptj= (j-1)*nlstate+i;
-      printf("%d|",(int)age);fflush(stdout);
+       for(i2=1; i2<=nlstate;i2++)
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+         for(j2=1; j2<=nlstate;j2++){
-      for(h=0;h<=nhstepm-1;h++){
+           cptj2= (j2-1)*nlstate+i2;
-       for(k=0;k<=nhstepm-1;k++){
+           if(cptj2 <= cptj)
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+         }
-         for(ij=1;ij<=nlstate*nlstate;ij++)
+     }
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+   fprintf(ficrescveij,"\n");
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-       }
+   if(estepm < stepm){
-     }
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-     /* Computing expectancies */
+   else  hstepm=estepm;
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+   /* We compute the life expectancy from trapezoids spaced every estepm months
-     for(i=1; i<=nlstate;i++)
+    * This is mainly to measure the difference between two models: for example
-       for(j=1; j<=nlstate;j++)
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-           /* 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]);*/
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+    * to compare the new estimate of Life expectancy with the same linear
-         }
+    * hypothesis. A more precise result, taking into account a more precise
+    * curvature will be obtained if estepm is as small as stepm. */
-     fprintf(ficresstdeij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++){
+   /* For example we decided to compute the life expectancy with the smallest unit */
-       eip=0.;
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       vip=0.;
+      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.
-         eip += eij[i][j][(int)age];
+      Look at hpijx to understand the reason of that which relies in memory size
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+      and note for a fixed period like estepm months */
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+      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(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+      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(ficresstdeij,"\n");
+   */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-     fprintf(ficrescveij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++)
+   /* If stepm=6 months */
-       for(j=1; j<=nlstate;j++){
+   /* nhstepm age range expressed in number of stepm */
-         cptj= (j-1)*nlstate+i;
+   agelim=AGESUP;
-         for(i2=1; i2<=nlstate;i2++)
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-           for(j2=1; j2<=nlstate;j2++){
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-             cptj2= (j2-1)*nlstate+i2;
+   /* if (stepm >= YEARM) hstepm=1;*/
-             if(cptj2 <= cptj)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-           }
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       }
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficrescveij,"\n");
+   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);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+   for (age=bage; age<=fage; age ++){
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /* if (stepm >= YEARM) hstepm=1;*/
-   printf("\n");
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-   fprintf(ficlog,"\n");
+     /* If stepm=6 months */
-   free_vector(xm,1,npar);
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   free_vector(xp,1,npar);
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
- }
+     /* Computing  Variances of health expectancies */
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
- /************ Variance ******************/
+        decrease memory allocation */
- 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[])
+     for(theta=1; theta <=npar; theta++){
- {
+       for(i=1; i<=npar; i++){
-   /* Variance of health expectancies */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
-   /* double **newm;*/
+       }
-   double **dnewm,**doldm;
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-   double **dnewmp,**doldmp;
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-   int i, j, nhstepm, hstepm, h, nstepm ;
-   int k, cptcode;
+       for(j=1; j<= nlstate; j++){
-   double *xp;
+         for(i=1; i<=nlstate; i++){
-   double **gp, **gm;  /* for var eij */
+           for(h=0; h<=nhstepm-1; h++){
-   double ***gradg, ***trgradg; /*for var eij */
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-   double **gradgp, **trgradgp; /* for var p point j */
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-   double *gpp, *gmp; /* for var p point j */
+           }
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+         }
-   double ***p3mat;
+       }
-   double age,agelim, hf;
-   double ***mobaverage;
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-   int theta;
+         for(h=0; h<=nhstepm-1; h++){
-   char digit[4];
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-   char digitp[25];
+         }
+     }/* End theta */
-   char fileresprobmorprev[FILENAMELENGTH];
-   if(popbased==1){
+     for(h=0; h<=nhstepm-1; h++)
-     if(mobilav!=0)
+       for(j=1; j<=nlstate*nlstate;j++)
-       strcpy(digitp,"-populbased-mobilav-");
+         for(theta=1; theta <=npar; theta++)
-     else strcpy(digitp,"-populbased-nomobil-");
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   }
-   else
-     strcpy(digitp,"-stablbased-");
+      for(ij=1;ij<=nlstate*nlstate;ij++)
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-   if (mobilav!=0) {
+         varhe[ij][ji][(int)age] =0.;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+      printf("%d|",(int)age);fflush(stdout);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+      for(h=0;h<=nhstepm-1;h++){
-     }
+       for(k=0;k<=nhstepm-1;k++){
-   }
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   strcpy(fileresprobmorprev,"prmorprev");
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   sprintf(digit,"%-d",ij);
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+       }
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+     }
-   strcat(fileresprobmorprev,fileres);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+     /* Computing expectancies */
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+     for(i=1; i<=nlstate;i++)
-   }
+       for(j=1; j<=nlstate;j++)
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   pstamp(ficresprobmorprev);
+           /* 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(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+         }
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+     fprintf(ficresstdeij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++)
+     for(i=1; i<=nlstate;i++){
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+       eip=0.;
-   }
+       vip=0.;
-   fprintf(ficresprobmorprev,"\n");
+       for(j=1; j<=nlstate;j++){
-   fprintf(ficgp,"\n# Routine varevsij");
+         eip += eij[i][j][(int)age];
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-   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");
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
- /*   } */
+       }
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   pstamp(ficresvij);
+     }
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+     fprintf(ficresstdeij,"\n");
-   if(popbased==1)
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+     fprintf(ficrescveij,"%3.0f",age );
-   else
+     for(i=1; i<=nlstate;i++)
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+       for(j=1; j<=nlstate;j++){
-   fprintf(ficresvij,"# Age");
+         cptj= (j-1)*nlstate+i;
-   for(i=1; i<=nlstate;i++)
+         for(i2=1; i2<=nlstate;i2++)
-     for(j=1; j<=nlstate;j++)
+           for(j2=1; j2<=nlstate;j2++){
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+             cptj2= (j2-1)*nlstate+i2;
-   fprintf(ficresvij,"\n");
+             if(cptj2 <= cptj)
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-   xp=vector(1,npar);
+           }
-   dnewm=matrix(1,nlstate,1,npar);
+       }
-   doldm=matrix(1,nlstate,1,nlstate);
+     fprintf(ficrescveij,"\n");
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   }
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   if(estepm < stepm){
+   printf("\n");
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   fprintf(ficlog,"\n");
-   }
-   else  hstepm=estepm;
+   free_vector(xm,1,npar);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   free_vector(xp,1,npar);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-      nhstepm is the number of hstepm from age to agelim
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-      nstepm is the number of stepm from age to agelin.
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-      Look at hpijx to understand the reason of that which relies in memory size
+ }
-      and note for a fixed period like k years */
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+ /************ Variance ******************/
-      survival function given by stepm (the optimization length). Unfortunately it
+ 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[])
-      means that if the survival funtion is printed every two years of age and if
+ {
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   /* Variance of health expectancies */
-      results. So we changed our mind and took the option of the best precision.
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   */
+   /* double **newm;*/
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   double **dnewm,**doldm;
-   agelim = AGESUP;
+   double **dnewmp,**doldmp;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   int i, j, nhstepm, hstepm, h, nstepm ;
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   int k, cptcode;
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   double *xp;
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   double **gp, **gm;  /* for var eij */
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+   double ***gradg, ***trgradg; /*for var eij */
-     gp=matrix(0,nhstepm,1,nlstate);
+   double **gradgp, **trgradgp; /* for var p point j */
-     gm=matrix(0,nhstepm,1,nlstate);
+   double *gpp, *gmp; /* for var p point j */
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+   double ***p3mat;
-     for(theta=1; theta <=npar; theta++){
+   double age,agelim, hf;
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   double ***mobaverage;
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   int theta;
-       }
+   char digit[4];
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   char digitp[25];
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   char fileresprobmorprev[FILENAMELENGTH];
-       if (popbased==1) {
-         if(mobilav ==0){
+   if(popbased==1){
-           for(i=1; i<=nlstate;i++)
+     if(mobilav!=0)
-             prlim[i][i]=probs[(int)age][i][ij];
+       strcpy(digitp,"-populbased-mobilav-");
-         }else{ /* mobilav */
+     else strcpy(digitp,"-populbased-nomobil-");
-           for(i=1; i<=nlstate;i++)
+   }
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   else
-         }
+     strcpy(digitp,"-stablbased-");
-       }
+   if (mobilav!=0) {
-       for(j=1; j<= nlstate; j++){
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         for(h=0; h<=nhstepm; h++){
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-         }
+     }
-       }
+   }
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
+   strcpy(fileresprobmorprev,"prmorprev");
-          as a weighted average of prlim.
+   sprintf(digit,"%-d",ij);
-       */
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+   strcat(fileresprobmorprev,fileres);
-       }
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-       /* end probability of death */
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+   }
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   pstamp(ficresprobmorprev);
-       if (popbased==1) {
+   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);
-         if(mobilav ==0){
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-           for(i=1; i<=nlstate;i++)
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-             prlim[i][i]=probs[(int)age][i][ij];
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-         }else{ /* mobilav */
+     for(i=1; i<=nlstate;i++)
-           for(i=1; i<=nlstate;i++)
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   }
-         }
+   fprintf(ficresprobmorprev,"\n");
-       }
+   fprintf(ficgp,"\n# Routine varevsij");
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-       for(j=1; j<= nlstate; j++){
+   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-         for(h=0; h<=nhstepm; h++){
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+ /*   } */
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+   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 ");
-       /* This for computing probability of death (h=1 means
+   if(popbased==1)
-          computed over hstepm matrices product = hstepm*stepm months)
+     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);
-          as a weighted average of prlim.
+   else
-       */
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   fprintf(ficresvij,"# Age");
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+   for(i=1; i<=nlstate;i++)
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+     for(j=1; j<=nlstate;j++)
-       }
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-       /* end probability of death */
+   fprintf(ficresvij,"\n");
-       for(j=1; j<= nlstate; j++) /* vareij */
+   xp=vector(1,npar);
-         for(h=0; h<=nhstepm; h++){
+   dnewm=matrix(1,nlstate,1,npar);
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+   doldm=matrix(1,nlstate,1,nlstate);
-         }
+   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-       }
+   gpp=vector(nlstate+1,nlstate+ndeath);
+   gmp=vector(nlstate+1,nlstate+ndeath);
-     } /* End theta */
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-     for(h=0; h<=nhstepm; h++) /* veij */
+   }
-       for(j=1; j<=nlstate;j++)
+   else  hstepm=estepm;
-         for(theta=1; theta <=npar; theta++)
+   /* For example we decided to compute the life expectancy with the smallest unit */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   /* 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
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+      nstepm is the number of stepm from age to agelin.
-       for(theta=1; theta <=npar; theta++)
+      Look at function hpijx to understand why (it is linked to memory size questions) */
-         trgradgp[j][theta]=gradgp[theta][j];
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed every two years of age and if
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     for(i=1;i<=nlstate;i++)
+      results. So we changed our mind and took the option of the best precision.
-       for(j=1;j<=nlstate;j++)
+   */
-         vareij[i][j][(int)age] =0.;
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   agelim = AGESUP;
-     for(h=0;h<=nhstepm;h++){
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       for(k=0;k<=nhstepm;k++){
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         for(i=1;i<=nlstate;i++)
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-           for(j=1;j<=nlstate;j++)
+     gp=matrix(0,nhstepm,1,nlstate);
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+     gm=matrix(0,nhstepm,1,nlstate);
-       }
-     }
+     for(theta=1; theta <=npar; theta++){
-     /* pptj */
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+       }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-         varppt[j][i]=doldmp[j][i];
-     /* end ppptj */
+       if (popbased==1) {
-     /*  x centered again */
+         if(mobilav ==0){
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+           for(i=1; i<=nlstate;i++)
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
-     if (popbased==1) {
+           for(i=1; i<=nlstate;i++)
-       if(mobilav ==0){
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-         for(i=1; i<=nlstate;i++)
+         }
-           prlim[i][i]=probs[(int)age][i][ij];
+       }
-       }else{ /* mobilav */
-         for(i=1; i<=nlstate;i++)
+       for(j=1; j<= nlstate; j++){
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+         for(h=0; h<=nhstepm; h++){
-       }
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-     }
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+         }
-     /* This for computing probability of death (h=1 means
+       }
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+       /* This for computing probability of death (h=1 means
-        as a weighted average of prlim.
+          computed over hstepm matrices product = hstepm*stepm months)
-     */
+          as a weighted average of prlim.
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-     }
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-     /* end probability of death */
+       }
+       /* end probability of death */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       for(i=1; i<=nlstate;i++){
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       }
-     }
+       if (popbased==1) {
-     fprintf(ficresprobmorprev,"\n");
+         if(mobilav ==0){
+           for(i=1; i<=nlstate;i++)
-     fprintf(ficresvij,"%.0f ",age );
+             prlim[i][i]=probs[(int)age][i][ij];
-     for(i=1; i<=nlstate;i++)
+         }else{ /* mobilav */
-       for(j=1; j<=nlstate;j++){
+           for(i=1; i<=nlstate;i++)
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-       }
+         }
-     fprintf(ficresvij,"\n");
+       }
-     free_matrix(gp,0,nhstepm,1,nlstate);
-     free_matrix(gm,0,nhstepm,1,nlstate);
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+         for(h=0; h<=nhstepm; h++){
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-   } /* End age */
+         }
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+       }
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+       /* This for computing probability of death (h=1 means
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+          computed over hstepm matrices product = hstepm*stepm months)
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+          as a weighted average of prlim.
-   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 */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       }
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       /* end probability of death */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+       for(j=1; j<= nlstate; j++) /* vareij */
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+         for(h=0; h<=nhstepm; h++){
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+         }
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
- */
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+       }
-   free_vector(xp,1,npar);
+     } /* End theta */
-   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+     for(h=0; h<=nhstepm; h++) /* veij */
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       for(j=1; j<=nlstate;j++)
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         for(theta=1; theta <=npar; theta++)
-   fclose(ficresprobmorprev);
+           trgradg[h][j][theta]=gradg[h][theta][j];
-   fflush(ficgp);
-   fflush(fichtm);
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
- }  /* end varevsij */
+       for(theta=1; theta <=npar; theta++)
+         trgradgp[j][theta]=gradgp[theta][j];
- /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
- {
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   /* Variance of prevalence limit */
+     for(i=1;i<=nlstate;i++)
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+       for(j=1;j<=nlstate;j++)
-   double **newm;
+         vareij[i][j][(int)age] =0.;
-   double **dnewm,**doldm;
-   int i, j, nhstepm, hstepm;
+     for(h=0;h<=nhstepm;h++){
-   int k, cptcode;
+       for(k=0;k<=nhstepm;k++){
-   double *xp;
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-   double *gp, *gm;
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-   double **gradg, **trgradg;
+         for(i=1;i<=nlstate;i++)
-   double age,agelim;
+           for(j=1;j<=nlstate;j++)
-   int theta;
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+       }
-   pstamp(ficresvpl);
+     }
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+     /* pptj */
-   for(i=1; i<=nlstate;i++)
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-       fprintf(ficresvpl," %1d-%1d",i,i);
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-   fprintf(ficresvpl,"\n");
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-   xp=vector(1,npar);
+         varppt[j][i]=doldmp[j][i];
-   dnewm=matrix(1,nlstate,1,npar);
+     /* end ppptj */
-   doldm=matrix(1,nlstate,1,nlstate);
+     /*  x centered again */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-   hstepm=1*YEARM; /* Every year of age */
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   agelim = AGESUP;
+     if (popbased==1) {
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+       if(mobilav ==0){
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         for(i=1; i<=nlstate;i++)
-     if (stepm >= YEARM) hstepm=1;
+           prlim[i][i]=probs[(int)age][i][ij];
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+       }else{ /* mobilav */
-     gradg=matrix(1,npar,1,nlstate);
+         for(i=1; i<=nlstate;i++)
-     gp=vector(1,nlstate);
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-     gm=vector(1,nlstate);
+       }
+     }
-     for(theta=1; theta <=npar; theta++){
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+     /* This for computing probability of death (h=1 means
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-       }
+        as a weighted average of prlim.
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     */
-       for(i=1;i<=nlstate;i++)
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         gp[i] = prlim[i][i];
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-       for(i=1; i<=npar; i++) /* Computes gradient */
+     }
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+     /* end probability of death */
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       for(i=1;i<=nlstate;i++)
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-         gm[i] = prlim[i][i];
+     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++)
+       for(i=1; i<=nlstate;i++){
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-     } /* End theta */
+       }
+     }
-     trgradg =matrix(1,nlstate,1,npar);
+     fprintf(ficresprobmorprev,"\n");
-     for(j=1; j<=nlstate;j++)
+     fprintf(ficresvij,"%.0f ",age );
-       for(theta=1; theta <=npar; theta++)
+     for(i=1; i<=nlstate;i++)
-         trgradg[j][theta]=gradg[theta][j];
+       for(j=1; j<=nlstate;j++){
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-     for(i=1;i<=nlstate;i++)
+       }
-       varpl[i][(int)age] =0.;
+     fprintf(ficresvij,"\n");
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     free_matrix(gp,0,nhstepm,1,nlstate);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     free_matrix(gm,0,nhstepm,1,nlstate);
-     for(i=1;i<=nlstate;i++)
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     fprintf(ficresvpl,"%.0f ",age );
+   } /* End age */
-     for(i=1; i<=nlstate;i++)
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-     fprintf(ficresvpl,"\n");
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-     free_vector(gp,1,nlstate);
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     free_vector(gm,1,nlstate);
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
-     free_matrix(gradg,1,npar,1,nlstate);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-     free_matrix(trgradg,1,nlstate,1,npar);
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-   } /* End age */
+ /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   free_vector(xp,1,npar);
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   free_matrix(doldm,1,nlstate,1,npar);
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   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));
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
- /************ Variance of one-step probabilities  ******************/
+   /*  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);
- 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,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   int i, j=0,  i1, k1, l1, t, tj;
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   int k2, l2, j1,  z1;
-   int k=0,l, cptcode;
+   free_vector(xp,1,npar);
-   int first=1, first1;
+   free_matrix(doldm,1,nlstate,1,nlstate);
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   free_matrix(dnewm,1,nlstate,1,npar);
-   double **dnewm,**doldm;
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   double *xp;
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   double *gp, *gm;
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   double **gradg, **trgradg;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   double **mu;
+   fclose(ficresprobmorprev);
-   double age,agelim, cov[NCOVMAX];
+   fflush(ficgp);
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+   fflush(fichtm);
-   int theta;
+ }  /* end varevsij */
-   char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+ /************ Variance of prevlim ******************/
-   char fileresprobcor[FILENAMELENGTH];
+ 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[])
+ {
-   double ***varpij;
+   /* Variance of prevalence limit */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   strcpy(fileresprob,"prob");
+   double **newm;
-   strcat(fileresprob,fileres);
+   double **dnewm,**doldm;
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+   int i, j, nhstepm, hstepm;
-     printf("Problem with resultfile: %s\n", fileresprob);
+   int k, cptcode;
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   double *xp;
-   }
+   double *gp, *gm;
-   strcpy(fileresprobcov,"probcov");
+   double **gradg, **trgradg;
-   strcat(fileresprobcov,fileres);
+   double age,agelim;
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+   int theta;
-     printf("Problem with resultfile: %s\n", fileresprobcov);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+   pstamp(ficresvpl);
-   }
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   strcpy(fileresprobcor,"probcor");
+   fprintf(ficresvpl,"# Age");
-   strcat(fileresprobcor,fileres);
+   for(i=1; i<=nlstate;i++)
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+       fprintf(ficresvpl," %1d-%1d",i,i);
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+   fprintf(ficresvpl,"\n");
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+   xp=vector(1,npar);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   dnewm=matrix(1,nlstate,1,npar);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   doldm=matrix(1,nlstate,1,nlstate);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+   hstepm=1*YEARM; /* Every year of age */
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   agelim = AGESUP;
-   pstamp(ficresprob);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   fprintf(ficresprob,"# Age");
+     if (stepm >= YEARM) hstepm=1;
-   pstamp(ficresprobcov);
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+     gradg=matrix(1,npar,1,nlstate);
-   fprintf(ficresprobcov,"# Age");
+     gp=vector(1,nlstate);
-   pstamp(ficresprobcor);
+     gm=vector(1,nlstate);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"# Age");
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   for(i=1; i<=nlstate;i++)
+       }
-     for(j=1; j<=(nlstate+ndeath);j++){
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       for(i=1;i<=nlstate;i++)
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+         gp[i] = prlim[i][i];
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+       for(i=1; i<=npar; i++) /* Computes gradient */
-  /* fprintf(ficresprob,"\n");
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   fprintf(ficresprobcov,"\n");
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   fprintf(ficresprobcor,"\n");
+       for(i=1;i<=nlstate;i++)
-  */
+         gm[i] = prlim[i][i];
-  xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+       for(i=1;i<=nlstate;i++)
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+     } /* End theta */
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   first=1;
+     trgradg =matrix(1,nlstate,1,npar);
-   fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     for(j=1; j<=nlstate;j++)
-   fprintf(fichtm,"\n");
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+     for(i=1;i<=nlstate;i++)
-   file %s<br>\n",optionfilehtmcov);
+       varpl[i][(int)age] =0.;
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
- and drawn. It helps understanding how is the covariance between two incidences.\
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+     for(i=1;i<=nlstate;i++)
-   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. \
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+     fprintf(ficresvpl,"%.0f ",age );
- standard deviations wide on each axis. <br>\
+     for(i=1; i<=nlstate;i++)
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+     fprintf(ficresvpl,"\n");
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+     free_vector(gp,1,nlstate);
+     free_vector(gm,1,nlstate);
-   cov[1]=1;
+     free_matrix(gradg,1,npar,1,nlstate);
-   tj=cptcoveff;
+     free_matrix(trgradg,1,nlstate,1,npar);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   } /* End age */
-   j1=0;
-   for(t=1; t<=tj;t++){
+   free_vector(xp,1,npar);
-     for(i1=1; i1<=ncodemax[t];i1++){
+   free_matrix(doldm,1,nlstate,1,npar);
-       j1++;
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-       if  (cptcovn>0) {
-         fprintf(ficresprob, "\n#********** Variable ");
+ }
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficresprob, "**********\n#\n");
+ /************ Variance of one-step probabilities  ******************/
-         fprintf(ficresprobcov, "\n#********** Variable ");
+ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ {
-         fprintf(ficresprobcov, "**********\n#\n");
+   int i, j=0,  i1, k1, l1, t, tj;
+   int k2, l2, j1,  z1;
-         fprintf(ficgp, "\n#********** Variable ");
+   int k=0,l, cptcode;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   int first=1, first1;
-         fprintf(ficgp, "**********\n#\n");
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+   double **dnewm,**doldm;
+   double *xp;
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+   double *gp, *gm;
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   double **gradg, **trgradg;
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   double **mu;
+   double age,agelim, cov[NCOVMAX];
-         fprintf(ficresprobcor, "\n#********** Variable ");
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   int theta;
-         fprintf(ficresprobcor, "**********\n#");
+   char fileresprob[FILENAMELENGTH];
-       }
+   char fileresprobcov[FILENAMELENGTH];
+   char fileresprobcor[FILENAMELENGTH];
-       for (age=bage; age<=fage; age ++){
-         cov[2]=age;
+   double ***varpij;
-         for (k=1; k<=cptcovn;k++) {
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   strcpy(fileresprob,"prob");
-         }
+   strcat(fileresprob,fileres);
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-         for (k=1; k<=cptcovprod;k++)
+     printf("Problem with resultfile: %s\n", fileresprob);
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   }
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   strcpy(fileresprobcov,"probcov");
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+   strcat(fileresprobcov,fileres);
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+     printf("Problem with resultfile: %s\n", fileresprobcov);
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-         for(theta=1; theta <=npar; theta++){
+   }
-           for(i=1; i<=npar; i++)
+   strcpy(fileresprobcor,"probcor");
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+   strcat(fileresprobcor,fileres);
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+     printf("Problem with resultfile: %s\n", fileresprobcor);
+     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);
-               gp[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<=npar; i++)
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+   fprintf(ficresprob,"# Age");
+   pstamp(ficresprobcov);
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-           k=0;
+   fprintf(ficresprobcov,"# Age");
-           for(i=1; i<=(nlstate); i++){
+   pstamp(ficresprobcor);
-             for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-               k=k+1;
+   fprintf(ficresprobcor,"# Age");
-               gm[k]=pmmij[i][j];
-             }
-           }
+   for(i=1; i<=nlstate;i++)
+     for(j=1; j<=(nlstate+ndeath);j++){
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
-         }
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+     }
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+  /* fprintf(ficresprob,"\n");
-           for(theta=1; theta <=npar; theta++)
+   fprintf(ficresprobcov,"\n");
-             trgradg[j][theta]=gradg[theta][j];
+   fprintf(ficresprobcor,"\n");
+  */
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+   xp=vector(1,npar);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+   first=1;
+   fprintf(ficgp,"\n# Routine varprob");
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+   fprintf(fichtm,"\n");
-         k=0;
-         for(i=1; i<=(nlstate); i++){
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-           for(j=1; j<=(nlstate+ndeath);j++){
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
-             k=k+1;
+   file %s<br>\n",optionfilehtmcov);
-             mu[k][(int) age]=pmmij[i][j];
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-           }
+ and drawn. It helps understanding how is the covariance between two incidences.\
-         }
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+   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. \
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-             varpij[i][j][(int)age] = doldm[i][j];
+ 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>\
-         /*printf("\n%d ",(int)age);
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
+   cov[1]=1;
+   tj=cptcoveff;
-         fprintf(ficresprob,"\n%d ",(int)age);
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+   j1=0;
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+   for(t=1; t<=tj;t++){
+     for(i1=1; i1<=ncodemax[t];i1++){
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+       j1++;
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+       if  (cptcovn>0) {
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+         fprintf(ficresprob, "\n#********** Variable ");
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+         fprintf(ficresprob, "**********\n#\n");
-         }
+         fprintf(ficresprobcov, "\n#********** Variable ");
-         i=0;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         for (k=1; k<=(nlstate);k++){
+         fprintf(ficresprobcov, "**********\n#\n");
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
+         fprintf(ficgp, "\n#********** Variable ");
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+         fprintf(ficgp, "**********\n#\n");
-             for (j=1; j<=i;j++){
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+         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\">");
-         }/* end of loop for state */
-       } /* end of loop for age */
+         fprintf(ficresprobcor, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-       /* Confidence intervalle of pij  */
+         fprintf(ficresprobcor, "**********\n#");
-       /*
+       }
-         fprintf(ficgp,"\nset noparametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+       for (age=bage; age<=fage; age ++){
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         cov[2]=age;
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+         for (k=1; k<=cptcovn;k++) {
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+         }
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       */
+         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]]];
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       for (k2=1; k2<=(nlstate);k2++){
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
-           if(l2==k2) continue;
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
+         for(theta=1; theta <=npar; theta++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
+           for(i=1; i<=npar; i++)
-               if(l1==k1) continue;
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-               i=(k1-1)*(nlstate+ndeath)+l1;
-               if(i<=j) continue;
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-               for (age=bage; age<=fage; age ++){
-                 if ((int)age %5==0){
+           k=0;
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+           for(i=1; i<= (nlstate); i++){
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+             for(j=1; j<=(nlstate+ndeath);j++){
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+               k=k+1;
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+               gp[k]=pmmij[i][j];
-                   mu2=mu[j][(int) age]/stepm*YEARM;
+             }
-                   c12=cv12/sqrt(v1*v2);
+           }
-                   /* Computing eigen value of matrix of covariance */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+           for(i=1; i<=npar; i++)
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-                   /* Eigen vectors */
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-                   /*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;
+               gm[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<= (nlstate)*(nlstate+ndeath); 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);
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-                   /*printf(fignu*/
+         }
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                   if(first==1){
+           for(theta=1; theta <=npar; theta++)
-                     first=0;
+             trgradg[j][theta]=gradg[theta][j];
-                     fprintf(ficgp,"\nset parametric;unset label");
-                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-                             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);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         k=0;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+         for(i=1; i<=(nlstate); i++){
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+           for(j=1; j<=(nlstate+ndeath);j++){
-                     fprintf(ficgp,"\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",\
+             k=k+1;
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+             mu[k][(int) age]=pmmij[i][j];
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+           }
-                   }else{
+         }
-                     first=0;
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+             varpij[i][j][(int)age] = doldm[i][j];
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+         /*printf("\n%d ",(int)age);
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                   }/* if first */
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                 } /* age mod 5 */
+           }*/
-               } /* end loop age */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         fprintf(ficresprob,"\n%d ",(int)age);
-               first=1;
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-             } /*l12 */
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-           } /* k12 */
-         } /*l1 */
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-       }/* k1 */
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-     } /* loop covariates */
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-   }
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+         }
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+         i=0;
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+         for (k=1; k<=(nlstate);k++){
-   free_vector(xp,1,npar);
+           for (l=1; l<=(nlstate+ndeath);l++){
-   fclose(ficresprob);
+             i=i++;
-   fclose(ficresprobcov);
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-   fclose(ficresprobcor);
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-   fflush(ficgp);
+             for (j=1; j<=i;j++){
-   fflush(fichtmcov);
+               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
- }
+               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+             }
+           }
- /******************* Printing html file ***********/
+         }/* end of loop for state */
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+       } /* end of loop for age */
-                   int lastpass, int stepm, int weightopt, char model[],\
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+       /* Confidence intervalle of pij  */
-                   int popforecast, int estepm ,\
+       /*
-                   double jprev1, double mprev1,double anprev1, \
+         fprintf(ficgp,"\nunset parametric;unset label");
-                   double jprev2, double mprev2,double anprev2){
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   int jj1, k1, i1, cpt;
+         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,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
- </ul>");
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+       */
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-    fprintf(fichtm,"\
+       first1=1;
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+       for (k2=1; k2<=(nlstate);k2++){
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-    fprintf(fichtm,"\
+           if(l2==k2) continue;
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+           j=(k2-1)*(nlstate+ndeath)+l2;
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+           for (k1=1; k1<=(nlstate);k1++){
-    fprintf(fichtm,"\
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+               if(l1==k1) continue;
-    <a href=\"%s\">%s</a> <br>\n",
+               i=(k1-1)*(nlstate+ndeath)+l1;
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+               if(i<=j) continue;
-    fprintf(fichtm,"\
+               for (age=bage; age<=fage; age ++){
-  - Population projections by age and states: \
+                 if ((int)age %5==0){
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-  m=cptcoveff;
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+                   c12=cv12/sqrt(v1*v2);
+                   /* Computing eigen value of matrix of covariance */
-  jj1=0;
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-  for(k1=1; k1<=m;k1++){
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-    for(i1=1; i1<=ncodemax[k1];i1++){
+                   if ((lc2 <0) || (lc1 <0) ){
-      jj1++;
+                     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);
-      if (cptcovn > 0) {
+                     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);
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+                     lc1=fabs(lc1);
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+                     lc2=fabs(lc2);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+                   }
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-      }
+                   /* Eigen vectors */
-      /* Pij */
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-      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> \
+                   /*v21=sqrt(1.-v11*v11); *//* error */
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+                   v21=(lc1-v1)/cv12*v11;
-      /* Quasi-incidences */
+                   v12=-v21;
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+                   v22=v11;
-  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> \
+                   tnalp=v21/v11;
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+                   if(first1==1){
-        /* Period (stable) prevalence in each health state */
+                     first1=0;
-        for(cpt=1; cpt<nlstate;cpt++){
+                     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,"<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(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
-        }
+                   /*printf(fignu*/
-      for(cpt=1; cpt<=nlstate;cpt++) {
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-         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> \
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+                   if(first==1){
-      }
+                     first=0;
-    } /* end i1 */
+                     fprintf(ficgp,"\nset parametric;unset label");
-  }/* End k1 */
+                     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(fichtm,"</ul>");
+                     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\">\
-  fprintf(fichtm,"\
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+                             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(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-  fprintf(fichtm,"\
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-  fprintf(fichtm,"\
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+                   }else{
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+                     first=0;
-  fprintf(fichtm,"\
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
-  fprintf(fichtm,"\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-  - (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): \
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-    <a href=\"%s\">%s</a> <br>\n</li>",
+                   }/* if first */
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+                 } /* age mod 5 */
-  fprintf(fichtm,"\
+               } /* end loop age */
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+               first=1;
-  fprintf(fichtm,"\
+             } /*l12 */
-  - 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",
+           } /* k12 */
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+         } /*l1 */
-  fprintf(fichtm,"\
+       }/* k1 */
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+     } /* loop covariates */
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+   }
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
- /*      <br>",fileres,fileres,fileres,fileres); */
+   free_vector(xp,1,npar);
- /*  else  */
+   fclose(ficresprob);
- /*    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); */
+   fclose(ficresprobcov);
-  fflush(fichtm);
+   fclose(ficresprobcor);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+   fflush(ficgp);
+   fflush(fichtmcov);
-  m=cptcoveff;
+ }
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+ /******************* Printing html file ***********/
-  for(k1=1; k1<=m;k1++){
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
-    for(i1=1; i1<=ncodemax[k1];i1++){
+                   int lastpass, int stepm, int weightopt, char model[],\
-      jj1++;
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-      if (cptcovn > 0) {
+                   int popforecast, int estepm ,\
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+                   double jprev1, double mprev1,double anprev1, \
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+                   double jprev2, double mprev2,double anprev2){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+   int jj1, k1, i1, cpt;
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-      }
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
-      for(cpt=1; cpt<=nlstate;cpt++) {
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+ </ul>");
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-      }
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+    fprintf(fichtm,"\
- health expectancies in states (1) and (2): %s%d.png<br>\
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
-    } /* end i1 */
+    fprintf(fichtm,"\
-  }/* End k1 */
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-  fprintf(fichtm,"</ul>");
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-  fflush(fichtm);
+    fprintf(fichtm,"\
- }
+  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n",
- /******************* Gnuplot file **************/
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+    fprintf(fichtm,"\
+  - Population projections by age and states: \
-   char dirfileres[132],optfileres[132];
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   int ng;
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
- /*     printf("Problem with file %s",optionfilegnuplot); */
+  m=cptcoveff;
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
- /*   } */
+  jj1=0;
-   /*#ifdef windows */
+  for(k1=1; k1<=m;k1++){
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+    for(i1=1; i1<=ncodemax[k1];i1++){
-     /*#endif */
+      jj1++;
-   m=pow(2,cptcoveff);
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-   strcpy(dirfileres,optionfilefiname);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-   strcpy(optfileres,"vpl");
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-  /* 1eme*/
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+      }
-    for (k1=1; k1<= m ; k1 ++) {
+      /* Pij */
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+      /* Quasi-incidences */
- set ylabel \"Probability\" \n\
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- set ter png small\n\
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
- set size 0.65,0.65\n\
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+        /* Period (stable) prevalence in each health state */
+        for(cpt=1; cpt<nlstate;cpt++){
-      for (i=1; i<= nlstate ; i ++) {
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        }
-      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
-      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,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-      for (i=1; i<= nlstate ; i ++) {
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+      }
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+    } /* end i1 */
-      }
+  }/* End k1 */
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+  fprintf(fichtm,"</ul>");
-      for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+  fprintf(fichtm,"\
-      }
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-    }
-   }
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-   /*2 eme*/
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+  fprintf(fichtm,"\
-   for (k1=1; k1<= m ; k1 ++) {
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+  fprintf(fichtm,"\
-     for (i=1; i<= nlstate+1 ; i ++) {
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-       k=2*i;
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+  fprintf(fichtm,"\
-       for (j=1; j<= nlstate+1 ; j ++) {
+  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+    <a href=\"%s\">%s</a> <br>\n</li>",
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
-       }
+  fprintf(fichtm,"\
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+    <a href=\"%s\">%s</a> <br>\n</li>",
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
-       for (j=1; j<= nlstate+1 ; j ++) {
+  fprintf(fichtm,"\
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  - 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",
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-       }
+  fprintf(fichtm,"\
-       fprintf(ficgp,"\" t\"\" w l 0,");
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-       for (j=1; j<= nlstate+1 ; j ++) {
+  fprintf(fichtm,"\
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-       }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-     }
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-   }
+ /*      <br>",fileres,fileres,fileres,fileres); */
+ /*  else  */
-   /*3eme*/
+ /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+  fflush(fichtm);
-   for (k1=1; k1<= m ; k1 ++) {
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       /*       k=2+nlstate*(2*cpt-2); */
+  m=cptcoveff;
-       k=2+(nlstate+1)*(cpt-1);
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+  jj1=0;
- set size 0.65,0.65\n\
+  for(k1=1; k1<=m;k1++){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+    for(i1=1; i1<=ncodemax[k1];i1++){
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+      jj1++;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+      if (cptcovn > 0) {
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+      }
-       */
+      for(cpt=1; cpt<=nlstate;cpt++) {
-       for (i=1; i< nlstate ; i ++) {
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-         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);
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
-         /*      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);*/
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+      }
-       }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+ 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\
-   }
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
-   /* CV preval stable (period) */
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-   for (k1=1; k1<= m ; k1 ++) {
+    } /* end i1 */
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
+  }/* End k1 */
-       k=3;
+  fprintf(fichtm,"</ul>");
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+  fflush(fichtm);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ }
- set ter png small\nset size 0.65,0.65\n\
- unset log y\n\
+ /******************* Gnuplot file **************/
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       for (i=1; i< nlstate ; i ++)
+   char dirfileres[132],optfileres[132];
-         fprintf(ficgp,"+$%d",k+i+1);
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+   int ng=0;
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-       l=3+(nlstate+ndeath)*cpt;
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-       for (i=1; i< nlstate ; i ++) {
+ /*   } */
-         l=3+(nlstate+ndeath)*cpt;
-         fprintf(ficgp,"+$%d",l+i+1);
+   /*#ifdef windows */
-       }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+     /*#endif */
-     }
+   m=pow(2,cptcoveff);
-   }
+   strcpy(dirfileres,optionfilefiname);
-   /* proba elementaires */
+   strcpy(optfileres,"vpl");
-   for(i=1,jk=1; i <=nlstate; i++){
+  /* 1eme*/
-     for(k=1; k <=(nlstate+ndeath); k++){
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-       if (k != i) {
+    for (k1=1; k1<= m ; k1 ++) {
-         for(j=1; j <=ncovmodel; j++){
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
-           jk++;
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-           fprintf(ficgp,"\n");
+ set ylabel \"Probability\" \n\
-         }
+ set ter png small\n\
-       }
+ set size 0.65,0.65\n\
-     }
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-    }
+      for (i=1; i<= nlstate ; i ++) {
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-      for(jk=1; jk <=m; jk++) {
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+      }
-        if (ng==2)
+      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(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+      for (i=1; i<= nlstate ; i ++) {
-        else
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+      }
-        i=1;
+      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
-        for(k2=1; k2<=nlstate; k2++) {
+      for (i=1; i<= nlstate ; i ++) {
-          k3=i;
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-          for(k=1; k<=(nlstate+ndeath); k++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-            if (k != k2){
+      }
-              if(ng==2)
+      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+    }
-              else
+   }
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+   /*2 eme*/
-              ij=1;
-              for(j=3; j <=ncovmodel; j++) {
+   for (k1=1; k1<= m ; k1 ++) {
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
-                  ij++;
-                }
+     for (i=1; i<= nlstate+1 ; i ++) {
-                else
+       k=2*i;
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-              }
+       for (j=1; j<= nlstate+1 ; j ++) {
-              fprintf(ficgp,")/(1");
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-              for(k1=1; k1 <=nlstate; k1++){
+       }
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-                ij=1;
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-                for(j=3; j <=ncovmodel; j++){
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       for (j=1; j<= nlstate+1 ; j ++) {
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-                    ij++;
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-                  }
+       }
-                  else
+       fprintf(ficgp,"\" t\"\" w l 0,");
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-                }
+       for (j=1; j<= nlstate+1 ; j ++) {
-                fprintf(ficgp,")");
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-              }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       }
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
-              i=i+ncovmodel;
+       else fprintf(ficgp,"\" t\"\" w l 0,");
-            }
+     }
-          } /* end k */
+   }
-        } /* end k2 */
-      } /* end jk */
+   /*3eme*/
-    } /* end ng */
-    fflush(ficgp);
+   for (k1=1; k1<= m ; k1 ++) {
- }  /* end gnuplot */
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       /*       k=2+nlstate*(2*cpt-2); */
+       k=2+(nlstate+1)*(cpt-1);
- /*************** Moving average **************/
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+       fprintf(ficgp,"set ter png small\n\
+ set size 0.65,0.65\n\
-   int i, cpt, cptcod;
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-   int modcovmax =1;
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-   int mobilavrange, mob;
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-   double age;
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-                            a covariate has 2 modalities */
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+       */
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+       for (i=1; i< nlstate ; i ++) {
-     if(mobilav==1) mobilavrange=5; /* default */
+         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);
-     else mobilavrange=mobilav;
+         /*      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 (age=bage; age<=fage; age++)
-       for (i=1; i<=nlstate;i++)
+       }
-         for (cptcod=1;cptcod<=modcovmax;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][i][cptcod];
+     }
-     /* We keep the original values on the extreme ages bage, fage and for
+   }
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-        we use a 5 terms etc. until the borders are no more concerned.
+   /* CV preval stable (period) */
-     */
+   for (k1=1; k1<= m ; k1 ++) {
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+       k=3;
-         for (i=1; i<=nlstate;i++){
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+ set ter png small\nset size 0.65,0.65\n\
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+ unset log y\n\
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               }
+       for (i=1; i< nlstate ; i ++)
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+         fprintf(ficgp,"+$%d",k+i+1);
-           }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-         }
-       }/* end age */
+       l=3+(nlstate+ndeath)*cpt;
-     }/* end mob */
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-   }else return -1;
+       for (i=1; i< nlstate ; i ++) {
-   return 0;
+         l=3+(nlstate+ndeath)*cpt;
- }/* End movingaverage */
+         fprintf(ficgp,"+$%d",l+i+1);
+       }
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+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){
+   }
-   /* proj1, year, month, day of starting projection
-      agemin, agemax range of age
+   /* proba elementaires */
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+   for(i=1,jk=1; i <=nlstate; i++){
-      anproj2 year of en of projection (same day and month as proj1).
+     for(k=1; k <=(nlstate+ndeath); k++){
-   */
+       if (k != i) {
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+         for(j=1; j <=ncovmodel; j++){
-   int *popage;
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-   double agec; /* generic age */
+           jk++;
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+           fprintf(ficgp,"\n");
-   double *popeffectif,*popcount;
+         }
-   double ***p3mat;
+       }
-   double ***mobaverage;
+     }
-   char fileresf[FILENAMELENGTH];
+    }
-   agelim=AGESUP;
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+      for(jk=1; jk <=m; jk++) {
+        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-   strcpy(fileresf,"f");
+        if (ng==2)
-   strcat(fileresf,fileres);
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+        else
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-   }
+        i=1;
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+        for(k2=1; k2<=nlstate; k2++) {
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+          k3=i;
+          for(k=1; k<=(nlstate+ndeath); k++) {
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+            if (k != k2){
+              if(ng==2)
-   if (mobilav!=0) {
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+              else
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+              ij=1;
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+              for(j=3; j <=ncovmodel; j++) {
-     }
+                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]]]);
+                  ij++;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+                }
-   if (stepm<=12) stepsize=1;
+                else
-   if(estepm < stepm){
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+              }
-   }
+              fprintf(ficgp,")/(1");
-   else  hstepm=estepm;
+              for(k1=1; k1 <=nlstate; k1++){
-   hstepm=hstepm/stepm;
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                ij=1;
-                                fractional in yp1 */
+                for(j=3; j <=ncovmodel; j++){
-   anprojmean=yp;
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-   yp2=modf((yp1*12),&yp);
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-   mprojmean=yp;
+                    ij++;
-   yp1=modf((yp2*30.5),&yp);
+                  }
-   jprojmean=yp;
+                  else
-   if(jprojmean==0) jprojmean=1;
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   if(mprojmean==0) jprojmean=1;
+                }
+                fprintf(ficgp,")");
-   i1=cptcoveff;
+              }
-   if (cptcovn < 1){i1=1;}
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+              i=i+ncovmodel;
+            }
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+          } /* end k */
+        } /* end k2 */
- /*            if (h==(int)(YEARM*yearp)){ */
+      } /* end jk */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+    } /* end ng */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+    fflush(ficgp);
-       k=k+1;
+ }  /* end gnuplot */
-       fprintf(ficresf,"\n#******");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ /*************** Moving average **************/
-       }
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-       fprintf(ficresf,"******\n");
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+   int i, cpt, cptcod;
-       for(j=1; j<=nlstate+ndeath;j++){
+   int modcovmax =1;
-         for(i=1; i<=nlstate;i++)
+   int mobilavrange, mob;
-           fprintf(ficresf," p%d%d",i,j);
+   double age;
-         fprintf(ficresf," p.%d",j);
-       }
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+                            a covariate has 2 modalities */
-         fprintf(ficresf,"\n");
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+     if(mobilav==1) mobilavrange=5; /* default */
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+     else mobilavrange=mobilav;
-           nhstepm = nhstepm/hstepm;
+     for (age=bage; age<=fage; age++)
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       for (i=1; i<=nlstate;i++)
-           oldm=oldms;savm=savms;
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+     /* We keep the original values on the extreme ages bage, fage and for
-           for (h=0; h<=nhstepm; h++){
+        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
-             if (h*hstepm/YEARM*stepm ==yearp) {
+        we use a 5 terms etc. until the borders are no more concerned.
-               fprintf(ficresf,"\n");
+     */
-               for(j=1;j<=cptcoveff;j++)
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+         for (i=1; i<=nlstate;i++){
-             }
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
-             for(j=1; j<=nlstate+ndeath;j++) {
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-               ppij=0.;
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-               for(i=1; i<=nlstate;i++) {
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                 if (mobilav==1)
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+               }
-                 else {
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+           }
-                 }
+         }
-                 if (h*hstepm/YEARM*stepm== yearp) {
+       }/* end age */
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+     }/* end mob */
-                 }
+   }else return -1;
-               } /* end i */
+   return 0;
-               if (h*hstepm/YEARM*stepm==yearp) {
+ }/* End movingaverage */
-                 fprintf(ficresf," %.3f", ppij);
-               }
-             }/* end j */
+ /************** Forecasting ******************/
-           } /* end h */
+ prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* proj1, year, month, day of starting projection
-         } /* end agec */
+      agemin, agemax range of age
-       } /* end yearp */
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-     } /* end cptcod */
+      anproj2 year of en of projection (same day and month as proj1).
-   } /* end  cptcov */
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   int *popage;
+   double agec; /* generic age */
-   fclose(ficresf);
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- }
+   double *popeffectif,*popcount;
+   double ***p3mat;
- /************** Forecasting *****not tested NB*************/
+   double ***mobaverage;
- 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){
+   char fileresf[FILENAMELENGTH];
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+   agelim=AGESUP;
-   int *popage;
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
+   strcpy(fileresf,"f");
-   double ***p3mat,***tabpop,***tabpopprev;
+   strcat(fileresf,fileres);
-   double ***mobaverage;
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
-   char filerespop[FILENAMELENGTH];
+     printf("Problem with forecast resultfile: %s\n", fileresf);
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   }
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-   agelim=AGESUP;
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   strcpy(filerespop,"pop");
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-   strcat(filerespop,fileres);
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+     }
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+   }
-   }
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   if (mobilav!=0) {
+   else  hstepm=estepm;
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   hstepm=hstepm/stepm;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                                fractional in yp1 */
-     }
+   anprojmean=yp;
-   }
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   yp1=modf((yp2*30.5),&yp);
-   if (stepm<=12) stepsize=1;
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
-   agelim=AGESUP;
+   if(mprojmean==0) jprojmean=1;
-   hstepm=1;
+   i1=cptcoveff;
-   hstepm=hstepm/stepm;
+   if (cptcovn < 1){i1=1;}
-   if (popforecast==1) {
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-     if((ficpop=fopen(popfile,"r"))==NULL) {
-       printf("Problem with population file : %s\n",popfile);exit(0);
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-     }
+ /*            if (h==(int)(YEARM*yearp)){ */
-     popage=ivector(0,AGESUP);
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
-     popeffectif=vector(0,AGESUP);
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-     popcount=vector(0,AGESUP);
+       k=k+1;
+       fprintf(ficresf,"\n#******");
-     i=1;
+       for(j=1;j<=cptcoveff;j++) {
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       }
-     imx=i;
+       fprintf(ficresf,"******\n");
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   }
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+           fprintf(ficresf," p%d%d",i,j);
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+         fprintf(ficresf," p.%d",j);
-       k=k+1;
+       }
-       fprintf(ficrespop,"\n#******");
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresf,"\n");
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-       }
-       fprintf(ficrespop,"******\n");
+         for (agec=fage; agec>=(ageminpar-1); agec--){
-       fprintf(ficrespop,"# Age");
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+           nhstepm = nhstepm/hstepm;
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
-       for (cpt=0; cpt<=0;cpt++) {
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+           for (h=0; h<=nhstepm; h++){
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+             if (h*hstepm/YEARM*stepm ==yearp) {
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+               fprintf(ficresf,"\n");
-           nhstepm = nhstepm/hstepm;
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-           oldm=oldms;savm=savms;
+             }
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               ppij=0.;
-           for (h=0; h<=nhstepm; h++){
+               for(i=1; i<=nlstate;i++) {
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+                 if (mobilav==1)
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-             }
+                 else {
-             for(j=1; j<=nlstate+ndeath;j++) {
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-               kk1=0.;kk2=0;
+                 }
-               for(i=1; i<=nlstate;i++) {
+                 if (h*hstepm/YEARM*stepm== yearp) {
-                 if (mobilav==1)
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+                 }
-                 else {
+               } /* end i */
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+               if (h*hstepm/YEARM*stepm==yearp) {
-                 }
+                 fprintf(ficresf," %.3f", ppij);
                }
-               if (h==(int)(calagedatem+12*cpt)){
+             }/* end j */
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+           } /* end h */
-                   /*fprintf(ficrespop," %.3f", kk1);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+         } /* end agec */
-               }
+       } /* end yearp */
-             }
+     } /* end cptcod */
-             for(i=1; i<=nlstate;i++){
+   } /* end  cptcov */
-               kk1=0.;
-                 for(j=1; j<=nlstate;j++){
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
+   fclose(ficresf);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+ }
-             }
+ /************** Forecasting *****not tested NB*************/
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-           }
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   int *popage;
-         }
+   double calagedatem, agelim, kk1, kk2;
-       }
+   double *popeffectif,*popcount;
+   double ***p3mat,***tabpop,***tabpopprev;
-   /******/
+   double ***mobaverage;
+   char filerespop[FILENAMELENGTH];
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   agelim=AGESUP;
-           nhstepm = nhstepm/hstepm;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-           for (h=0; h<=nhstepm; h++){
+   strcpy(filerespop,"pop");
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+   strcat(filerespop,fileres);
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-             }
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-             for(j=1; j<=nlstate+ndeath;j++) {
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-               kk1=0.;kk2=0;
+   }
-               for(i=1; i<=nlstate;i++) {
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-               }
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-             }
-           }
+   if (mobilav!=0) {
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         }
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-       }
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-    }
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   }
+     }
+   }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-   if (popforecast==1) {
+   if (stepm<=12) stepsize=1;
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
+   agelim=AGESUP;
-     free_vector(popcount,0,AGESUP);
-   }
+   hstepm=1;
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   hstepm=hstepm/stepm;
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficrespop);
+   if (popforecast==1) {
- } /* End of popforecast */
+     if((ficpop=fopen(popfile,"r"))==NULL) {
+       printf("Problem with population file : %s\n",popfile);exit(0);
- int fileappend(FILE *fichier, char *optionfich)
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- {
+     }
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+     popage=ivector(0,AGESUP);
-     printf("Problem with file: %s\n", optionfich);
+     popeffectif=vector(0,AGESUP);
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+     popcount=vector(0,AGESUP);
-     return (0);
-   }
+     i=1;
-   fflush(fichier);
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-   return (1);
- }
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+   }
- /**************** function prwizard **********************/
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
- {
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
-   /* Wizard to print covariance matrix template */
+       fprintf(ficrespop,"\n#******");
+       for(j=1;j<=cptcoveff;j++) {
-   char ca[32], cb[32], cc[32];
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+       }
-   int numlinepar;
+       fprintf(ficrespop,"******\n");
+       fprintf(ficrespop,"# Age");
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-   for(i=1; i <=nlstate; i++){
-     jj=0;
+       for (cpt=0; cpt<=0;cpt++) {
-     for(j=1; j <=nlstate+ndeath; j++){
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-       if(j==i) continue;
-       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);
-       printf("%1d%1d",i,j);
+           nhstepm = nhstepm/hstepm;
-       fprintf(ficparo,"%1d%1d",i,j);
-       for(k=1; k<=ncovmodel;k++){
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         /*        printf(" %lf",param[i][j][k]); */
+           oldm=oldms;savm=savms;
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         printf(" 0.");
-         fprintf(ficparo," 0.");
+           for (h=0; h<=nhstepm; h++){
-       }
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       printf("\n");
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       fprintf(ficparo,"\n");
+             }
-     }
+             for(j=1; j<=nlstate+ndeath;j++) {
-   }
+               kk1=0.;kk2=0;
-   printf("# Scales (for hessian or gradient estimation)\n");
+               for(i=1; i<=nlstate;i++) {
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+                 if (mobilav==1)
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-   for(i=1; i <=nlstate; i++){
+                 else {
-     jj=0;
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-     for(j=1; j <=nlstate+ndeath; j++){
+                 }
-       if(j==i) continue;
+               }
-       jj++;
+               if (h==(int)(calagedatem+12*cpt)){
-       fprintf(ficparo,"%1d%1d",i,j);
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-       printf("%1d%1d",i,j);
+                   /*fprintf(ficrespop," %.3f", kk1);
-       fflush(stdout);
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-       for(k=1; k<=ncovmodel;k++){
+               }
-         /*      printf(" %le",delti3[i][j][k]); */
+             }
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+             for(i=1; i<=nlstate;i++){
-         printf(" 0.");
+               kk1=0.;
-         fprintf(ficparo," 0.");
+                 for(j=1; j<=nlstate;j++){
-       }
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-       numlinepar++;
+                 }
-       printf("\n");
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-       fprintf(ficparo,"\n");
+             }
-     }
-   }
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-   printf("# Covariance matrix\n");
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
- /* # 121 Var(a12)\n\ */
+           }
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+         }
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+       }
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+   /******/
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-   fflush(stdout);
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   fprintf(ficparo,"# Covariance matrix\n");
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   /* # 121 Var(a12)\n\ */
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
+           nhstepm = nhstepm/hstepm;
-   /* #   ...\n\ */
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
-   for(itimes=1;itimes<=2;itimes++){
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     jj=0;
+           for (h=0; h<=nhstepm; h++){
-     for(i=1; i <=nlstate; i++){
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       for(j=1; j <=nlstate+ndeath; j++){
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-         if(j==i) continue;
+             }
-         for(k=1; k<=ncovmodel;k++){
+             for(j=1; j<=nlstate+ndeath;j++) {
-           jj++;
+               kk1=0.;kk2=0;
-           ca[0]= k+'a'-1;ca[1]='\0';
+               for(i=1; i<=nlstate;i++) {
-           if(itimes==1){
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-             printf("#%1d%1d%d",i,j,k);
+               }
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-           }else{
+             }
-             printf("%1d%1d%d",i,j,k);
+           }
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             /*  printf(" %.5le",matcov[i][j]); */
+         }
-           }
+       }
-           ll=0;
+    }
-           for(li=1;li <=nlstate; li++){
+   }
-             for(lj=1;lj <=nlstate+ndeath; lj++){
-               if(lj==li) continue;
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               for(lk=1;lk<=ncovmodel;lk++){
-                 ll++;
+   if (popforecast==1) {
-                 if(ll<=jj){
+     free_ivector(popage,0,AGESUP);
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+     free_vector(popeffectif,0,AGESUP);
-                   if(ll<jj){
+     free_vector(popcount,0,AGESUP);
-                     if(itimes==1){
+   }
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-                     }else{
+   fclose(ficrespop);
-                       printf(" 0.");
+ } /* End of popforecast */
-                       fprintf(ficparo," 0.");
-                     }
+ int fileappend(FILE *fichier, char *optionfich)
-                   }else{
+ {
-                     if(itimes==1){
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+     printf("Problem with file: %s\n", optionfich);
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-                     }else{
+     return (0);
-                       printf(" 0.");
+   }
-                       fprintf(ficparo," 0.");
+   fflush(fichier);
-                     }
+   return (1);
-                   }
+ }
-                 }
-               } /* end lk */
-             } /* end lj */
+ /**************** function prwizard **********************/
-           } /* end li */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-           printf("\n");
+ {
-           fprintf(ficparo,"\n");
-           numlinepar++;
+   /* Wizard to print covariance matrix template */
-         } /* end k*/
-       } /*end j */
+   char ca[32], cb[32], cc[32];
-     } /* end i */
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   } /* end itimes */
+   int numlinepar;
- } /* end of prwizard */
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- /******************* Gompertz Likelihood ******************************/
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- double gompertz(double x[])
+   for(i=1; i <=nlstate; i++){
- {
+     jj=0;
-   double A,B,L=0.0,sump=0.,num=0.;
+     for(j=1; j <=nlstate+ndeath; j++){
-   int i,n=0; /* n is the size of the sample */
+       if(j==i) continue;
+       jj++;
-   for (i=0;i<=imx-1 ; i++) {
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-     sump=sump+weight[i];
+       printf("%1d%1d",i,j);
-     /*    sump=sump+1;*/
+       fprintf(ficparo,"%1d%1d",i,j);
-     num=num+1;
+       for(k=1; k<=ncovmodel;k++){
-   }
+         /*        printf(" %lf",param[i][j][k]); */
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+         printf(" 0.");
-   /* for (i=0; i<=imx; i++)
+         fprintf(ficparo," 0.");
-      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
+       }
+       printf("\n");
-   for (i=1;i<=imx ; i++)
+       fprintf(ficparo,"\n");
-     {
+     }
-       if (cens[i] == 1 && wav[i]>1)
+   }
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+   printf("# Scales (for hessian or gradient estimation)\n");
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-       if (cens[i] == 0 && wav[i]>1)
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+   for(i=1; i <=nlstate; i++){
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+     jj=0;
+     for(j=1; j <=nlstate+ndeath; j++){
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if(j==i) continue;
-       if (wav[i] > 1 ) { /* ??? */
+       jj++;
-         L=L+A*weight[i];
+       fprintf(ficparo,"%1d%1d",i,j);
-         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
+       printf("%1d%1d",i,j);
-       }
+       fflush(stdout);
-     }
+       for(k=1; k<=ncovmodel;k++){
+         /*      printf(" %le",delti3[i][j][k]); */
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+         printf(" 0.");
-   return -2*L*num/sump;
+         fprintf(ficparo," 0.");
- }
+       }
+       numlinepar++;
- /******************* Printing html file ***********/
+       printf("\n");
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+       fprintf(ficparo,"\n");
-                   int lastpass, int stepm, int weightopt, char model[],\
+     }
-                   int imx,  double p[],double **matcov,double agemortsup){
+   }
-   int i,k;
+   printf("# Covariance matrix\n");
+ /* # 121 Var(a12)\n\ */
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-   for (i=1;i<=2;i++)
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-   fprintf(fichtm,"</ul>");
+ /* # 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" */
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+   fflush(stdout);
+   fprintf(ficparo,"# Covariance matrix\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>");
+   /* # 121 Var(a12)\n\ */
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-  for (k=agegomp;k<(agemortsup-2);k++)
+   /* #   ...\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]);
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   for(itimes=1;itimes<=2;itimes++){
-   fflush(fichtm);
+     jj=0;
- }
+     for(i=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
- /******************* Gnuplot file **************/
+         if(j==i) continue;
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
-   char dirfileres[132],optfileres[132];
+           ca[0]= k+'a'-1;ca[1]='\0';
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+           if(itimes==1){
-   int ng;
+             printf("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+           }else{
-   /*#ifdef windows */
+             printf("%1d%1d%d",i,j,k);
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-     /*#endif */
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
+           ll=0;
-   strcpy(dirfileres,optionfilefiname);
+           for(li=1;li <=nlstate; li++){
-   strcpy(optfileres,"vpl");
+             for(lj=1;lj <=nlstate+ndeath; lj++){
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+               if(lj==li) continue;
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+               for(lk=1;lk<=ncovmodel;lk++){
-   fprintf(ficgp, "set ter png small\n set log y\n");
+                 ll++;
-   fprintf(ficgp, "set size 0.65,0.65\n");
+                 if(ll<=jj){
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+                   cb[0]= lk +'a'-1;cb[1]='\0';
+                   if(ll<jj){
- }
+                     if(itimes==1){
+                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
+                       printf(" 0.");
+                       fprintf(ficparo," 0.");
- /***********************************************/
+                     }
- /**************** Main Program *****************/
+                   }else{
- /***********************************************/
+                     if(itimes==1){
+                       printf(" Var(%s%1d%1d)",ca,i,j);
- int main(int argc, char *argv[])
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
- {
+                     }else{
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+                       printf(" 0.");
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+                       fprintf(ficparo," 0.");
-   int linei, month, year,iout;
+                     }
-   int jj, ll, li, lj, lk, imk;
+                   }
-   int numlinepar=0; /* Current linenumber of parameter file */
+                 }
-   int itimes;
+               } /* end lk */
-   int NDIM=2;
+             } /* end lj */
+           } /* end li */
-   char ca[32], cb[32], cc[32];
+           printf("\n");
-   char dummy[]="                         ";
+           fprintf(ficparo,"\n");
-   /*  FILE *fichtm; *//* Html File */
+           numlinepar++;
-   /* FILE *ficgp;*/ /*Gnuplot File */
+         } /* end k*/
-   struct stat info;
+       } /*end j */
-   double agedeb, agefin,hf;
+     } /* end i */
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   } /* end itimes */
-   double fret;
+ } /* end of prwizard */
-   double **xi,tmp,delta;
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
-   double dum; /* Dummy variable */
+ {
-   double ***p3mat;
+   double A,B,L=0.0,sump=0.,num=0.;
-   double ***mobaverage;
+   int i,n=0; /* n is the size of the sample */
-   int *indx;
-   char line[MAXLINE], linepar[MAXLINE];
+   for (i=0;i<=imx-1 ; i++) {
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
+     sump=sump+weight[i];
-   char pathr[MAXLINE], pathimach[MAXLINE];
+     /*    sump=sump+1;*/
-   char **bp, *tok, *val; /* pathtot */
+     num=num+1;
-   int firstobs=1, lastobs=10;
+   }
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
-   int ju,jl, mi;
+   /* for (i=0; i<=imx; i++)
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+      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]);*/
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   for (i=1;i<=imx ; i++)
-   int mobilav=0,popforecast=0;
+     {
-   int hstepm, nhstepm;
+       if (cens[i] == 1 && wav[i]>1)
-   int agemortsup;
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   float  sumlpop=0.;
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
+       if (cens[i] == 0 && wav[i]>1)
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-   double bage, fage, age, agelim, agebase;
-   double ftolpl=FTOL;
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   double **prlim;
+       if (wav[i] > 1 ) { /* ??? */
-   double *severity;
+         L=L+A*weight[i];
-   double ***param; /* Matrix of parameters */
+         /*      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]);*/
-   double  *p;
+       }
-   double **matcov; /* Matrix of covariance */
+     }
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   double ***eij, ***vareij;
-   double **varpl; /* Variances of prevalence limits by age */
+   return -2*L*num/sump;
-   double *epj, vepp;
+ }
-   double kk1, kk2;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+ #ifdef GSL
-   double **ximort;
+ /******************* Gompertz_f Likelihood ******************************/
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+ double gompertz_f(const gsl_vector *v, void *params)
-   int *dcwave;
+ {
+   double A,B,LL=0.0,sump=0.,num=0.;
-   char z[1]="c", occ;
+   double *x= (double *) v->data;
+   int i,n=0; /* n is the size of the sample */
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
+   for (i=0;i<=imx-1 ; i++) {
-   char *stratrunc;
+     sump=sump+weight[i];
-   int lstra;
+     /*    sump=sump+1;*/
+     num=num+1;
-   long total_usecs;
+   }
- /*   setlocale (LC_ALL, ""); */
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+   /* for (i=0; i<=imx; i++)
- /*   textdomain (PACKAGE); */
+      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]);*/
- /*   setlocale (LC_CTYPE, ""); */
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
- /*   setlocale (LC_MESSAGES, ""); */
+   for (i=1;i<=imx ; i++)
+     {
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+       if (cens[i] == 1 && wav[i]>1)
-   (void) gettimeofday(&start_time,&tzp);
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-   curr_time=start_time;
-   tm = *localtime(&start_time.tv_sec);
+       if (cens[i] == 0 && wav[i]>1)
-   tmg = *gmtime(&start_time.tv_sec);
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-   strcpy(strstart,asctime(&tm));
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
- /*  printf("Localtime (at start)=%s",strstart); */
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+       if (wav[i] > 1 ) { /* ??? */
- /*  tm = *localtime(&start_time.tv_sec); */
+         LL=LL+A*weight[i];
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+         /*      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]);*/
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+       }
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+     }
- /*   tp.tv_sec = mktime(&tmg); */
- /*   strt=asctime(&tmg); */
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
- /*   printf("Time(after) =%s",strstart);  */
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
- /*  (void) time (&time_value);
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+   return -2*LL*num/sump;
- *  tm = *localtime(&time_value);
+ }
- *  strstart=asctime(&tm);
+ #endif
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
- */
+ /******************* Printing html file ***********/
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   nberr=0; /* Number of errors and warnings */
+                   int lastpass, int stepm, int weightopt, char model[],\
-   nbwarn=0;
+                   int imx,  double p[],double **matcov,double agemortsup){
-   getcwd(pathcd, size);
+   int i,k;
-   printf("\n%s\n%s",version,fullversion);
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-   if(argc <=1){
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-     printf("\nEnter the parameter file name: ");
+   for (i=1;i<=2;i++)
-     fgets(pathr,FILENAMELENGTH,stdin);
+     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]));
-     i=strlen(pathr);
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-     if(pathr[i-1]=='\n')
+   fprintf(fichtm,"</ul>");
-       pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-       printf("Pathr |%s|\n",pathr);
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+  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("val= |%s| pathr=%s\n",val,pathr);
-       strcpy (pathtot, val);
+  for (k=agegomp;k<(agemortsup-2);k++)
-       if(pathr[0] == '\0') break; /* Dirty */
+    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]);
-     }
-   }
-   else{
+   fflush(fichtm);
-     strcpy(pathtot,argv[1]);
+ }
-   }
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+ /******************* Gnuplot file **************/
-   /*cygwin_split_path(pathtot,path,optionfile);
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-   /* cutv(path,optionfile,pathtot,'\\');*/
+   char dirfileres[132],optfileres[132];
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
-   /* Split argv[0], imach program to get pathimach */
+   int ng;
-   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);
+   /*#ifdef windows */
-  /*   strcpy(pathimach,argv[0]); */
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+     /*#endif */
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path); /* Can be a relative path */
+   strcpy(dirfileres,optionfilefiname);
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   strcpy(optfileres,"vpl");
-     printf("Current directory %s!\n",pathcd);
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
-   strcpy(command,"mkdir ");
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   strcat(command,optionfilefiname);
+   fprintf(ficgp, "set ter png small\n set log y\n");
-   if((outcmd=system(command)) != 0){
+   fprintf(ficgp, "set size 0.65,0.65\n");
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-     /* fclose(ficlog); */
+ }
- /*     exit(1); */
-   }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+ {
- /*     perror("mkdir"); */
- /*   } */
+   /*-------- data file ----------*/
+   FILE *fic;
-   /*-------- arguments in the command line --------*/
+   char dummy[]="                         ";
+   int i, j, n;
-   /* Log file */
+   int linei, month, year,iout;
-   strcat(filelog, optionfilefiname);
+   char line[MAXLINE], linetmp[MAXLINE];
-   strcat(filelog,".log");    /* */
+   char stra[80], strb[80];
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+   char *stratrunc;
-     printf("Problem with logfile %s\n",filelog);
+   int lstra;
-     goto end;
-   }
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+   }
-  path=%s \n\
-  optionfile=%s\n\
+   i=1;
-  optionfilext=%s\n\
+   linei=0;
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+     linei=linei+1;
-   printf("Local time (at start):%s",strstart);
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+       if(line[j] == '\t')
-   fflush(ficlog);
+         line[j] = ' ';
- /*   (void) gettimeofday(&curr_time,&tzp); */
+     }
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+       ;
-   /* */
+     };
-   strcpy(fileres,"r");
+     line[j+1]=0;  /* Trims blanks at end of line */
-   strcat(fileres, optionfilefiname);
+     if(line[0]=='#'){
-   strcat(fileres,".txt");    /* Other files have txt extension */
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
-   /*---------arguments file --------*/
+       continue;
+     }
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-     printf("Problem with optionfile %s\n",optionfile);
+     for (j=0; line[j]!='\0';j++){
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+       line[j]=linetmp[j];
-     fflush(ficlog);
+     }
-     goto end;
-   }
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
-   strcpy(filereso,"o");
+         lval=-1;
-   strcat(filereso,fileres);
+       }else{
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+         errno=0;
-     printf("Problem with Output resultfile: %s\n", filereso);
+         lval=strtol(strb,&endptr,10);
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     fflush(ficlog);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-     goto end;
+           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-   }
+           fprintf(ficlog,"Error reading data around '%s' at line number %ld 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;
-   /* Reads comments: lines beginning with '#' */
+         }
-   numlinepar=0;
+       }
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       s[j][i]=lval;
-     ungetc(c,ficpar);
-     fgets(line, MAXLINE, ficpar);
+       strcpy(line,stra);
-     numlinepar++;
+       cutv(stra, strb,line,' ');
-     puts(line);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     fputs(line,ficparo);
+       }
-     fputs(line,ficlog);
+       else  if(iout=sscanf(strb,"%s.") != 0){
-   }
+         month=99;
-   ungetc(c,ficpar);
+         year=9999;
+       }else{
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
-   numlinepar++;
+         fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);
-   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);
+         return 1;
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       }
-   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);
+       anint[j][i]= (double) year;
-   fflush(ficlog);
+       mint[j][i]= (double)month;
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       strcpy(line,stra);
-     ungetc(c,ficpar);
+     } /* ENd Waves */
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
+     cutv(stra, strb,line,' ');
-     puts(line);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     fputs(line,ficparo);
+     }
-     fputs(line,ficlog);
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
-   }
+       month=99;
-   ungetc(c,ficpar);
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-   covar=matrix(0,NCOVMAX,1,n);
+         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+         return 1;
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+     }
+     andc[i]=(double) year;
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+     moisdc[i]=(double) month;
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+     strcpy(line,stra);
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+     cutv(stra, strb,line,' ');
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   delti=delti3[1][1];
+     }
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+     else  if(iout=sscanf(strb,"%s.") != 0){
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+       month=99;
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+       year=9999;
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     }else{
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+       printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-     fclose (ficparo);
+         return 1;
-     fclose (ficlog);
+     }
-     goto end;
+     if (year==9999) {
-     exit(0);
+       printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
-   }
+       fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);
-   else if(mle==-3) {
+         return 1;
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     }
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     annais[i]=(double)(year);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     moisnais[i]=(double)(month);
-     matcov=matrix(1,npar,1,npar);
+     strcpy(line,stra);
-   }
-   else{
+     cutv(stra, strb,line,' ');
-     /* Read guess parameters */
+     errno=0;
-     /* Reads comments: lines beginning with '#' */
+     dval=strtod(strb,&endptr);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     if( strb[0]=='\0' || (*endptr != '\0')){
-       ungetc(c,ficpar);
+       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-       numlinepar++;
+       fflush(ficlog);
-       puts(line);
+       return 1;
-       fputs(line,ficparo);
+     }
-       fputs(line,ficlog);
+     weight[i]=dval;
-     }
+     strcpy(line,stra);
-     ungetc(c,ficpar);
+     for (j=ncovcol;j>=1;j--){
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+       cutv(stra, strb,line,' ');
-     for(i=1; i <=nlstate; i++){
+       if(strb[0]=='.') { /* Missing status */
-       j=0;
+         lval=-1;
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+       }else{
-         if(jj==i) continue;
+         errno=0;
-         j++;
+         lval=strtol(strb,&endptr,10);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-         if ((i1 != i) && (j1 != j)){
+           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+           fprintf(ficlog,"Error reading data around '%d' at line number %ld 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);
- It might be a problem of design; if ncovcol and the model are correct\n \
+           return 1;
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
+         }
-           exit(1);
+       }
-         }
+       if(lval <-1 || lval >1){
-         fprintf(ficparo,"%1d%1d",i1,j1);
+         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
-         if(mle==1)
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-           printf("%1d%1d",i,j);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-         fprintf(ficlog,"%1d%1d",i,j);
+  For example, for multinomial values like 1, 2 and 3,\n \
-         for(k=1; k<=ncovmodel;k++){
+  build V1=0 V2=0 for the reference value (1),\n \
-           fscanf(ficpar," %lf",&param[i][j][k]);
+         V1=1 V2=0 for (2) \n \
-           if(mle==1){
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-             printf(" %lf",param[i][j][k]);
+  output of IMaCh is often meaningless.\n \
-             fprintf(ficlog," %lf",param[i][j][k]);
+  Exiting.\n",lval,linei, i,line,j);
-           }
+         fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
-           else
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-             fprintf(ficlog," %lf",param[i][j][k]);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-           fprintf(ficparo," %lf",param[i][j][k]);
+  For example, for multinomial values like 1, 2 and 3,\n \
-         }
+  build V1=0 V2=0 for the reference value (1),\n \
-         fscanf(ficpar,"\n");
+         V1=1 V2=0 for (2) \n \
-         numlinepar++;
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-         if(mle==1)
+  output of IMaCh is often meaningless.\n \
-           printf("\n");
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-         fprintf(ficlog,"\n");
+         return 1;
-         fprintf(ficparo,"\n");
+       }
-       }
+       covar[j][i]=(double)(lval);
-     }
+       strcpy(line,stra);
-     fflush(ficlog);
+     }
+     lstra=strlen(stra);
-     p=param[1][1];
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-     /* Reads comments: lines beginning with '#' */
+       stratrunc = &(stra[lstra-9]);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       num[i]=atol(stratrunc);
-       ungetc(c,ficpar);
+     }
-       fgets(line, MAXLINE, ficpar);
+     else
-       numlinepar++;
+       num[i]=atol(stra);
-       puts(line);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       fputs(line,ficparo);
+       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;}*/
-       fputs(line,ficlog);
-     }
+     i=i+1;
-     ungetc(c,ficpar);
+   } /* End loop reading  data */
-     for(i=1; i <=nlstate; i++){
+   *imax=i-1; /* Number of individuals */
-       for(j=1; j <=nlstate+ndeath-1; j++){
+   fclose(fic);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+   return (0);
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+   endread:
-           exit(1);
+     printf("Exiting readdata: ");
-         }
+     fclose(fic);
-         printf("%1d%1d",i,j);
+     return (1);
-         fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+ }
-           printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+ int decodemodel ( char model[], int lastobs)
-           fprintf(ficlog," %le",delti3[i][j][k]);
+ {
-         }
+   int i, j, k;
-         fscanf(ficpar,"\n");
+   int i1, j1, k1, k2;
-         numlinepar++;
+   char modelsav[80];
-         printf("\n");
+    char stra[80], strb[80], strc[80], strd[80],stre[80];
-         fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-       }
+     j=0, j1=0, k1=1, k2=1;
-     }
+     j=nbocc(model,'+'); /* j=Number of '+' */
-     fflush(ficlog);
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
+     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
-     delti=delti3[1][1];
+                   but the covariates which are product must be computed and stored. */
+     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+     strcpy(modelsav,model);
+     if (strstr(model,"AGE") !=0){
-     /* Reads comments: lines beginning with '#' */
+       printf("Error. AGE must be in lower case 'age' model=%s ",model);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
-       ungetc(c,ficpar);
+       return 1;
-       fgets(line, MAXLINE, ficpar);
+     }
-       numlinepar++;
-       puts(line);
+     /* This loop fills the array Tvar from the string 'model'.*/
-       fputs(line,ficparo);
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-       fputs(line,ficlog);
+     /*   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 */
-     ungetc(c,ficpar);
+     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
-     matcov=matrix(1,npar,1,npar);
+     /*  k=1 Tvar[1]=2 (from V2) */
-     for(i=1; i <=npar; i++){
+     /*  k=5 Tvar[5] */
-       fscanf(ficpar,"%s",&str);
+     /* for (k=1; k<=cptcovn;k++) { */
-       if(mle==1)
+     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
-         printf("%s",str);
+     /*  } */
-       fprintf(ficlog,"%s",str);
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       fprintf(ficparo,"%s",str);
+     for(k=cptcovn; k>=1;k--){
-       for(j=1; j <=i; j++){
+       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-         fscanf(ficpar," %le",&matcov[i][j]);
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
-         if(mle==1){
+                                     */
-           printf(" %.5le",matcov[i][j]);
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-         }
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-         fprintf(ficlog," %.5le",matcov[i][j]);
+       /*scanf("%d",i);*/
-         fprintf(ficparo," %.5le",matcov[i][j]);
+       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 */
-       fscanf(ficpar,"\n");
+         if (strcmp(strc,"age")==0) { /* Vn*age */
-       numlinepar++;
+           cptcovprod--;
-       if(mle==1)
+           cutv(strb,stre,strd,'V'); /* stre="V3" */
-         printf("\n");
+           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
-       fprintf(ficlog,"\n");
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-       fprintf(ficparo,"\n");
+           Tage[cptcovage]=k;  /* Tage[1] = 4 */
-     }
+           /*printf("stre=%s ", stre);*/
-     for(i=1; i <=npar; i++)
+         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-       for(j=i+1;j<=npar;j++)
+           cptcovprod--;
-         matcov[i][j]=matcov[j][i];
+           cutv(strb,stre,strc,'V');
+           Tvar[k]=atoi(stre);
-     if(mle==1)
+           cptcovage++;
-       printf("\n");
+           Tage[cptcovage]=k;
-     fprintf(ficlog,"\n");
+         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-     fflush(ficlog);
+           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
-     /*-------- Rewriting parameter file ----------*/
+                                   because this model-covariate is a construction we invent a new column
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+                                   ncovcol + k1
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-     strcat(rfileres,".");    /* */
+                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
-     }
+           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
-     fprintf(ficres,"#%s\n",version);
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
-   }    /* End of mle != -3 */
+           for (i=1; i<=lastobs;i++){
+             /* Computes the new covariate which is a product of
-   /*-------- data file ----------*/
+                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
-   if((fic=fopen(datafile,"r"))==NULL)    {
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
+           }
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+           k1++;
-   }
+           k2=k2+2;
+         } /* End age is not in the model */
-   n= lastobs;
+       } /* End if model includes a product */
-   severity = vector(1,maxwav);
+       else { /* no more sum */
-   outcome=imatrix(1,maxwav+1,1,n);
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-   num=lvector(1,n);
+        /*  scanf("%d",i);*/
-   moisnais=vector(1,n);
+         cutv(strd,strc,strb,'V');
-   annais=vector(1,n);
+         Tvar[k]=atoi(strc);
-   moisdc=vector(1,n);
+       }
-   andc=vector(1,n);
+       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-   agedc=vector(1,n);
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-   cod=ivector(1,n);
+         scanf("%d",i);*/
-   weight=vector(1,n);
+     } /* end of loop + */
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+   } /* end model */
-   mint=matrix(1,maxwav,1,n);
-   anint=matrix(1,maxwav,1,n);
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-   s=imatrix(1,maxwav+1,1,n);
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-   tab=ivector(1,NCOVMAX);
-   ncodemax=ivector(1,8);
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   printf("cptcovprod=%d ", cptcovprod);
-   i=1;
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-   linei=0;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+   scanf("%d ",i);*/
-     linei=linei+1;
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-       if(line[j] == '\t')
+   return (0); /* with covar[new additional covariate if product] and Tage if age */
-         line[j] = ' ';
+   endread:
-     }
+     printf("Exiting decodemodel: ");
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+     return (1);
-       ;
+ }
-     };
-     line[j+1]=0;  /* Trims blanks at end of line */
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-     if(line[0]=='#'){
+ {
-       fprintf(ficlog,"Comment line\n%s\n",line);
+   int i, m;
-       printf("Comment line\n%s\n",line);
-       continue;
+   for (i=1; i<=imx; i++) {
-     }
+     for(m=2; (m<= maxwav); m++) {
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
-     for (j=maxwav;j>=1;j--){
+         anint[m][i]=9999;
-       cutv(stra, strb,line,' ');
+         s[m][i]=-1;
-       errno=0;
+       }
-       lval=strtol(strb,&endptr,10);
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         *nberr++;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+         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);
-         printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+         fprintf(ficlog,"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);
-         exit(1);
+         s[m][i]=-1;
        }
-       s[j][i]=lval;
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+         *nberr++;
-       strcpy(line,stra);
+         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]);
-       cutv(stra, strb,line,' ');
+         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]);
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
-       else  if(iout=sscanf(strb,"%s.") != 0){
+     }
-         month=99;
+   }
-         year=9999;
-       }else{
+   for (i=1; i<=imx; i++)  {
-         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);
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-         exit(1);
+     for(m=firstpass; (m<= lastpass); m++){
-       }
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-       anint[j][i]= (double) year;
+         if (s[m][i] >= nlstate+1) {
-       mint[j][i]= (double)month;
+           if(agedc[i]>0)
-       strcpy(line,stra);
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-     } /* ENd Waves */
+               agev[m][i]=agedc[i];
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-     cutv(stra, strb,line,' ');
+             else {
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+               if ((int)andc[i]!=9999){
-     }
+                 nbwarn++;
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-       month=99;
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-       year=9999;
+                 agev[m][i]=-1;
-     }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);
+         }
-     }
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-     andc[i]=(double) year;
+                                  years but with the precision of a month */
-     moisdc[i]=(double) month;
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-     strcpy(line,stra);
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+             agev[m][i]=1;
-     cutv(stra, strb,line,' ');
+           else if(agev[m][i] < *agemin){
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+             *agemin=agev[m][i];
-     }
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-     else  if(iout=sscanf(strb,"%s.") != 0){
+           }
-       month=99;
+           else if(agev[m][i] >*agemax){
-       year=9999;
+             *agemax=agev[m][i];
-     }else{
+             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
+           }
-       exit(1);
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-     }
+           /*     agev[m][i] = age[i]+2*m;*/
-     annais[i]=(double)(year);
+         }
-     moisnais[i]=(double)(month);
+         else { /* =9 */
-     strcpy(line,stra);
+           agev[m][i]=1;
+           s[m][i]=-1;
-     cutv(stra, strb,line,' ');
+         }
-     errno=0;
+       }
-     dval=strtod(strb,&endptr);
+       else /*= 0 Unknown */
-     if( strb[0]=='\0' || (*endptr != '\0')){
+         agev[m][i]=1;
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+     }
-       exit(1);
-     }
+   }
-     weight[i]=dval;
+   for (i=1; i<=imx; i++)  {
-     strcpy(line,stra);
+     for(m=firstpass; (m<=lastpass); m++){
+       if (s[m][i] > (nlstate+ndeath)) {
-     for (j=ncovcol;j>=1;j--){
+         *nberr++;
-       cutv(stra, strb,line,' ');
+         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);
-       errno=0;
+         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);
-       lval=strtol(strb,&endptr,10);
+         return 1;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+       }
-         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
+     }
-         exit(1);
+   }
-       }
-       if(lval <-1 || lval >1){
+   /*for (i=1; i<=imx; i++){
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+   for (m=firstpass; (m<lastpass); m++){
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+ }
-  For example, for multinomial values like 1, 2 and 3,\n \
-  build V1=0 V2=0 for the reference value (1),\n \
+ }*/
-         V1=1 V2=0 for (2) \n \
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n \
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-  Exiting.\n",lval,linei, i,line,j);
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
-         exit(1);
-       }
+   return (0);
-       covar[j][i]=(double)(lval);
+   endread:
-       strcpy(line,stra);
+     printf("Exiting calandcheckages: ");
-     }
+     return (1);
-     lstra=strlen(stra);
+ }
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-       stratrunc = &(stra[lstra-9]);
+ /***********************************************/
-       num[i]=atol(stratrunc);
+ /**************** Main Program *****************/
-     }
+ /***********************************************/
-     else
-       num[i]=atol(stra);
+ int main(int argc, char *argv[])
-     /*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;}*/
+ #ifdef GSL
+   const gsl_multimin_fminimizer_type *T;
-     i=i+1;
+   size_t iteri = 0, it;
-   } /* End loop reading  data */
+   int rval = GSL_CONTINUE;
-   fclose(fic);
+   int status = GSL_SUCCESS;
-   /* printf("ii=%d", ij);
+   double ssval;
-      scanf("%d",i);*/
+ #endif
-   imx=i-1; /* Number of individuals */
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   /* for (i=1; i<=imx; i++){
+   int linei, month, year,iout;
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   int jj, ll, li, lj, lk, imk;
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   int numlinepar=0; /* Current linenumber of parameter file */
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+   int itimes;
-     }*/
+   int NDIM=2;
-    /*  for (i=1; i<=imx; i++){
+   int vpopbased=0;
-      if (s[4][i]==9)  s[4][i]=-1;
-      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+   char ca[32], cb[32], cc[32];
+   /*  FILE *fichtm; *//* Html File */
-   /* for (i=1; i<=imx; i++) */
+   /* FILE *ficgp;*/ /*Gnuplot File */
+   struct stat info;
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
+   double agedeb, agefin,hf;
-      else weight[i]=1;*/
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-   /* Calculation of the number of parameters from char model */
+   double fret;
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+   double **xi,tmp,delta;
-   Tprod=ivector(1,15);
-   Tvaraff=ivector(1,15);
+   double dum; /* Dummy variable */
-   Tvard=imatrix(1,15,1,2);
+   double ***p3mat;
-   Tage=ivector(1,15);
+   double ***mobaverage;
+   int *indx;
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+   char line[MAXLINE], linepar[MAXLINE];
-     j=0, j1=0, k1=1, k2=1;
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-     j=nbocc(model,'+'); /* j=Number of '+' */
+   char pathr[MAXLINE], pathimach[MAXLINE];
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+   char **bp, *tok, *val; /* pathtot */
-     cptcovn=j+1;
+   int firstobs=1, lastobs=10;
-     cptcovprod=j1; /*Number of products */
+   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt,l;
-     strcpy(modelsav,model);
+   int ju,jl, mi;
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+   int i1,j1, jk,aa,bb, stepsize, ij;
-       printf("Error. Non available option model=%s ",model);
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-       goto end;
+   int mobilav=0,popforecast=0;
-     }
+   int hstepm, nhstepm;
+   int agemortsup;
-     /* This loop fills the array Tvar from the string 'model'.*/
+   float  sumlpop=0.;
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-     for(i=(j+1); i>=1;i--){
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   double bage, fage, age, agelim, agebase;
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+   double ftolpl=FTOL;
-       /*scanf("%d",i);*/
+   double **prlim;
-       if (strchr(strb,'*')) {  /* Model includes a product */
+   double ***param; /* Matrix of parameters */
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+   double  *p;
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+   double **matcov; /* Matrix of covariance */
-           cptcovprod--;
+   double ***delti3; /* Scale */
-           cutv(strb,stre,strd,'V');
+   double *delti; /* Scale */
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+   double ***eij, ***vareij;
-           cptcovage++;
+   double **varpl; /* Variances of prevalence limits by age */
-             Tage[cptcovage]=i;
+   double *epj, vepp;
-             /*printf("stre=%s ", stre);*/
+   double kk1, kk2;
-         }
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+   double **ximort;
-           cptcovprod--;
+   char *alph[]={"a","a","b","c","d","e"}, str[4];
-           cutv(strb,stre,strc,'V');
+   int *dcwave;
-           Tvar[i]=atoi(stre);
-           cptcovage++;
+   char z[1]="c", occ;
-           Tage[cptcovage]=i;
-         }
+   /*char  *strt;*/
-         else {  /* Age is not in the model */
+   char strtend[80];
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
-           Tvar[i]=ncovcol+k1;
+   long total_usecs;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-           Tprod[k1]=i;
+ /*   setlocale (LC_ALL, ""); */
-           Tvard[k1][1]=atoi(strc); /* m*/
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
-           Tvard[k1][2]=atoi(stre); /* n */
+ /*   textdomain (PACKAGE); */
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+ /*   setlocale (LC_CTYPE, ""); */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+ /*   setlocale (LC_MESSAGES, ""); */
-           for (k=1; k<=lastobs;k++)
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-           k1++;
+   (void) gettimeofday(&start_time,&tzp);
-           k2=k2+2;
+   curr_time=start_time;
-         }
+   tm = *localtime(&start_time.tv_sec);
-       }
+   tmg = *gmtime(&start_time.tv_sec);
-       else { /* no more sum */
+   strcpy(strstart,asctime(&tm));
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-        /*  scanf("%d",i);*/
+ /*  printf("Localtime (at start)=%s",strstart); */
-       cutv(strd,strc,strb,'V');
+ /*  tp.tv_sec = tp.tv_sec +86400; */
-       Tvar[i]=atoi(strc);
+ /*  tm = *localtime(&start_time.tv_sec); */
-       }
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-       strcpy(modelsav,stra);
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-         scanf("%d",i);*/
+ /*   tp.tv_sec = mktime(&tmg); */
-     } /* end of loop + */
+ /*   strt=asctime(&tmg); */
-   } /* end model */
+ /*   printf("Time(after) =%s",strstart);  */
+ /*  (void) time (&time_value);
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+ *  tm = *localtime(&time_value);
+ *  strstart=asctime(&tm);
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-   printf("cptcovprod=%d ", cptcovprod);
+ */
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   nberr=0; /* Number of errors and warnings */
-   scanf("%d ",i);*/
+   nbwarn=0;
+   getcwd(pathcd, size);
-     /*  if(mle==1){*/
-   if (weightopt != 1) { /* Maximisation without weights*/
+   printf("\n%s\n%s",version,fullversion);
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   if(argc <=1){
-   }
+     printf("\nEnter the parameter file name: ");
-     /*-calculation of age at interview from date of interview and age at death -*/
+     fgets(pathr,FILENAMELENGTH,stdin);
-   agev=matrix(1,maxwav,1,imx);
+     i=strlen(pathr);
+     if(pathr[i-1]=='\n')
-   for (i=1; i<=imx; i++) {
+       pathr[i-1]='\0';
-     for(m=2; (m<= maxwav); m++) {
+    for (tok = pathr; tok != NULL; ){
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+       printf("Pathr |%s|\n",pathr);
-         anint[m][i]=9999;
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-         s[m][i]=-1;
+       printf("val= |%s| pathr=%s\n",val,pathr);
-       }
+       strcpy (pathtot, val);
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+       if(pathr[0] == '\0') break; /* Dirty */
-         nberr++;
+     }
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+   }
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
+   else{
-         s[m][i]=-1;
+     strcpy(pathtot,argv[1]);
-       }
+   }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-         nberr++;
+   /*cygwin_split_path(pathtot,path,optionfile);
-         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]);
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-         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]);
+   /* cutv(path,optionfile,pathtot,'\\');*/
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
-       }
+   /* Split argv[0], imach program to get pathimach */
-     }
+   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);
-   for (i=1; i<=imx; i++)  {
+  /*   strcpy(pathimach,argv[0]); */
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-     for(m=firstpass; (m<= lastpass); m++){
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-         if (s[m][i] >= nlstate+1) {
+   chdir(path); /* Can be a relative path */
-           if(agedc[i]>0)
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     printf("Current directory %s!\n",pathcd);
-               agev[m][i]=agedc[i];
+   strcpy(command,"mkdir ");
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+   strcat(command,optionfilefiname);
-             else {
+   if((outcmd=system(command)) != 0){
-               if ((int)andc[i]!=9999){
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-                 nbwarn++;
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+     /* fclose(ficlog); */
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+ /*     exit(1); */
-                 agev[m][i]=-1;
+   }
-               }
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-             }
+ /*     perror("mkdir"); */
-         }
+ /*   } */
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
-                                  years but with the precision of a month */
+   /*-------- arguments in the command line --------*/
-           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
+   /* Log file */
-             agev[m][i]=1;
+   strcat(filelog, optionfilefiname);
-           else if(agev[m][i] <agemin){
+   strcat(filelog,".log");    /* */
-             agemin=agev[m][i];
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+     printf("Problem with logfile %s\n",filelog);
-           }
+     goto end;
-           else if(agev[m][i] >agemax){
+   }
-             agemax=agev[m][i];
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-           }
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-           /*     agev[m][i] = age[i]+2*m;*/
+  path=%s \n\
-         }
+  optionfile=%s\n\
-         else { /* =9 */
+  optionfilext=%s\n\
-           agev[m][i]=1;
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-           s[m][i]=-1;
-         }
+   printf("Local time (at start):%s",strstart);
-       }
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-       else /*= 0 Unknown */
+   fflush(ficlog);
-         agev[m][i]=1;
+ /*   (void) gettimeofday(&curr_time,&tzp); */
-     }
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
-   }
+   /* */
-   for (i=1; i<=imx; i++)  {
+   strcpy(fileres,"r");
-     for(m=firstpass; (m<=lastpass); m++){
+   strcat(fileres, optionfilefiname);
-       if (s[m][i] > (nlstate+ndeath)) {
+   strcat(fileres,".txt");    /* Other files have txt extension */
-         nberr++;
-         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+   /*---------arguments file --------*/
-         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-         goto end;
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-       }
+     printf("Problem with optionfile %s\n",optionfile);
-     }
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-   }
+     fflush(ficlog);
+     goto end;
-   /*for (i=1; i<=imx; i++){
+   }
-   for (m=firstpass; (m<lastpass); m++){
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
- }
+   strcpy(filereso,"o");
- }*/
+   strcat(filereso,fileres);
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+     printf("Problem with Output resultfile: %s\n", filereso);
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     fflush(ficlog);
+     goto end;
-   agegomp=(int)agemin;
+   }
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
+   /* Reads comments: lines beginning with '#' */
-   free_vector(moisnais,1,n);
+   numlinepar=0;
-   free_vector(annais,1,n);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-   /* free_matrix(mint,1,maxwav,1,n);
+     ungetc(c,ficpar);
-      free_matrix(anint,1,maxwav,1,n);*/
+     fgets(line, MAXLINE, ficpar);
-   free_vector(moisdc,1,n);
+     numlinepar++;
-   free_vector(andc,1,n);
+     puts(line);
+     fputs(line,ficparo);
+     fputs(line,ficlog);
-   wav=ivector(1,imx);
+   }
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   ungetc(c,ficpar);
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   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++;
-   /* Concatenates waves */
+   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);
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+   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);
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   fflush(ficlog);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-   Tcode=ivector(1,100);
+     ungetc(c,ficpar);
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+     fgets(line, MAXLINE, ficpar);
-   ncodemax[1]=1;
+     numlinepar++;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+     puts(line);
+     fputs(line,ficparo);
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     fputs(line,ficlog);
-                                  the estimations*/
+   }
-   h=0;
+   ungetc(c,ficpar);
-   m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){
+   covar=matrix(0,NCOVMAX,1,n);
-     for(i=1; i <=(m/pow(2,k));i++){
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
-       for(j=1; j <= ncodemax[k]; j++){
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+      v1+v2*age+v2*v3 makes cptcovn = 3
-           h++;
+   */
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+   if (strlen(model)>1)
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+     cptcovn=nbocc(model,'+')+1;
-         }
+   /* 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*/
-     }
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-   }
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-      codtab[1][2]=1;codtab[2][2]=2; */
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-   /* for(i=1; i <=m ;i++){
+     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);
-      for(k=1; k <=cptcovn; k++){
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+     fflush(stdout);
-      }
+     fclose (ficlog);
-      printf("\n");
+     goto end;
-      }
+   }
-      scanf("%d",i);*/
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+   delti=delti3[1][1];
-   /*------------ gnuplot -------------*/
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
-   strcpy(optionfilegnuplot,optionfilefiname);
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-   if(mle==-3)
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     strcat(optionfilegnuplot,"-mort");
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-   strcat(optionfilegnuplot,".gp");
+     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);
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+     fclose (ficparo);
-     printf("Problem with file %s",optionfilegnuplot);
+     fclose (ficlog);
-   }
+     goto end;
-   else{
+     exit(0);
-     fprintf(ficgp,"\n# %s\n", version);
+   }
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+   else if(mle==-3) {
-     fprintf(ficgp,"set missing 'NaNq'\n");
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   }
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-   /*  fclose(ficgp);*/
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-   /*--------- index.htm --------*/
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     matcov=matrix(1,npar,1,npar);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+   }
-   if(mle==-3)
+   else{
-     strcat(optionfilehtm,"-mort");
+     /* Read guess parameters */
-   strcat(optionfilehtm,".htm");
+     /* Reads comments: lines beginning with '#' */
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+       ungetc(c,ficpar);
-   }
+       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+       puts(line);
-   strcat(optionfilehtmcov,"-cov.htm");
+       fputs(line,ficparo);
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+       fputs(line,ficlog);
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+     }
-   }
+     ungetc(c,ficpar);
-   else{
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+     for(i=1; i <=nlstate; i++){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+       j=0;
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
-   }
+         if(jj==i) continue;
+         j++;
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         if ((i1 != i) && (j1 != j)){
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
- \n\
+ It might be a problem of design; if ncovcol and the model are correct\n \
- <hr  size=\"2\" color=\"#EC5E5E\">\
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-  <ul><li><h4>Parameter files</h4>\n\
+           exit(1);
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+         }
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+         fprintf(ficparo,"%1d%1d",i1,j1);
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+         if(mle==1)
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+           printf("%1d%1d",i,j);
-  - Date and time at start: %s</ul>\n",\
+         fprintf(ficlog,"%1d%1d",i,j);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+         for(k=1; k<=ncovmodel;k++){
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+           fscanf(ficpar," %lf",&param[i][j][k]);
-           fileres,fileres,\
+           if(mle==1){
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
+             printf(" %lf",param[i][j][k]);
-   fflush(fichtm);
+             fprintf(ficlog," %lf",param[i][j][k]);
+           }
-   strcpy(pathr,path);
+           else
-   strcat(pathr,optionfilefiname);
+             fprintf(ficlog," %lf",param[i][j][k]);
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+           fprintf(ficparo," %lf",param[i][j][k]);
+         }
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+         fscanf(ficpar,"\n");
-      and prints on file fileres'p'. */
+         numlinepar++;
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+         if(mle==1)
+           printf("\n");
-   fprintf(fichtm,"\n");
+         fprintf(ficlog,"\n");
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+         fprintf(ficparo,"\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",\
+     }
-           imx,agemin,agemax,jmin,jmax,jmean);
+     fflush(ficlog);
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     p=param[1][1];
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     /* Reads comments: lines beginning with '#' */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       numlinepar++;
-      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);
+       fputs(line,ficlog);
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+     }
+     ungetc(c,ficpar);
-   if (mle==-3){
-     ximort=matrix(1,NDIM,1,NDIM);
+     for(i=1; i <=nlstate; i++){
-     cens=ivector(1,n);
+       for(j=1; j <=nlstate+ndeath-1; j++){
-     ageexmed=vector(1,n);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-     agecens=vector(1,n);
+         if ((i1-i)*(j1-j)!=0){
-     dcwave=ivector(1,n);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           exit(1);
-     for (i=1; i<=imx; i++){
+         }
-       dcwave[i]=-1;
+         printf("%1d%1d",i,j);
-       for (m=firstpass; m<=lastpass; m++)
+         fprintf(ficparo,"%1d%1d",i1,j1);
-         if (s[m][i]>nlstate) {
+         fprintf(ficlog,"%1d%1d",i1,j1);
-           dcwave[i]=m;
+         for(k=1; k<=ncovmodel;k++){
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-           break;
+           printf(" %le",delti3[i][j][k]);
-         }
+           fprintf(ficparo," %le",delti3[i][j][k]);
-     }
+           fprintf(ficlog," %le",delti3[i][j][k]);
+         }
-     for (i=1; i<=imx; i++) {
+         fscanf(ficpar,"\n");
-       if (wav[i]>0){
+         numlinepar++;
-         ageexmed[i]=agev[mw[1][i]][i];
+         printf("\n");
-         j=wav[i];
+         fprintf(ficparo,"\n");
-         agecens[i]=1.;
+         fprintf(ficlog,"\n");
+       }
-         if (ageexmed[i]> 1 && wav[i] > 0){
+     }
-           agecens[i]=agev[mw[j][i]][i];
+     fflush(ficlog);
-           cens[i]= 1;
-         }else if (ageexmed[i]< 1)
+     delti=delti3[1][1];
-           cens[i]= -1;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           cens[i]=0 ;
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-       }
-       else cens[i]=-1;
+     /* Reads comments: lines beginning with '#' */
-     }
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
-     for (i=1;i<=NDIM;i++) {
+       fgets(line, MAXLINE, ficpar);
-       for (j=1;j<=NDIM;j++)
+       numlinepar++;
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+       puts(line);
-     }
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-     p[1]=0.0268; p[NDIM]=0.083;
+     }
-     /*printf("%lf %lf", p[1], p[2]);*/
+     ungetc(c,ficpar);
+     matcov=matrix(1,npar,1,npar);
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+     for(i=1; i <=npar; i++)
-     strcpy(filerespow,"pow-mort");
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-     strcat(filerespow,fileres);
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+     for(i=1; i <=npar; i++){
-       printf("Problem with resultfile: %s\n", filerespow);
+       fscanf(ficpar,"%s",&str);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+       if(mle==1)
-     }
+         printf("%s",str);
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+       fprintf(ficlog,"%s",str);
-     /*  for (i=1;i<=nlstate;i++)
+       fprintf(ficparo,"%s",str);
-         for(j=1;j<=nlstate+ndeath;j++)
+       for(j=1; j <=i; j++){
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+         fscanf(ficpar," %le",&matcov[i][j]);
-     */
+         if(mle==1){
-     fprintf(ficrespow,"\n");
+           printf(" %.5le",matcov[i][j]);
+         }
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     fclose(ficrespow);
+         fprintf(ficparo," %.5le",matcov[i][j]);
+       }
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+       fscanf(ficpar,"\n");
+       numlinepar++;
-     for(i=1; i <=NDIM; i++)
+       if(mle==1)
-       for(j=i+1;j<=NDIM;j++)
+         printf("\n");
-         matcov[i][j]=matcov[j][i];
+       fprintf(ficlog,"\n");
+       fprintf(ficparo,"\n");
-     printf("\nCovariance matrix\n ");
+     }
-     for(i=1; i <=NDIM; i++) {
+     for(i=1; i <=npar; i++)
-       for(j=1;j<=NDIM;j++){
+       for(j=i+1;j<=npar;j++)
-         printf("%f ",matcov[i][j]);
+         matcov[i][j]=matcov[j][i];
-       }
-       printf("\n ");
+     if(mle==1)
-     }
+       printf("\n");
+     fprintf(ficlog,"\n");
-     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-     for (i=1;i<=NDIM;i++)
+     fflush(ficlog);
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     /*-------- Rewriting parameter file ----------*/
-     lsurv=vector(1,AGESUP);
+     strcpy(rfileres,"r");    /* "Rparameterfile */
-     lpop=vector(1,AGESUP);
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     tpop=vector(1,AGESUP);
+     strcat(rfileres,".");    /* */
-     lsurv[agegomp]=100000;
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-     for (k=agegomp;k<=AGESUP;k++) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-       agemortsup=k;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+     }
-     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   n= lastobs;
-     for (k=agegomp;k<agemortsup;k++){
+   num=lvector(1,n);
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   moisnais=vector(1,n);
-       sumlpop=sumlpop+lpop[k];
+   annais=vector(1,n);
-     }
+   moisdc=vector(1,n);
+   andc=vector(1,n);
-     tpop[agegomp]=sumlpop;
+   agedc=vector(1,n);
-     for (k=agegomp;k<(agemortsup-3);k++){
+   cod=ivector(1,n);
-       /*  tpop[k+1]=2;*/
+   weight=vector(1,n);
-       tpop[k+1]=tpop[k]-lpop[k];
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-     }
+   mint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,1,n);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   tab=ivector(1,NCOVMAX);
-     for (k=agegomp;k<(agemortsup-2);k++)
+   ncodemax=ivector(1,8); /* hard coded ? */
-       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]);
+   /* Reads data from file datafile */
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+     goto end;
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+   /* Calculation of the number of parameters from char model */
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
-                      stepm, weightopt,\
+         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
-                      model,imx,p,matcov,agemortsup);
+         k=3 V4 Tvar[k=3]= 4 (from V4)
+         k=2 V1 Tvar[k=2]= 1 (from V1)
-     free_vector(lsurv,1,AGESUP);
+         k=1 Tvar[1]=2 (from V2)
-     free_vector(lpop,1,AGESUP);
+     */
-     free_vector(tpop,1,AGESUP);
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
-   } /* Endof if mle==-3 */
+   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
+       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
-   else{ /* For mle >=1 */
+       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
+   */
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   /* For model-covariate k tells which data-covariate to use but
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+     because this model-covariate is a construction we invent a new column
-     for (k=1; k<=npar;k++)
+     ncovcol + k1
-       printf(" %d %8.5f",k,p[k]);
+     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
-     printf("\n");
+     Tvar[3=V1*V4]=4+1 etc */
-     globpr=1; /* to print the contributions */
+   Tprod=ivector(1,15);
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
-     for (k=1; k<=npar;k++)
+   */
-       printf(" %d %8.5f",k,p[k]);
+   Tvaraff=ivector(1,15);
-     printf("\n");
+   Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
-     if(mle>=1){ /* Could be 1 or 2 */
+   Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+covariates (3 plus signs)
-     }
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
-     /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   if((double)(lastobs-imx)/(double)imx > 1.10){
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     nbwarn++;
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     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);
-     for(i=1,jk=1; i <=nlstate; i++){
+     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);
-       for(k=1; k <=(nlstate+ndeath); k++){
+   }
-         if (k != i) {
+     /*  if(mle==1){*/
-           printf("%d%d ",i,k);
+   if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
-           fprintf(ficlog,"%d%d ",i,k);
+     for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
-           fprintf(ficres,"%1d%1d ",i,k);
+   }
-           for(j=1; j <=ncovmodel; j++){
-             printf("%lf ",p[jk]);
+     /*-calculation of age at interview from date of interview and age at death -*/
-             fprintf(ficlog,"%lf ",p[jk]);
+   agev=matrix(1,maxwav,1,imx);
-             fprintf(ficres,"%lf ",p[jk]);
-             jk++;
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-           }
+     goto end;
-           printf("\n");
-           fprintf(ficlog,"\n");
-           fprintf(ficres,"\n");
+   agegomp=(int)agemin;
-         }
+   free_vector(moisnais,1,n);
-       }
+   free_vector(annais,1,n);
-     }
+   /* free_matrix(mint,1,maxwav,1,n);
-     if(mle!=0){
+      free_matrix(anint,1,maxwav,1,n);*/
-       /* Computing hessian and covariance matrix */
+   free_vector(moisdc,1,n);
-       ftolhess=ftol; /* Usually correct */
+   free_vector(andc,1,n);
-       hesscov(matcov, p, npar, delti, ftolhess, func);
-     }
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+   wav=ivector(1,imx);
-     printf("# Scales (for hessian or gradient estimation)\n");
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
-     for(i=1,jk=1; i <=nlstate; i++){
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-       for(j=1; j <=nlstate+ndeath; j++){
-         if (j!=i) {
+   /* Concatenates waves */
-           fprintf(ficres,"%1d%1d",i,j);
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-           printf("%1d%1d",i,j);
-           fprintf(ficlog,"%1d%1d",i,j);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-           for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
-             fprintf(ficlog," %.5e",delti[jk]);
+   ncodemax[1]=1;
-             fprintf(ficres," %.5e",delti[jk]);
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-             jk++;
-           }
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
-           printf("\n");
+                                  the estimations*/
-           fprintf(ficlog,"\n");
+   h=0;
-           fprintf(ficres,"\n");
+   m=pow(2,cptcoveff);
-         }
-       }
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     }
+     for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
-     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");
+         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-     if(mle>=1)
+           h++;
-       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");
+           if (h>m) {
-     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");
+             h=1;
-     /* # 121 Var(a12)\n\ */
+             codtab[h][k]=j;
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+             codtab[h][Tvar[k]]=j;
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+           }
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+         }
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+       }
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     }
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   }
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
-     /* Just to have a covariance matrix which will be more understandable
+   /* for(i=1; i <=m ;i++){
-        even is we still don't want to manage dictionary of variables
+      for(k=1; k <=cptcovn; k++){
-     */
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-     for(itimes=1;itimes<=2;itimes++){
+      }
-       jj=0;
+      printf("\n");
-       for(i=1; i <=nlstate; i++){
+      }
-         for(j=1; j <=nlstate+ndeath; j++){
+      scanf("%d",i);*/
-           if(j==i) continue;
-           for(k=1; k<=ncovmodel;k++){
+   /*------------ gnuplot -------------*/
-             jj++;
+   strcpy(optionfilegnuplot,optionfilefiname);
-             ca[0]= k+'a'-1;ca[1]='\0';
+   if(mle==-3)
-             if(itimes==1){
+     strcat(optionfilegnuplot,"-mort");
-               if(mle>=1)
+   strcat(optionfilegnuplot,".gp");
-                 printf("#%1d%1d%d",i,j,k);
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+     printf("Problem with file %s",optionfilegnuplot);
-             }else{
+   }
-               if(mle>=1)
+   else{
-                 printf("%1d%1d%d",i,j,k);
+     fprintf(ficgp,"\n# %s\n", version);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+     fprintf(ficgp,"set missing 'NaNq'\n");
-             }
+   }
-             ll=0;
+   /*  fclose(ficgp);*/
-             for(li=1;li <=nlstate; li++){
+   /*--------- index.htm --------*/
-               for(lj=1;lj <=nlstate+ndeath; lj++){
-                 if(lj==li) continue;
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-                 for(lk=1;lk<=ncovmodel;lk++){
+   if(mle==-3)
-                   ll++;
+     strcat(optionfilehtm,"-mort");
-                   if(ll<=jj){
+   strcat(optionfilehtm,".htm");
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-                     if(ll<jj){
+     printf("Problem with %s \n",optionfilehtm);
-                       if(itimes==1){
+     exit(0);
-                         if(mle>=1)
+   }
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+   strcat(optionfilehtmcov,"-cov.htm");
-                       }else{
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-                         if(mle>=1)
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-                           printf(" %.5e",matcov[jj][ll]);
+   }
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+   else{
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-                       }
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-                     }else{
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-                       if(itimes==1){
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-                         if(mle>=1)
+   }
-                           printf(" Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-                       }else{
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-                         if(mle>=1)
+ \n\
-                           printf(" %.5e",matcov[jj][ll]);
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+  <ul><li><h4>Parameter files</h4>\n\
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-                       }
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-                     }
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-                   }
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-                 } /* end lk */
+  - Date and time at start: %s</ul>\n",\
-               } /* end lj */
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-             } /* end li */
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-             if(mle>=1)
+           fileres,fileres,\
-               printf("\n");
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-             fprintf(ficlog,"\n");
+   fflush(fichtm);
-             fprintf(ficres,"\n");
-             numlinepar++;
+   strcpy(pathr,path);
-           } /* end k*/
+   strcat(pathr,optionfilefiname);
-         } /*end j */
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-       } /* end i */
-     } /* end itimes */
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
-     fflush(ficlog);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-     fflush(ficres);
+   fprintf(fichtm,"\n");
-     while((c=getc(ficpar))=='#' && c!= EOF){
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-       ungetc(c,ficpar);
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-       fgets(line, MAXLINE, ficpar);
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-       puts(line);
+           imx,agemin,agemax,jmin,jmax,jmean);
-       fputs(line,ficparo);
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     }
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     ungetc(c,ficpar);
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     estepm=0;
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     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) {
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-       bage = ageminpar;
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-       fage = agemaxpar;
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-     }
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+   if (mle==-3){
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     cens=ivector(1,n);
-       ungetc(c,ficpar);
+     ageexmed=vector(1,n);
-       fgets(line, MAXLINE, ficpar);
+     agecens=vector(1,n);
-       puts(line);
+     dcwave=ivector(1,n);
-       fputs(line,ficparo);
-     }
+     for (i=1; i<=imx; i++){
-     ungetc(c,ficpar);
+       dcwave[i]=-1;
+       for (m=firstpass; m<=lastpass; m++)
-     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);
+         if (s[m][i]>nlstate) {
-     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);
+           dcwave[i]=m;
-     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("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+           break;
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         }
+     }
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+     for (i=1; i<=imx; i++) {
-       fgets(line, MAXLINE, ficpar);
+       if (wav[i]>0){
-       puts(line);
+         ageexmed[i]=agev[mw[1][i]][i];
-       fputs(line,ficparo);
+         j=wav[i];
-     }
+         agecens[i]=1.;
-     ungetc(c,ficpar);
+         if (ageexmed[i]> 1 && wav[i] > 0){
+           agecens[i]=agev[mw[j][i]][i];
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+           cens[i]= 1;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+         }else if (ageexmed[i]< 1)
+           cens[i]= -1;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+           cens[i]=0 ;
-     fprintf(ficres,"pop_based=%d\n",popbased);
+       }
+       else cens[i]=-1;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     }
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+     for (i=1;i<=NDIM;i++) {
-       puts(line);
+       for (j=1;j<=NDIM;j++)
-       fputs(line,ficparo);
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     ungetc(c,ficpar);
+     p[1]=0.0268; p[NDIM]=0.083;
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
+     /*printf("%lf %lf", p[1], p[2]);*/
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+ #ifdef GSL
-     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);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-     /* day and month of proj2 are not used but only year anproj2.*/
+ #elsedef
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
+     strcpy(filerespow,"pow-mort");
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     strcat(filerespow,fileres);
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+       printf("Problem with resultfile: %s\n", filerespow);
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     }
+ #ifdef GSL
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ #elsedef
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
-    /*------------ free_vector  -------------*/
+     /*  for (i=1;i<=nlstate;i++)
-    /*  chdir(path); */
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     free_ivector(wav,1,imx);
+     */
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     fprintf(ficrespow,"\n");
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+ #ifdef GSL
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     /* gsl starts here */
-     free_lvector(num,1,n);
+     T = gsl_multimin_fminimizer_nmsimplex;
-     free_vector(agedc,1,n);
+     gsl_multimin_fminimizer *sfm = NULL;
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     gsl_vector *ss, *x;
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     gsl_multimin_function minex_func;
-     fclose(ficparo);
-     fclose(ficres);
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-     strcpy(filerespl,"pl");
+     }
-     strcat(filerespl,fileres);
+     /* Set all step sizes to 1 */
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     gsl_vector_set_all (ss, 0.001);
-       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;
+     /* Starting point */
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     x = gsl_vector_alloc (NDIM);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     pstamp(ficrespl);
+     if (x == NULL){
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+       gsl_vector_free(ss);
-     fprintf(ficrespl,"#Age ");
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+     }
-     fprintf(ficrespl,"\n");
+     /* Initialize method and iterate */
-     prlim=matrix(1,nlstate,1,nlstate);
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
-     agebase=ageminpar;
+ /*     gsl_vector_set(x, 1, 0.083); */
-     agelim=agemaxpar;
+     gsl_vector_set(x, 0, p[1]);
-     ftolpl=1.e-10;
+     gsl_vector_set(x, 1, p[2]);
-     i1=cptcoveff;
-     if (cptcovn < 1){i1=1;}
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     minex_func.params = (void *)&p; /* ??? */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
+     printf("Iterations beginning .....\n\n");
-         fprintf(ficlog,"\n#******");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     iteri=0;
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     while (rval == GSL_CONTINUE){
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       iteri++;
-         }
+       status = gsl_multimin_fminimizer_iterate(sfm);
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
+       if (status) printf("error: %s\n", gsl_strerror (status));
-         fprintf(ficlog,"******\n");
+       fflush(0);
-         for (age=agebase; age<=agelim; age++){
+       if (status)
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+         break;
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       ssval = gsl_multimin_fminimizer_size (sfm);
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+       if (rval == GSL_SUCCESS)
-           fprintf(ficrespl,"\n");
+         printf ("converged to a local maximum at\n");
-         }
-       }
+       printf("%5d ", iteri);
-     }
+       for (it = 0; it < NDIM; it++){
-     fclose(ficrespl);
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
-     /*------------- h Pij x at various ages ------------*/
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     gsl_vector_free(x); /* initial values */
-     }
+     gsl_vector_free(ss); /* inital step size */
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     for (it=0; it<NDIM; it++){
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+       p[it+1]=gsl_vector_get(sfm->x,it);
+       fprintf(ficrespow," %.12lf", p[it]);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     }
-     /*if (stepm<=24) stepsize=2;*/
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
+ #endif
-     agelim=AGESUP;
+ #ifdef POWELL
-     hstepm=stepsize*YEARM; /* Every year of age */
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+ #endif
+     fclose(ficrespow);
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     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(i=1; i <=NDIM; i++)
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       for(j=i+1;j<=NDIM;j++)
-         k=k+1;
+         matcov[i][j]=matcov[j][i];
-         fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+     printf("\nCovariance matrix\n ");
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(i=1; i <=NDIM; i++) {
-         fprintf(ficrespij,"******\n");
+       for(j=1;j<=NDIM;j++){
+         printf("%f ",matcov[i][j]);
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+       }
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       printf("\n ");
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     }
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+     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++)
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     lsurv=vector(1,AGESUP);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     lpop=vector(1,AGESUP);
-           for(i=1; i<=nlstate;i++)
+     tpop=vector(1,AGESUP);
-             for(j=1; j<=nlstate+ndeath;j++)
+     lsurv[agegomp]=100000;
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
+     for (k=agegomp;k<=AGESUP;k++) {
-           for (h=0; h<=nhstepm; h++){
+       agemortsup=k;
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-             for(i=1; i<=nlstate;i++)
+     }
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+     for (k=agegomp;k<agemortsup;k++)
-             fprintf(ficrespij,"\n");
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     for (k=agegomp;k<agemortsup;k++){
-           fprintf(ficrespij,"\n");
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
-         }
+       sumlpop=sumlpop+lpop[k];
-       }
+     }
-     }
+     tpop[agegomp]=sumlpop;
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     for (k=agegomp;k<(agemortsup-3);k++){
+       /*  tpop[k+1]=2;*/
-     fclose(ficrespij);
+       tpop[k+1]=tpop[k]-lpop[k];
+     }
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     for(i=1;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-         for(k=1;k<=NCOVMAX;k++)
+     for (k=agegomp;k<(agemortsup-2);k++)
-           probs[i][j][k]=0.;
+       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]);
-     /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     if(prevfcast==1){
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-       /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+                      stepm, weightopt,\
-       /*      }  */
+                      model,imx,p,matcov,agemortsup);
-       /*      else{ */
-       /*        erreur=108; */
+     free_vector(lsurv,1,AGESUP);
-       /*        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); */
+     free_vector(lpop,1,AGESUP);
-       /*        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); */
+     free_vector(tpop,1,AGESUP);
-       /*      } */
+ #ifdef GSL
-     }
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
-     /*---------- Health expectancies and variances ------------*/
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
-     strcpy(filerest,"t");
+   } /* Endof if mle==-3 */
-     strcat(filerest,fileres);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+   else{ /* For mle >=1 */
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+     globpr=0;/* debug */
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     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);
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     for (k=1; k<=npar;k++)
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       printf(" %d %8.5f",k,p[k]);
+     printf("\n");
+     globpr=1; /* to print the contributions */
-     strcpy(filerese,"e");
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-     strcat(filerese,fileres);
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+     for (k=1; k<=npar;k++)
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+       printf(" %d %8.5f",k,p[k]);
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+     printf("\n");
-     }
+     if(mle>=1){ /* Could be 1 or 2 */
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     }
-     strcpy(fileresstde,"stde");
+     /*--------- results files --------------*/
-     strcat(fileresstde,fileres);
+     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);
-     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);
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     }
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     for(i=1,jk=1; i <=nlstate; i++){
+       for(k=1; k <=(nlstate+ndeath); k++){
-     strcpy(filerescve,"cve");
+         if (k != i) {
-     strcat(filerescve,fileres);
+           printf("%d%d ",i,k);
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+           fprintf(ficlog,"%d%d ",i,k);
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+           fprintf(ficres,"%1d%1d ",i,k);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+           for(j=1; j <=ncovmodel; j++){
-     }
+             printf("%lf ",p[jk]);
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+             fprintf(ficlog,"%lf ",p[jk]);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+             fprintf(ficres,"%lf ",p[jk]);
+             jk++;
-     strcpy(fileresv,"v");
+           }
-     strcat(fileresv,fileres);
+           printf("\n");
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+           fprintf(ficlog,"\n");
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+           fprintf(ficres,"\n");
-       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);
+     if(mle!=0){
+       /* Computing hessian and covariance matrix */
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+       ftolhess=ftol; /* Usually correct */
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-     /*  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);
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-     */
+     printf("# Scales (for hessian or gradient estimation)\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-     if (mobilav!=0) {
+     for(i=1,jk=1; i <=nlstate; i++){
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       for(j=1; j <=nlstate+ndeath; j++){
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+         if (j!=i) {
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+           fprintf(ficres,"%1d%1d",i,j);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+           printf("%1d%1d",i,j);
-       }
+           fprintf(ficlog,"%1d%1d",i,j);
-     }
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+             fprintf(ficlog," %.5e",delti[jk]);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+             fprintf(ficres," %.5e",delti[jk]);
-         k=k+1;
+             jk++;
-         fprintf(ficrest,"\n#****** ");
+           }
-         for(j=1;j<=cptcoveff;j++)
+           printf("\n");
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficlog,"\n");
-         fprintf(ficrest,"******\n");
+           fprintf(ficres,"\n");
+         }
-         fprintf(ficreseij,"\n#****** ");
+       }
-         fprintf(ficresstdeij,"\n#****** ");
+     }
-         fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     if(mle>=1)
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       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(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-         }
+     /* # 121 Var(a12)\n\ */
-         fprintf(ficreseij,"******\n");
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-         fprintf(ficresstdeij,"******\n");
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-         fprintf(ficrescveij,"******\n");
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-         fprintf(ficresvij,"\n#****** ");
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-         for(j=1;j<=cptcoveff;j++)
+     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-         fprintf(ficresvij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     /* Just to have a covariance matrix which will be more understandable
-         oldm=oldms;savm=savms;
+        even is we still don't want to manage dictionary of variables
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+     */
-         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+     for(itimes=1;itimes<=2;itimes++){
+       jj=0;
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       for(i=1; i <=nlstate; i++){
-         oldm=oldms;savm=savms;
+         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,0, mobilav, strstart);
+           if(j==i) continue;
-         if(popbased==1){
+           for(k=1; k<=ncovmodel;k++){
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+             jj++;
-         }
+             ca[0]= k+'a'-1;ca[1]='\0';
+             if(itimes==1){
-         pstamp(ficrest);
+               if(mle>=1)
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+                 printf("#%1d%1d%d",i,j,k);
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-         fprintf(ficrest,"\n");
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
-         epj=vector(1,nlstate+1);
+               if(mle>=1)
-         for(age=bage; age <=fage ;age++){
+                 printf("%1d%1d%d",i,j,k);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
-           if (popbased==1) {
+               fprintf(ficres,"%1d%1d%d",i,j,k);
-             if(mobilav ==0){
+             }
-               for(i=1; i<=nlstate;i++)
+             ll=0;
-                 prlim[i][i]=probs[(int)age][i][k];
+             for(li=1;li <=nlstate; li++){
-             }else{ /* mobilav */
+               for(lj=1;lj <=nlstate+ndeath; lj++){
-               for(i=1; i<=nlstate;i++)
+                 if(lj==li) continue;
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+                 for(lk=1;lk<=ncovmodel;lk++){
-             }
+                   ll++;
-           }
+                   if(ll<=jj){
+                     cb[0]= lk +'a'-1;cb[1]='\0';
-           fprintf(ficrest," %4.0f",age);
+                     if(ll<jj){
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+                       if(itimes==1){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                         if(mle>=1)
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+                         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);
-             epj[nlstate+1] +=epj[j];
+                       }else{
-           }
+                         if(mle>=1)
+                           printf(" %.5e",matcov[jj][ll]);
-           for(i=1, vepp=0.;i <=nlstate;i++)
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-             for(j=1;j <=nlstate;j++)
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-               vepp += vareij[i][j][(int)age];
+                       }
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+                     }else{
-           for(j=1;j <=nlstate;j++){
+                       if(itimes==1){
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+                         if(mle>=1)
-           }
+                           printf(" Var(%s%1d%1d)",ca,i,j);
-           fprintf(ficrest,"\n");
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-         }
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+                       }else{
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+                         if(mle>=1)
-         free_vector(epj,1,nlstate+1);
+                           printf(" %.5e",matcov[jj][ll]);
-       }
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-     }
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-     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);
+                 } /* end lk */
-     free_matrix(mint,1,maxwav,1,n);
+               } /* end lj */
-     free_ivector(cod,1,n);
+             } /* end li */
-     free_ivector(tab,1,NCOVMAX);
+             if(mle>=1)
-     fclose(ficreseij);
+               printf("\n");
-     fclose(ficresstdeij);
+             fprintf(ficlog,"\n");
-     fclose(ficrescveij);
+             fprintf(ficres,"\n");
-     fclose(ficresvij);
+             numlinepar++;
-     fclose(ficrest);
+           } /* end k*/
-     fclose(ficpar);
+         } /*end j */
+       } /* end i */
-     /*------- Variance of period (stable) prevalence------*/
+     } /* end itimes */
-     strcpy(fileresvpl,"vpl");
+     fflush(ficlog);
-     strcat(fileresvpl,fileres);
+     fflush(ficres);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-       exit(0);
+       ungetc(c,ficpar);
-     }
+       fgets(line, MAXLINE, ficpar);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+       puts(line);
+       fputs(line,ficparo);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     }
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     ungetc(c,ficpar);
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
+     estepm=0;
-         for(j=1;j<=cptcoveff;j++)
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
-         fprintf(ficresvpl,"******\n");
+     if (fage <= 2) {
+       bage = ageminpar;
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       fage = agemaxpar;
-         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);
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-       }
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     }
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-     fclose(ficresvpl);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
-     /*---------- End : free ----------------*/
+       fgets(line, MAXLINE, ficpar);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       puts(line);
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       fputs(line,ficparo);
+     }
-   }  /* mle==-3 arrives here for freeing */
+     ungetc(c,ficpar);
-   free_matrix(prlim,1,nlstate,1,nlstate);
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     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);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     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);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     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);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     free_matrix(covar,0,NCOVMAX,1,n);
+     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     free_matrix(matcov,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       ungetc(c,ficpar);
-     free_matrix(agev,1,maxwav,1,imx);
+       fgets(line, MAXLINE, ficpar);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+       puts(line);
+       fputs(line,ficparo);
-     free_ivector(ncodemax,1,8);
+     }
-     free_ivector(Tvar,1,15);
+     ungetc(c,ficpar);
-     free_ivector(Tprod,1,15);
-     free_ivector(Tvaraff,1,15);
-     free_ivector(Tage,1,15);
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     free_ivector(Tcode,1,100);
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     free_imatrix(codtab,1,100,1,10);
+     fprintf(ficparo,"pop_based=%d\n",popbased);
-   fflush(fichtm);
+     fprintf(ficres,"pop_based=%d\n",popbased);
-   fflush(ficgp);
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
-   if((nberr >0) || (nbwarn>0)){
+       fgets(line, MAXLINE, ficpar);
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+       puts(line);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+       fputs(line,ficparo);
-   }else{
+     }
-     printf("End of Imach\n");
+     ungetc(c,ficpar);
-     fprintf(ficlog,"End of Imach\n");
-   }
+     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-   printf("See log file on %s\n",filelog);
+     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);
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     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);
-   (void) gettimeofday(&end_time,&tzp);
+     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);
-   tm = *localtime(&end_time.tv_sec);
+     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);
-   tmg = *gmtime(&end_time.tv_sec);
+     /* day and month of proj2 are not used but only year anproj2.*/
-   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));
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
-   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-   fclose(fichtm);
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
-   fclose(fichtmcov);
+    /*------------ free_vector  -------------*/
-   fclose(ficgp);
+    /*  chdir(path); */
-   fclose(ficlog);
-   /*------ End -----------*/
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-    printf("Before Current directory %s!\n",pathcd);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-    if(chdir(pathcd) != 0)
+     free_lvector(num,1,n);
-     printf("Can't move to directory %s!\n",path);
+     free_vector(agedc,1,n);
-   if(getcwd(pathcd,MAXLINE) > 0)
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
-     printf("Current directory %s!\n",pathcd);
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+     fclose(ficparo);
-   sprintf(plotcmd,"gnuplot");
+     fclose(ficres);
- #ifndef UNIX
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
- #endif
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   if(!stat(plotcmd,&info)){
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     strcpy(filerespl,"pl");
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+     strcat(filerespl,fileres);
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     }else
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-       strcpy(pplotcmd,plotcmd);
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
- #ifdef UNIX
+     }
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     if(!stat(plotcmd,&info)){
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+     pstamp(ficrespl);
-     }else
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
-       strcpy(pplotcmd,plotcmd);
+     fprintf(ficrespl,"#Age ");
- #endif
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-   }else
+     fprintf(ficrespl,"\n");
-     strcpy(pplotcmd,plotcmd);
+     prlim=matrix(1,nlstate,1,nlstate);
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+     agebase=ageminpar;
+     agelim=agemaxpar;
-   if((outcmd=system(plotcmd)) != 0){
+     ftolpl=1.e-10;
-     printf("\n Problem with gnuplot\n");
+     i1=cptcoveff;
-   }
+     if (cptcovn < 1){i1=1;}
-   printf(" Wait...");
-   while (z[0] != 'q') {
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     /* chdir(path); */
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+         k=k+1;
-     scanf("%s",z);
+         /* to clean */
- /*     if (z[0] == 'c') system("./imach"); */
+         printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
-     if (z[0] == 'e') {
+         fprintf(ficrespl,"\n#******");
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+         printf("\n#******");
-       system(optionfilehtm);
+         fprintf(ficlog,"\n#******");
-     }
+         for(j=1;j<=cptcoveff;j++) {
-     else if (z[0] == 'g') system(plotcmd);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     else if (z[0] == 'q') exit(0);
+           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]]);
-   end:
+         }
-   while (z[0] != 'q') {
+         fprintf(ficrespl,"******\n");
-     printf("\nType  q for exiting: ");
+         printf("******\n");
-     scanf("%s",z);
+         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");
+         }
+       }
+     }
+     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);
+     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 %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+   /*  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.1.139