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Diff for /imach/src/imach.c between versions 1.125 and 1.136

-version 1.125, 2006/04/04 15:20:31
+version 1.136, 2010/04/26 20:30:53
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 */
-   }
+   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;
+ int nbocc(char *s, char occ)
-   }
+ {
+   int i,j=0;
-   lg=strlen(t);
+   int lg=20;
-   for(j=0; j<p; j++) {
+   i=0;
-     (u[j] = t[j]);
+   lg=strlen(s);
-   }
+   for(i=0; i<= lg; i++) {
-      u[p]='\0';
+   if  (s[i] == occ ) j++;
+   }
-    for(j=0; j<= lg; j++) {
+   return j;
-     if (j>=(p+1))(v[j-p-1] = t[j]);
+ }
-   }
- }
+ void cutv(char *u,char *v, char*t, char occ)
+ {
- /********************** nrerror ********************/
+   /* cuts string t into u and v where u ends before first occurence of char 'occ'
+      and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
- void nrerror(char error_text[])
+      gives u="abcedf" and v="ghi2j" */
- {
+   int i,lg,j,p=0;
-   fprintf(stderr,"ERREUR ...\n");
+   i=0;
-   fprintf(stderr,"%s\n",error_text);
+   for(j=0; j<=strlen(t)-1; j++) {
-   exit(EXIT_FAILURE);
+     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
- }
+   }
- /*********************** vector *******************/
- double *vector(int nl, int nh)
+   lg=strlen(t);
- {
+   for(j=0; j<p; j++) {
-   double *v;
+     (u[j] = t[j]);
-   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+   }
-   if (!v) nrerror("allocation failure in vector");
+      u[p]='\0';
-   return v-nl+NR_END;
- }
+    for(j=0; j<= lg; j++) {
+     if (j>=(p+1))(v[j-p-1] = t[j]);
- /************************ free vector ******************/
+   }
- void free_vector(double*v, int nl, int nh)
+ }
- {
-   free((FREE_ARG)(v+nl-NR_END));
+ /********************** nrerror ********************/
- }
+ void nrerror(char error_text[])
- /************************ivector *******************************/
+ {
- int *ivector(long nl,long nh)
+   fprintf(stderr,"ERREUR ...\n");
- {
+   fprintf(stderr,"%s\n",error_text);
-   int *v;
+   exit(EXIT_FAILURE);
-   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ }
-   if (!v) nrerror("allocation failure in ivector");
+ /*********************** vector *******************/
-   return v-nl+NR_END;
+ double *vector(int nl, int nh)
- }
+ {
+   double *v;
- /******************free ivector **************************/
+   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
- void free_ivector(int *v, long nl, long nh)
+   if (!v) nrerror("allocation failure in vector");
- {
+   return v-nl+NR_END;
-   free((FREE_ARG)(v+nl-NR_END));
+ }
- }
+ /************************ free vector ******************/
- /************************lvector *******************************/
+ void free_vector(double*v, int nl, int nh)
- long *lvector(long nl,long nh)
+ {
- {
+   free((FREE_ARG)(v+nl-NR_END));
-   long *v;
+ }
-   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   if (!v) nrerror("allocation failure in ivector");
+ /************************ivector *******************************/
-   return v-nl+NR_END;
+ int *ivector(long nl,long nh)
- }
+ {
+   int *v;
- /******************free lvector **************************/
+   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- void free_lvector(long *v, long nl, long nh)
+   if (!v) nrerror("allocation failure in ivector");
- {
+   return v-nl+NR_END;
-   free((FREE_ARG)(v+nl-NR_END));
+ }
- }
+ /******************free ivector **************************/
- /******************* imatrix *******************************/
+ void free_ivector(int *v, long nl, long nh)
- int **imatrix(long nrl, long nrh, long ncl, long nch)
+ {
-      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+   free((FREE_ARG)(v+nl-NR_END));
- {
+ }
-   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
-   int **m;
+ /************************lvector *******************************/
+ long *lvector(long nl,long nh)
-   /* allocate pointers to rows */
+ {
-   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+   long *v;
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
-   m += NR_END;
+   if (!v) nrerror("allocation failure in ivector");
-   m -= nrl;
+   return v-nl+NR_END;
+ }
-   /* allocate rows and set pointers to them */
+ /******************free lvector **************************/
-   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ void free_lvector(long *v, long nl, long nh)
-   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ {
-   m[nrl] += NR_END;
+   free((FREE_ARG)(v+nl-NR_END));
-   m[nrl] -= ncl;
+ }
-   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+ /******************* imatrix *******************************/
+ int **imatrix(long nrl, long nrh, long ncl, long nch)
-   /* return pointer to array of pointers to rows */
+      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-   return m;
+ {
- }
+   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+   int **m;
- /****************** free_imatrix *************************/
- void free_imatrix(m,nrl,nrh,ncl,nch)
+   /* allocate pointers to rows */
-       int **m;
+   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
-       long nch,ncl,nrh,nrl;
+   if (!m) nrerror("allocation failure 1 in matrix()");
-      /* free an int matrix allocated by imatrix() */
+   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)));
- /******************* matrix *******************************/
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- double **matrix(long nrl, long nrh, long ncl, long nch)
+   m[nrl] += NR_END;
- {
+   m[nrl] -= ncl;
-   long i, nrow=nrh-nrl+1, ncol=nch-ncl+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));
-   return m;
+   free((FREE_ARG) (m+nrl-NR_END));
-   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ }
-    */
- }
+ /******************* matrix *******************************/
+ double **matrix(long nrl, long nrh, long ncl, long nch)
- /*************************free matrix ************************/
+ {
- void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
- {
+   double **m;
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   free((FREE_ARG)(m+nrl-NR_END));
+   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- }
+   if (!m) nrerror("allocation failure 1 in matrix()");
+   m += NR_END;
- /******************* ma3x *******************************/
+   m -= nrl;
- double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
- {
+   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
-   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
-   double ***m;
+   m[nrl] += NR_END;
+   m[nrl] -= ncl;
-   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
-   if (!m) nrerror("allocation failure 1 in matrix()");
+   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-   m += NR_END;
+   return m;
-   m -= nrl;
+   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+    */
-   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;
+ /*************************free matrix ************************/
-   m[nrl] -= ncl;
+ void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+ {
-   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;
+ /******************* ma3x *******************************/
-   m[nrl][ncl] -= nll;
+ double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-   for (j=ncl+1; j<=nch; j++)
+ {
-     m[nrl][j]=m[nrl][j-1]+nlay;
+   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][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)
- {
+   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
-   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
-   free((FREE_ARG)(m[nrl]+ncl-NR_END));
+   m[nrl][ncl] += NR_END;
-   free((FREE_ARG)(m+nrl-NR_END));
+   m[nrl][ncl] -= nll;
- }
+   for (j=ncl+1; j<=nch; j++)
+     m[nrl][j]=m[nrl][j-1]+nlay;
- /*************** function subdirf ***********/
- char *subdirf(char fileres[])
+   for (i=nrl+1; i<=nrh; i++) {
- {
+     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
-   /* Caution optionfilefiname is hidden */
+     for (j=ncl+1; j<=nch; j++)
-   strcpy(tmpout,optionfilefiname);
+       m[i][j]=m[i][j-1]+nlay;
-   strcat(tmpout,"/"); /* Add to the right */
+   }
-   strcat(tmpout,fileres);
+   return m;
-   return tmpout;
+   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
- }
+            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
+   */
- /*************** function subdirf2 ***********/
+ }
- char *subdirf2(char fileres[], char *preop)
- {
+ /*************************free ma3x ************************/
+ void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-   /* Caution optionfilefiname is hidden */
+ {
-   strcpy(tmpout,optionfilefiname);
+   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
-   strcat(tmpout,"/");
+   free((FREE_ARG)(m[nrl]+ncl-NR_END));
-   strcat(tmpout,preop);
+   free((FREE_ARG)(m+nrl-NR_END));
-   strcat(tmpout,fileres);
+ }
-   return tmpout;
- }
+ /*************** function subdirf ***********/
+ char *subdirf(char fileres[])
- /*************** function subdirf3 ***********/
+ {
- char *subdirf3(char fileres[], char *preop, char *preop2)
+   /* Caution optionfilefiname is hidden */
- {
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/"); /* Add to the right */
-   /* Caution optionfilefiname is hidden */
+   strcat(tmpout,fileres);
-   strcpy(tmpout,optionfilefiname);
+   return tmpout;
-   strcat(tmpout,"/");
+ }
-   strcat(tmpout,preop);
-   strcat(tmpout,preop2);
+ /*************** function subdirf2 ***********/
-   strcat(tmpout,fileres);
+ char *subdirf2(char fileres[], char *preop)
-   return tmpout;
+ {
- }
+   /* Caution optionfilefiname is hidden */
- /***************** f1dim *************************/
+   strcpy(tmpout,optionfilefiname);
- extern int ncom;
+   strcat(tmpout,"/");
- extern double *pcom,*xicom;
+   strcat(tmpout,preop);
- extern double (*nrfunc)(double []);
+   strcat(tmpout,fileres);
+   return tmpout;
- double f1dim(double x)
+ }
- {
-   int j;
+ /*************** function subdirf3 ***********/
-   double f;
+ char *subdirf3(char fileres[], char *preop, char *preop2)
-   double *xt;
+ {
-   xt=vector(1,ncom);
+   /* Caution optionfilefiname is hidden */
-   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+   strcpy(tmpout,optionfilefiname);
-   f=(*nrfunc)(xt);
+   strcat(tmpout,"/");
-   free_vector(xt,1,ncom);
+   strcat(tmpout,preop);
-   return f;
+   strcat(tmpout,preop2);
- }
+   strcat(tmpout,fileres);
+   return tmpout;
- /*****************brent *************************/
+ }
- double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
- {
+ /***************** f1dim *************************/
-   int iter;
+ extern int ncom;
-   double a,b,d,etemp;
+ extern double *pcom,*xicom;
-   double fu,fv,fw,fx;
+ extern double (*nrfunc)(double []);
-   double ftemp;
-   double p,q,r,tol1,tol2,u,v,w,x,xm;
+ double f1dim(double x)
-   double e=0.0;
+ {
+   int j;
-   a=(ax < cx ? ax : cx);
+   double f;
-   b=(ax > cx ? ax : cx);
+   double *xt;
-   x=w=v=bx;
-   fw=fv=fx=(*f)(x);
+   xt=vector(1,ncom);
-   for (iter=1;iter<=ITMAX;iter++) {
+   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
-     xm=0.5*(a+b);
+   f=(*nrfunc)(xt);
-     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+   free_vector(xt,1,ncom);
-     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+   return f;
-     printf(".");fflush(stdout);
+ }
-     fprintf(ficlog,".");fflush(ficlog);
- #ifdef DEBUG
+ /*****************brent *************************/
-     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
-     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)))) { */
+   int iter;
- #endif
+   double a,b,d,etemp;
-     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+   double fu,fv,fw,fx;
-       *xmin=x;
+   double ftemp;
-       return fx;
+   double p,q,r,tol1,tol2,u,v,w,x,xm;
-     }
+   double e=0.0;
-     ftemp=fu;
-     if (fabs(e) > tol1) {
+   a=(ax < cx ? ax : cx);
-       r=(x-w)*(fx-fv);
+   b=(ax > cx ? ax : cx);
-       q=(x-v)*(fx-fw);
+   x=w=v=bx;
-       p=(x-v)*q-(x-w)*r;
+   fw=fv=fx=(*f)(x);
-       q=2.0*(q-r);
+   for (iter=1;iter<=ITMAX;iter++) {
-       if (q > 0.0) p = -p;
+     xm=0.5*(a+b);
-       q=fabs(q);
+     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
-       etemp=e;
+     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
-       e=d;
+     printf(".");fflush(stdout);
-       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+     fprintf(ficlog,".");fflush(ficlog);
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ #ifdef DEBUG
-       else {
+     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);
-         d=p/q;
+     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);
-         u=x+d;
+     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-         if (u-a < tol2 || b-u < tol2)
+ #endif
-           d=SIGN(tol1,xm-x);
+     if (fabs(x-xm) <= (tol2-0.5*(b-a))){
-       }
+       *xmin=x;
-     } else {
+       return fx;
-       d=CGOLD*(e=(x >= xm ? a-x : b-x));
+     }
-     }
+     ftemp=fu;
-     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+     if (fabs(e) > tol1) {
-     fu=(*f)(u);
+       r=(x-w)*(fx-fv);
-     if (fu <= fx) {
+       q=(x-v)*(fx-fw);
-       if (u >= x) a=x; else b=x;
+       p=(x-v)*q-(x-w)*r;
-       SHFT(v,w,x,u)
+       q=2.0*(q-r);
-         SHFT(fv,fw,fx,fu)
+       if (q > 0.0) p = -p;
-         } else {
+       q=fabs(q);
-           if (u < x) a=u; else b=u;
+       etemp=e;
-           if (fu <= fw || w == x) {
+       e=d;
-             v=w;
+       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-             w=u;
+         d=CGOLD*(e=(x >= xm ? a-x : b-x));
-             fv=fw;
+       else {
-             fw=fu;
+         d=p/q;
-           } else if (fu <= fv || v == x || v == w) {
+         u=x+d;
-             v=u;
+         if (u-a < tol2 || b-u < tol2)
-             fv=fu;
+           d=SIGN(tol1,xm-x);
-           }
+       }
-         }
+     } else {
-   }
+       d=CGOLD*(e=(x >= xm ? a-x : b-x));
-   nrerror("Too many iterations in brent");
+     }
-   *xmin=x;
+     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
-   return fx;
+     fu=(*f)(u);
- }
+     if (fu <= fx) {
+       if (u >= x) a=x; else b=x;
- /****************** mnbrak ***********************/
+       SHFT(v,w,x,u)
+         SHFT(fv,fw,fx,fu)
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+         } else {
-             double (*func)(double))
+           if (u < x) a=u; else b=u;
- {
+           if (fu <= fw || w == x) {
-   double ulim,u,r,q, dum;
+             v=w;
-   double fu;
+             w=u;
+             fv=fw;
-   *fa=(*func)(*ax);
+             fw=fu;
-   *fb=(*func)(*bx);
+           } else if (fu <= fv || v == x || v == w) {
-   if (*fb > *fa) {
+             v=u;
-     SHFT(dum,*ax,*bx,dum)
+             fv=fu;
-       SHFT(dum,*fb,*fa,dum)
+           }
-       }
+         }
-   *cx=(*bx)+GOLD*(*bx-*ax);
+   }
-   *fc=(*func)(*cx);
+   nrerror("Too many iterations in brent");
-   while (*fb > *fc) {
+   *xmin=x;
-     r=(*bx-*ax)*(*fb-*fc);
+   return fx;
-     q=(*bx-*cx)*(*fb-*fa);
+ }
-     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+ /****************** mnbrak ***********************/
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
-     if ((*bx-u)*(u-*cx) > 0.0) {
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
-       fu=(*func)(u);
+             double (*func)(double))
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ {
-       fu=(*func)(u);
+   double ulim,u,r,q, dum;
-       if (fu < *fc) {
+   double fu;
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-           SHFT(*fb,*fc,fu,(*func)(u))
+   *fa=(*func)(*ax);
-           }
+   *fb=(*func)(*bx);
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+   if (*fb > *fa) {
-       u=ulim;
+     SHFT(dum,*ax,*bx,dum)
-       fu=(*func)(u);
+       SHFT(dum,*fb,*fa,dum)
-     } else {
+       }
-       u=(*cx)+GOLD*(*cx-*bx);
+   *cx=(*bx)+GOLD*(*bx-*ax);
-       fu=(*func)(u);
+   *fc=(*func)(*cx);
-     }
+   while (*fb > *fc) {
-     SHFT(*ax,*bx,*cx,u)
+     r=(*bx-*ax)*(*fb-*fc);
-       SHFT(*fa,*fb,*fc,fu)
+     q=(*bx-*cx)*(*fb-*fa);
-       }
+     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
- }
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+     ulim=(*bx)+GLIMIT*(*cx-*bx);
- /*************** linmin ************************/
+     if ((*bx-u)*(u-*cx) > 0.0) {
+       fu=(*func)(u);
- int ncom;
+     } else if ((*cx-u)*(u-ulim) > 0.0) {
- double *pcom,*xicom;
+       fu=(*func)(u);
- double (*nrfunc)(double []);
+       if (fu < *fc) {
+         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
- void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+           SHFT(*fb,*fc,fu,(*func)(u))
- {
+           }
-   double brent(double ax, double bx, double cx,
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
-                double (*f)(double), double tol, double *xmin);
+       u=ulim;
-   double f1dim(double x);
+       fu=(*func)(u);
-   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+     } else {
-               double *fc, double (*func)(double));
+       u=(*cx)+GOLD*(*cx-*bx);
-   int j;
+       fu=(*func)(u);
-   double xx,xmin,bx,ax;
+     }
-   double fx,fb,fa;
+     SHFT(*ax,*bx,*cx,u)
+       SHFT(*fa,*fb,*fc,fu)
-   ncom=n;
+       }
-   pcom=vector(1,n);
+ }
-   xicom=vector(1,n);
-   nrfunc=func;
+ /*************** linmin ************************/
-   for (j=1;j<=n;j++) {
-     pcom[j]=p[j];
+ int ncom;
-     xicom[j]=xi[j];
+ double *pcom,*xicom;
-   }
+ double (*nrfunc)(double []);
-   ax=0.0;
-   xx=1.0;
+ void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ {
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+   double brent(double ax, double bx, double cx,
- #ifdef DEBUG
+                double (*f)(double), double tol, double *xmin);
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   double f1dim(double x);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
- #endif
+               double *fc, double (*func)(double));
-   for (j=1;j<=n;j++) {
+   int j;
-     xi[j] *= xmin;
+   double xx,xmin,bx,ax;
-     p[j] += xi[j];
+   double fx,fb,fa;
-   }
-   free_vector(xicom,1,n);
+   ncom=n;
-   free_vector(pcom,1,n);
+   pcom=vector(1,n);
- }
+   xicom=vector(1,n);
+   nrfunc=func;
- char *asc_diff_time(long time_sec, char ascdiff[])
+   for (j=1;j<=n;j++) {
- {
+     pcom[j]=p[j];
-   long sec_left, days, hours, minutes;
+     xicom[j]=xi[j];
-   days = (time_sec) / (60*60*24);
+   }
-   sec_left = (time_sec) % (60*60*24);
+   ax=0.0;
-   hours = (sec_left) / (60*60) ;
+   xx=1.0;
-   sec_left = (sec_left) %(60*60);
+   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
-   minutes = (sec_left) /60;
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-   sec_left = (sec_left) % (60);
+ #ifdef DEBUG
-   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-   return ascdiff;
+   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- }
+ #endif
+   for (j=1;j<=n;j++) {
- /*************** powell ************************/
+     xi[j] *= xmin;
- void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+     p[j] += xi[j];
-             double (*func)(double []))
+   }
- {
+   free_vector(xicom,1,n);
-   void linmin(double p[], double xi[], int n, double *fret,
+   free_vector(pcom,1,n);
-               double (*func)(double []));
+ }
-   int i,ibig,j;
-   double del,t,*pt,*ptt,*xit;
+ char *asc_diff_time(long time_sec, char ascdiff[])
-   double fp,fptt;
+ {
-   double *xits;
+   long sec_left, days, hours, minutes;
-   int niterf, itmp;
+   days = (time_sec) / (60*60*24);
+   sec_left = (time_sec) % (60*60*24);
-   pt=vector(1,n);
+   hours = (sec_left) / (60*60) ;
-   ptt=vector(1,n);
+   sec_left = (sec_left) %(60*60);
-   xit=vector(1,n);
+   minutes = (sec_left) /60;
-   xits=vector(1,n);
+   sec_left = (sec_left) % (60);
-   *fret=(*func)(p);
+   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
-   for (j=1;j<=n;j++) pt[j]=p[j];
+   return ascdiff;
-   for (*iter=1;;++(*iter)) {
+ }
-     fp=(*fret);
-     ibig=0;
+ /*************** powell ************************/
-     del=0.0;
+ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
-     last_time=curr_time;
+             double (*func)(double []))
-     (void) gettimeofday(&curr_time,&tzp);
+ {
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+   void linmin(double p[], double xi[], int n, double *fret,
-     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);
+               double (*func)(double []));
- /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
+   int i,ibig,j;
-    for (i=1;i<=n;i++) {
+   double del,t,*pt,*ptt,*xit;
-       printf(" %d %.12f",i, p[i]);
+   double fp,fptt;
-       fprintf(ficlog," %d %.12lf",i, p[i]);
+   double *xits;
-       fprintf(ficrespow," %.12lf", p[i]);
+   int niterf, itmp;
-     }
-     printf("\n");
+   pt=vector(1,n);
-     fprintf(ficlog,"\n");
+   ptt=vector(1,n);
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+   xit=vector(1,n);
-     if(*iter <=3){
+   xits=vector(1,n);
-       tm = *localtime(&curr_time.tv_sec);
+   *fret=(*func)(p);
-       strcpy(strcurr,asctime(&tm));
+   for (j=1;j<=n;j++) pt[j]=p[j];
- /*       asctime_r(&tm,strcurr); */
+   for (*iter=1;;++(*iter)) {
-       forecast_time=curr_time;
+     fp=(*fret);
-       itmp = strlen(strcurr);
+     ibig=0;
-       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
+     del=0.0;
-         strcurr[itmp-1]='\0';
+     last_time=curr_time;
-       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     (void) gettimeofday(&curr_time,&tzp);
-       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
+     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(niterf=10;niterf<=30;niterf+=10){
+     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);
-         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
-         tmf = *localtime(&forecast_time.tv_sec);
+    for (i=1;i<=n;i++) {
- /*      asctime_r(&tmf,strfor); */
+       printf(" %d %.12f",i, p[i]);
-         strcpy(strfor,asctime(&tmf));
+       fprintf(ficlog," %d %.12lf",i, p[i]);
-         itmp = strlen(strfor);
+       fprintf(ficrespow," %.12lf", p[i]);
-         if(strfor[itmp-1]=='\n')
+     }
-         strfor[itmp-1]='\0';
+     printf("\n");
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     fprintf(ficlog,"\n");
-         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+     fprintf(ficrespow,"\n");fflush(ficrespow);
-       }
+     if(*iter <=3){
-     }
+       tm = *localtime(&curr_time.tv_sec);
-     for (i=1;i<=n;i++) {
+       strcpy(strcurr,asctime(&tm));
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+ /*       asctime_r(&tm,strcurr); */
-       fptt=(*fret);
+       forecast_time=curr_time;
- #ifdef DEBUG
+       itmp = strlen(strcurr);
-       printf("fret=%lf \n",*fret);
+       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-       fprintf(ficlog,"fret=%lf \n",*fret);
+         strcurr[itmp-1]='\0';
- #endif
+       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       printf("%d",i);fflush(stdout);
+       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
-       fprintf(ficlog,"%d",i);fflush(ficlog);
+       for(niterf=10;niterf<=30;niterf+=10){
-       linmin(p,xit,n,fret,func);
+         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
-       if (fabs(fptt-(*fret)) > del) {
+         tmf = *localtime(&forecast_time.tv_sec);
-         del=fabs(fptt-(*fret));
+ /*      asctime_r(&tmf,strfor); */
-         ibig=i;
+         strcpy(strfor,asctime(&tmf));
-       }
+         itmp = strlen(strfor);
- #ifdef DEBUG
+         if(strfor[itmp-1]=='\n')
-       printf("%d %.12e",i,(*fret));
+         strfor[itmp-1]='\0';
-       fprintf(ficlog,"%d %.12e",i,(*fret));
+         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);
-       for (j=1;j<=n;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);
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+       }
-         printf(" x(%d)=%.12e",j,xit[j]);
+     }
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+     for (i=1;i<=n;i++) {
-       }
+       for (j=1;j<=n;j++) xit[j]=xi[j][i];
-       for(j=1;j<=n;j++) {
+       fptt=(*fret);
-         printf(" p=%.12e",p[j]);
+ #ifdef DEBUG
-         fprintf(ficlog," p=%.12e",p[j]);
+       printf("fret=%lf \n",*fret);
-       }
+       fprintf(ficlog,"fret=%lf \n",*fret);
-       printf("\n");
+ #endif
-       fprintf(ficlog,"\n");
+       printf("%d",i);fflush(stdout);
- #endif
+       fprintf(ficlog,"%d",i);fflush(ficlog);
-     }
+       linmin(p,xit,n,fret,func);
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+       if (fabs(fptt-(*fret)) > del) {
- #ifdef DEBUG
+         del=fabs(fptt-(*fret));
-       int k[2],l;
+         ibig=i;
-       k[0]=1;
+       }
-       k[1]=-1;
+ #ifdef DEBUG
-       printf("Max: %.12e",(*func)(p));
+       printf("%d %.12e",i,(*fret));
-       fprintf(ficlog,"Max: %.12e",(*func)(p));
+       fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
-         printf(" %.12e",p[j]);
+         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         fprintf(ficlog," %.12e",p[j]);
+         printf(" x(%d)=%.12e",j,xit[j]);
-       }
+         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
-       printf("\n");
+       }
-       fprintf(ficlog,"\n");
+       for(j=1;j<=n;j++) {
-       for(l=0;l<=1;l++) {
+         printf(" p=%.12e",p[j]);
-         for (j=1;j<=n;j++) {
+         fprintf(ficlog," p=%.12e",p[j]);
-           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+       }
-           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       printf("\n");
-           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+       fprintf(ficlog,"\n");
-         }
+ #endif
-         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     }
-         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-       }
+ #ifdef DEBUG
- #endif
+       int k[2],l;
+       k[0]=1;
+       k[1]=-1;
-       free_vector(xit,1,n);
+       printf("Max: %.12e",(*func)(p));
-       free_vector(xits,1,n);
+       fprintf(ficlog,"Max: %.12e",(*func)(p));
-       free_vector(ptt,1,n);
+       for (j=1;j<=n;j++) {
-       free_vector(pt,1,n);
+         printf(" %.12e",p[j]);
-       return;
+         fprintf(ficlog," %.12e",p[j]);
-     }
+       }
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+       printf("\n");
-     for (j=1;j<=n;j++) {
+       fprintf(ficlog,"\n");
-       ptt[j]=2.0*p[j]-pt[j];
+       for(l=0;l<=1;l++) {
-       xit[j]=p[j]-pt[j];
+         for (j=1;j<=n;j++) {
-       pt[j]=p[j];
+           ptt[j]=p[j]+(p[j]-pt[j])*k[l];
-     }
+           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     fptt=(*func)(ptt);
+           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
-     if (fptt < fp) {
+         }
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-       if (t < 0.0) {
+         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
-         linmin(p,xit,n,fret,func);
+       }
-         for (j=1;j<=n;j++) {
+ #endif
-           xi[j][ibig]=xi[j][n];
-           xi[j][n]=xit[j];
-         }
+       free_vector(xit,1,n);
- #ifdef DEBUG
+       free_vector(xits,1,n);
-         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+       free_vector(ptt,1,n);
-         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+       free_vector(pt,1,n);
-         for(j=1;j<=n;j++){
+       return;
-           printf(" %.12e",xit[j]);
+     }
-           fprintf(ficlog," %.12e",xit[j]);
+     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-         }
+     for (j=1;j<=n;j++) {
-         printf("\n");
+       ptt[j]=2.0*p[j]-pt[j];
-         fprintf(ficlog,"\n");
+       xit[j]=p[j]-pt[j];
- #endif
+       pt[j]=p[j];
-       }
+     }
-     }
+     fptt=(*func)(ptt);
-   }
+     if (fptt < fp) {
- }
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+       if (t < 0.0) {
- /**** Prevalence limit (stable or period prevalence)  ****************/
+         linmin(p,xit,n,fret,func);
+         for (j=1;j<=n;j++) {
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+           xi[j][ibig]=xi[j][n];
- {
+           xi[j][n]=xit[j];
-   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+         }
-      matrix by transitions matrix until convergence is reached */
+ #ifdef DEBUG
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   int i, ii,j,k;
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-   double min, max, maxmin, maxmax,sumnew=0.;
+         for(j=1;j<=n;j++){
-   double **matprod2();
+           printf(" %.12e",xit[j]);
-   double **out, cov[NCOVMAX], **pmij();
+           fprintf(ficlog," %.12e",xit[j]);
-   double **newm;
+         }
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+         printf("\n");
+         fprintf(ficlog,"\n");
-   for (ii=1;ii<=nlstate+ndeath;ii++)
+ #endif
-     for (j=1;j<=nlstate+ndeath;j++){
+       }
-       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
-     }
+   }
+ }
-    cov[1]=1.;
+ /**** Prevalence limit (stable or period prevalence)  ****************/
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-     newm=savm;
+ {
-     /* Covariates have to be included here again */
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-      cov[2]=agefin;
+      matrix by transitions matrix until convergence is reached */
-       for (k=1; k<=cptcovn;k++) {
+   int i, ii,j,k;
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+   double min, max, maxmin, maxmax,sumnew=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]]);*/
+   double **matprod2();
-       }
+   double **out, cov[NCOVMAX+1], **pmij();
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   double **newm;
-       for (k=1; k<=cptcovprod;k++)
+   double agefin, delaymax=50 ; /* Max number of years to converge */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     for (j=1;j<=nlstate+ndeath;j++){
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       /*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);
+    cov[1]=1.;
-     savm=oldm;
-     oldm=newm;
+  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-     maxmax=0.;
+   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
-     for(j=1;j<=nlstate;j++){
+     newm=savm;
-       min=1.;
+     /* Covariates have to be included here again */
-       max=0.;
+      cov[2]=agefin;
-       for(i=1; i<=nlstate; i++) {
-         sumnew=0;
+       for (k=1; k<=cptcovn;k++) {
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         prlim[i][j]= newm[i][j]/(1-sumnew);
+         /*      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]]);*/
-         max=FMAX(max,prlim[i][j]);
+       }
-         min=FMIN(min,prlim[i][j]);
+       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       }
+       for (k=1; k<=cptcovprod;k++)
-       maxmin=max-min;
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-       maxmax=FMAX(maxmax,maxmin);
-     }
+       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-     if(maxmax < ftolpl){
+       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       return prlim;
+       /*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);
-   }
- }
+     savm=oldm;
+     oldm=newm;
- /*************** transition probabilities ***************/
+     maxmax=0.;
+     for(j=1;j<=nlstate;j++){
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+       min=1.;
- {
+       max=0.;
-   double s1, s2;
+       for(i=1; i<=nlstate; i++) {
-   /*double t34;*/
+         sumnew=0;
-   int i,j,j1, nc, ii, jj;
+         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+         prlim[i][j]= newm[i][j]/(1-sumnew);
-     for(i=1; i<= nlstate; i++){
+         max=FMAX(max,prlim[i][j]);
-       for(j=1; j<i;j++){
+         min=FMIN(min,prlim[i][j]);
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+       }
-           /*s2 += param[i][j][nc]*cov[nc];*/
+       maxmin=max-min;
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+       maxmax=FMAX(maxmax,maxmin);
- /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
+     }
-         }
+     if(maxmax < ftolpl){
-         ps[i][j]=s2;
+       return prlim;
- /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
+     }
-       }
+   }
-       for(j=i+1; j<=nlstate+ndeath;j++){
+ }
-         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*************** transition probabilities ***************/
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
-         }
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-         ps[i][j]=s2;
+ {
-       }
+   double s1, s2;
-     }
+   /*double t34;*/
-     /*ps[3][2]=1;*/
+   int i,j,j1, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
-       s1=0;
+       for(j=1; j<i;j++){
-       for(j=1; j<i; j++)
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-         s1+=exp(ps[i][j]);
+           /*s2 += param[i][j][nc]*cov[nc];*/
-       for(j=i+1; j<=nlstate+ndeath; j++)
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-         s1+=exp(ps[i][j]);
+ /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
-       ps[i][i]=1./(s1+1.);
+         }
-       for(j=1; j<i; j++)
+         ps[i][j]=s2;
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+       }
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       for(j=i+1; j<=nlstate+ndeath;j++){
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
-     } /* end i */
+           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+         }
-       for(jj=1; jj<= nlstate+ndeath; jj++){
+         ps[i][j]=s2;
-         ps[ii][jj]=0;
+       }
-         ps[ii][ii]=1;
+     }
-       }
+     /*ps[3][2]=1;*/
-     }
+     for(i=1; i<= nlstate; i++){
+       s1=0;
- /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
+       for(j=1; j<i; j++){
- /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
+         s1+=exp(ps[i][j]);
- /*         printf("ddd %lf ",ps[ii][jj]); */
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
- /*       } */
+       }
- /*       printf("\n "); */
+       for(j=i+1; j<=nlstate+ndeath; j++){
- /*        } */
+         s1+=exp(ps[i][j]);
- /*        printf("\n ");printf("%lf ",cov[2]); */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-        /*
+       }
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       ps[i][i]=1./(s1+1.);
-       goto end;*/
+       for(j=1; j<i; j++)
-     return ps;
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
- }
+       for(j=i+1; j<=nlstate+ndeath; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
- /**************** Product of 2 matrices ******************/
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
- double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
- {
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+       for(jj=1; jj<= nlstate+ndeath; jj++){
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+         ps[ii][jj]=0;
-   /* in, b, out are matrice of pointers which should have been initialized
+         ps[ii][ii]=1;
-      before: only the contents of out is modified. The function returns
+       }
-      a pointer to pointers identical to out */
+     }
-   long i, j, k;
-   for(i=nrl; i<= nrh; i++)
-     for(k=ncolol; k<=ncoloh; k++)
+ /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
-       for(j=ncl,out[i][k]=0.; j<=nch; j++)
+ /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
-         out[i][k] +=in[i][j]*b[j][k];
+ /*         printf("ddd %lf ",ps[ii][jj]); */
+ /*       } */
-   return out;
+ /*       printf("\n "); */
- }
+ /*        } */
+ /*        printf("\n ");printf("%lf ",cov[2]); */
+        /*
- /************* Higher Matrix Product ***************/
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       goto end;*/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+     return ps;
- {
+ }
-   /* Computes the transition matrix starting at age 'age' over
-      'nhstepm*hstepm*stepm' months (i.e. until
+ /**************** Product of 2 matrices ******************/
-      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-      nhstepm*hstepm matrices.
+ double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
-      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+ {
-      (typically every 2 years instead of every month which is too big
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
-      for the memory).
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
-      Model is determined by parameters x and covariates have to be
+   /* in, b, out are matrice of pointers which should have been initialized
-      included manually here.
+      before: only the contents of out is modified. The function returns
+      a pointer to pointers identical to out */
-      */
+   long i, j, k;
+   for(i=nrl; i<= nrh; i++)
-   int i, j, d, h, k;
+     for(k=ncolol; k<=ncoloh; k++)
-   double **out, cov[NCOVMAX];
+       for(j=ncl,out[i][k]=0.; j<=nch; j++)
-   double **newm;
+         out[i][k] +=in[i][j]*b[j][k];
-   /* Hstepm could be zero and should return the unit matrix */
+   return out;
-   for (i=1;i<=nlstate+ndeath;i++)
+ }
-     for (j=1;j<=nlstate+ndeath;j++){
-       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       po[i][j][0]=(i==j ? 1.0 : 0.0);
+ /************* Higher Matrix Product ***************/
-     }
-   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-   for(h=1; h <=nhstepm; h++){
+ {
-     for(d=1; d <=hstepm; d++){
+   /* Computes the transition matrix starting at age 'age' over
-       newm=savm;
+      'nhstepm*hstepm*stepm' months (i.e. until
-       /* Covariates have to be included here again */
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-       cov[1]=1.;
+      nhstepm*hstepm matrices.
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+      (typically every 2 years instead of every month which is too big
-       for (k=1; k<=cptcovage;k++)
+      for the memory).
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+      Model is determined by parameters x and covariates have to be
-       for (k=1; k<=cptcovprod;k++)
+      included manually here.
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+      */
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+   int i, j, d, h, k;
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+   double **out, cov[NCOVMAX+1];
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+   double **newm;
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-       savm=oldm;
+   /* Hstepm could be zero and should return the unit matrix */
-       oldm=newm;
+   for (i=1;i<=nlstate+ndeath;i++)
-     }
+     for (j=1;j<=nlstate+ndeath;j++){
-     for(i=1; i<=nlstate+ndeath; i++)
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
-       for(j=1;j<=nlstate+ndeath;j++) {
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
-         po[i][j][h]=newm[i][j];
+     }
-         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
-          */
+   for(h=1; h <=nhstepm; h++){
-       }
+     for(d=1; d <=hstepm; d++){
-   } /* end h */
+       newm=savm;
-   return po;
+       /* Covariates have to be included here again */
- }
+       cov[1]=1.;
+       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       for (k=1; k<=cptcovn;k++)
- /*************** log-likelihood *************/
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- double func( double *x)
+       for (k=1; k<=cptcovage;k++)
- {
+         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-   int i, ii, j, k, mi, d, kk;
+       for (k=1; k<=cptcovprod;k++)
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-   double **out;
-   double sw; /* Sum of weights */
-   double lli; /* Individual log likelihood */
+       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
-   int s1, s2;
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-   double bbh, survp;
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
-   long ipmx;
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
-   /*extern weight */
+       savm=oldm;
-   /* We are differentiating ll according to initial status */
+       oldm=newm;
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+     }
-   /*for(i=1;i<imx;i++)
+     for(i=1; i<=nlstate+ndeath; i++)
-     printf(" %d\n",s[4][i]);
+       for(j=1;j<=nlstate+ndeath;j++) {
-   */
+         po[i][j][h]=newm[i][j];
-   cov[1]=1.;
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+     /*printf("h=%d ",h);*/
+   } /* end h */
-   if(mle==1){
+ /*     printf("\n H=%d \n",h); */
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   return po;
-       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++){
+ /*************** log-likelihood *************/
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ double func( double *x)
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ {
-           }
+   int i, ii, j, k, mi, d, kk;
-         for(d=0; d<dh[mi][i]; d++){
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-           newm=savm;
+   double **out;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   double sw; /* Sum of weights */
-           for (kk=1; kk<=cptcovage;kk++) {
+   double lli; /* Individual log likelihood */
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   int s1, s2;
-           }
+   double bbh, survp;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   long ipmx;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   /*extern weight */
-           savm=oldm;
+   /* We are differentiating ll according to initial status */
-           oldm=newm;
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
-         } /* end mult */
+   /*for(i=1;i<imx;i++)
+     printf(" %d\n",s[4][i]);
-         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+   */
-         /* But now since version 0.9 we anticipate for bias at large stepm.
+   cov[1]=1.;
-          * If stepm is larger than one month (smallest stepm) and if the exact delay
-          * (in months) between two waves is not a multiple of stepm, we rounded to
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-          * the nearest (and in case of equal distance, to the lowest) interval but now
-          * we keep into memory the bias bh[mi][i] and also the previous matrix product
+   if(mle==1){
-          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-          * probability in order to take into account the bias as a fraction of the way
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+       for(mi=1; mi<= wav[i]-1; mi++){
-          * -stepm/2 to stepm/2 .
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-          * For stepm=1 the results are the same as for previous versions of Imach.
+           for (j=1;j<=nlstate+ndeath;j++){
-          * For stepm > 1 the results are less biased than in previous versions.
+             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++){
-         bbh=(double)bh[mi][i]/(double)stepm;
+           newm=savm;
-         /* bias bh is positive if real duration
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-          * is higher than the multiple of stepm and negative otherwise.
+           for (kk=1; kk<=cptcovage;kk++) {
-          */
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         /* 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){
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           /* i.e. if s2 is a death state and if the date of death is known
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-              then the contribution to the likelihood is the probability to
+           savm=oldm;
-              die between last step unit time and current  step unit time,
+           oldm=newm;
-              which is also equal to probability to die before dh
+         } /* end mult */
-              minus probability to die before dh-stepm .
-              In version up to 0.92 likelihood was computed
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-         as if date of death was unknown. Death was treated as any other
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-         health state: the date of the interview describes the actual state
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-         and not the date of a change in health state. The former idea was
+          * (in months) between two waves is not a multiple of stepm, we rounded to
-         to consider that at each interview the state was recorded
+          * the nearest (and in case of equal distance, to the lowest) interval but now
-         (healthy, disable or death) and IMaCh was corrected; but when we
+          * we keep into memory the bias bh[mi][i] and also the previous matrix product
-         introduced the exact date of death then we should have modified
+          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
-         the contribution of an exact death to the likelihood. This new
+          * probability in order to take into account the bias as a fraction of the way
-         contribution is smaller and very dependent of the step unit
+          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-         stepm. It is no more the probability to die between last interview
+          * -stepm/2 to stepm/2 .
-         and month of death but the probability to survive from last
+          * For stepm=1 the results are the same as for previous versions of Imach.
-         interview up to one month before death multiplied by the
+          * For stepm > 1 the results are less biased than in previous versions.
-         probability to die within a month. Thanks to Chris
+          */
-         Jackson for correcting this bug.  Former versions increased
+         s1=s[mw[mi][i]][i];
-         mortality artificially. The bad side is that we add another loop
+         s2=s[mw[mi+1][i]][i];
-         which slows down the processing. The difference can be up to 10%
+         bbh=(double)bh[mi][i]/(double)stepm;
-         lower mortality.
+         /* bias bh is positive if real duration
-           */
+          * is higher than the multiple of stepm and negative otherwise.
-           lli=log(out[s1][s2] - savm[s1][s2]);
+          */
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         if( s2 > nlstate){
-         } else if  (s2==-2) {
+           /* i.e. if s2 is a death state and if the date of death is known
-           for (j=1,survp=0. ; j<=nlstate; j++)
+              then the contribution to the likelihood is the probability to
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+              die between last step unit time and current  step unit time,
-           /*survp += out[s1][j]; */
+              which is also equal to probability to die before dh
-           lli= log(survp);
+              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
-         else if  (s2==-4) {
+         health state: the date of the interview describes the actual state
-           for (j=3,survp=0. ; j<=nlstate; j++)
+         and not the date of a change in health state. The former idea was
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         to consider that at each interview the state was recorded
-           lli= log(survp);
+         (healthy, disable or death) and IMaCh was corrected; but when we
-         }
+         introduced the exact date of death then we should have modified
+         the contribution of an exact death to the likelihood. This new
-         else if  (s2==-5) {
+         contribution is smaller and very dependent of the step unit
-           for (j=1,survp=0. ; j<=2; j++)
+         stepm. It is no more the probability to die between last interview
-             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+         and month of death but the probability to survive from last
-           lli= log(survp);
+         interview up to one month before death multiplied by the
-         }
+         probability to die within a month. Thanks to Chris
+         Jackson for correcting this bug.  Former versions increased
-         else{
+         mortality artificially. The bad side is that we add another loop
-           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         which slows down the processing. The difference can be up to 10%
-           /*  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 */
+         lower mortality.
-         }
+           */
-         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         /*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); */
-         ipmx +=1;
+         } else if  (s2==-2) {
-         sw += weight[i];
+           for (j=1,survp=0. ; j<=nlstate; j++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       } /* end of wave */
+           /*survp += out[s1][j]; */
-     } /* end of individual */
+           lli= log(survp);
-   }  else if(mle==2){
+         }
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+         else if  (s2==-4) {
-       for(mi=1; mi<= wav[i]-1; mi++){
+           for (j=3,survp=0. ; j<=nlstate; 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 if  (s2==-5) {
-         for(d=0; d<=dh[mi][i]; d++){
+           for (j=1,survp=0. ; j<=2; 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++) {
+         }
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           }
+         else{
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
-           savm=oldm;
+         }
-           oldm=newm;
+         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
-         } /* end mult */
+         /*if(lli ==000.0)*/
+         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
-         s1=s[mw[mi][i]][i];
+         ipmx +=1;
-         s2=s[mw[mi+1][i]][i];
+         sw += weight[i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         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 */
+       } /* end of wave */
-         ipmx +=1;
+     } /* end of individual */
-         sw += weight[i];
+   }  else if(mle==2){
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       } /* end of wave */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     } /* end of individual */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   }  else if(mle==3){  /* exponential inter-extrapolation */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           for (j=1;j<=nlstate+ndeath;j++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(mi=1; mi<= wav[i]-1; mi++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+           }
-           for (j=1;j<=nlstate+ndeath;j++){
+         for(d=0; d<=dh[mi][i]; d++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           newm=savm;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           }
+           for (kk=1; kk<=cptcovage;kk++) {
-         for(d=0; d<dh[mi][i]; d++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           newm=savm;
+           }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           for (kk=1; kk<=cptcovage;kk++) {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           savm=oldm;
-           }
+           oldm=newm;
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+         } /* end mult */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-           savm=oldm;
+         s1=s[mw[mi][i]][i];
-           oldm=newm;
+         s2=s[mw[mi+1][i]][i];
-         } /* end mult */
+         bbh=(double)bh[mi][i]/(double)stepm;
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
-         s1=s[mw[mi][i]][i];
+         ipmx +=1;
-         s2=s[mw[mi+1][i]][i];
+         sw += weight[i];
-         bbh=(double)bh[mi][i]/(double)stepm;
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+       } /* end of wave */
-         ipmx +=1;
+     } /* end of individual */
-         sw += weight[i];
+   }  else if(mle==3){  /* exponential inter-extrapolation */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       } /* end of wave */
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-     } /* end of individual */
+       for(mi=1; mi<= wav[i]-1; mi++){
-   }else if (mle==4){  /* ml=4 no inter-extrapolation */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           for (j=1;j<=nlstate+ndeath;j++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       for(mi=1; mi<= wav[i]-1; mi++){
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+           }
-           for (j=1;j<=nlstate+ndeath;j++){
+         for(d=0; d<dh[mi][i]; d++){
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           newm=savm;
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-           }
+           for (kk=1; kk<=cptcovage;kk++) {
-         for(d=0; d<dh[mi][i]; d++){
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           newm=savm;
+           }
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           for (kk=1; kk<=cptcovage;kk++) {
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           savm=oldm;
-           }
+           oldm=newm;
+         } /* end mult */
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         s1=s[mw[mi][i]][i];
-           savm=oldm;
+         s2=s[mw[mi+1][i]][i];
-           oldm=newm;
+         bbh=(double)bh[mi][i]/(double)stepm;
-         } /* 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])); /* exponential inter-extrapolation */
+         ipmx +=1;
-         s1=s[mw[mi][i]][i];
+         sw += weight[i];
-         s2=s[mw[mi+1][i]][i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         if( s2 > nlstate){
+       } /* end of wave */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+     } /* end of individual */
-         }else{
+   }else if (mle==4){  /* ml=4 no inter-extrapolation */
-           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++){
-         }
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-         ipmx +=1;
+       for(mi=1; mi<= wav[i]-1; mi++){
-         sw += weight[i];
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+           for (j=1;j<=nlstate+ndeath;j++){
- /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-       } /* end of wave */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-     } /* end of individual */
+           }
-   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
+         for(d=0; d<dh[mi][i]; d++){
-     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+           newm=savm;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-       for(mi=1; mi<= wav[i]-1; mi++){
+           for (kk=1; kk<=cptcovage;kk++) {
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-           for (j=1;j<=nlstate+ndeath;j++){
+           }
-             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-             savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-           }
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-         for(d=0; d<dh[mi][i]; d++){
+           savm=oldm;
-           newm=savm;
+           oldm=newm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         } /* end mult */
-           for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+         s1=s[mw[mi][i]][i];
-           }
+         s2=s[mw[mi+1][i]][i];
+         if( s2 > nlstate){
-           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+           lli=log(out[s1][s2] - savm[s1][s2]);
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         }else{
-           savm=oldm;
+           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-           oldm=newm;
+         }
-         } /* end mult */
+         ipmx +=1;
+         sw += weight[i];
-         s1=s[mw[mi][i]][i];
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-         s2=s[mw[mi+1][i]][i];
+ /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
-         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
+       } /* end of wave */
-         ipmx +=1;
+     } /* end of individual */
-         sw += weight[i];
+   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
-         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
+       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       } /* end of wave */
+       for(mi=1; mi<= wav[i]-1; mi++){
-     } /* end of individual */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-   } /* End of if */
+           for (j=1;j<=nlstate+ndeath;j++){
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+           }
-   return -l;
+         for(d=0; d<dh[mi][i]; d++){
- }
+           newm=savm;
+           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- /*************** log-likelihood *************/
+           for (kk=1; kk<=cptcovage;kk++) {
- double funcone( double *x)
+             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- {
+           }
-   /* Same as likeli but slower because of a lot of printf and if */
-   int i, ii, j, k, mi, d, kk;
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-   double **out;
+           savm=oldm;
-   double lli; /* Individual log likelihood */
+           oldm=newm;
-   double llt;
+         } /* end mult */
-   int s1, s2;
-   double bbh, survp;
+         s1=s[mw[mi][i]][i];
-   /*extern weight */
+         s2=s[mw[mi+1][i]][i];
-   /* We are differentiating ll according to initial status */
+         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
-   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+         ipmx +=1;
-   /*for(i=1;i<imx;i++)
+         sw += weight[i];
-     printf(" %d\n",s[4][i]);
+         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-   */
+         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
-   cov[1]=1.;
+       } /* end of wave */
+     } /* end of individual */
-   for(k=1; k<=nlstate; k++) ll[k]=0.;
+   } /* End of if */
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     for(mi=1; mi<= wav[i]-1; mi++){
+   return -l;
-       for (ii=1;ii<=nlstate+ndeath;ii++)
+ }
-         for (j=1;j<=nlstate+ndeath;j++){
-           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ /*************** log-likelihood *************/
-           savm[ii][j]=(ii==j ? 1.0 : 0.0);
+ double funcone( double *x)
-         }
+ {
-       for(d=0; d<dh[mi][i]; d++){
+   /* Same as likeli but slower because of a lot of printf and if */
-         newm=savm;
+   int i, ii, j, k, mi, d, kk;
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
-         for (kk=1; kk<=cptcovage;kk++) {
+   double **out;
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+   double lli; /* Individual log likelihood */
-         }
+   double llt;
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+   int s1, s2;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+   double bbh, survp;
-         savm=oldm;
+   /*extern weight */
-         oldm=newm;
+   /* We are differentiating ll according to initial status */
-       } /* end mult */
+   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+   /*for(i=1;i<imx;i++)
-       s1=s[mw[mi][i]][i];
+     printf(" %d\n",s[4][i]);
-       s2=s[mw[mi+1][i]][i];
+   */
-       bbh=(double)bh[mi][i]/(double)stepm;
+   cov[1]=1.;
-       /* bias is positive if real duration
-        * is higher than the multiple of stepm and negative otherwise.
+   for(k=1; k<=nlstate; k++) ll[k]=0.;
-        */
-       if( s2 > nlstate && (mle <5) ){  /* Jackson */
+   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-         lli=log(out[s1][s2] - savm[s1][s2]);
+     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
-       } else if  (s2==-2) {
+     for(mi=1; mi<= wav[i]-1; mi++){
-         for (j=1,survp=0. ; j<=nlstate; 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);
-       }else if (mle==1){
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         }
-       } else if(mle==2){
+       for(d=0; d<dh[mi][i]; d++){
-         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 */
+         newm=savm;
-       } else if(mle==3){  /* exponential inter-extrapolation */
+         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-         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 (kk=1; kk<=cptcovage;kk++) {
-       } else if (mle==4){  /* mle=4 no inter-extrapolation */
+           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-         lli=log(out[s1][s2]); /* Original formula */
+         }
-       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-         lli=log(out[s1][s2]); /* Original formula */
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-       } /* End of if */
+         savm=oldm;
-       ipmx +=1;
+         oldm=newm;
-       sw += weight[i];
+       } /* end mult */
-       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]); */
+       s1=s[mw[mi][i]][i];
-       if(globpr){
+       s2=s[mw[mi+1][i]][i];
-         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+       bbh=(double)bh[mi][i]/(double)stepm;
-  %11.6f %11.6f %11.6f ", \
+       /* bias is positive if real duration
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+        * is higher than the multiple of stepm and negative otherwise.
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+        */
-         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+       if( s2 > nlstate && (mle <5) ){  /* Jackson */
-           llt +=ll[k]*gipmx/gsw;
+         lli=log(out[s1][s2] - savm[s1][s2]);
-           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+       } else if  (s2==-2) {
-         }
+         for (j=1,survp=0. ; j<=nlstate; j++)
-         fprintf(ficresilk," %10.6f\n", -llt);
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-       }
+         lli= log(survp);
-     } /* end of wave */
+       }else if (mle==1){
-   } /* end of individual */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+       } else if(mle==2){
-   /* printf("l1=%f l2=%f ",ll[1],ll[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 */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+       } else if(mle==3){  /* exponential inter-extrapolation */
-   if(globpr==0){ /* First time we count the contributions and weights */
+         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 */
-     gipmx=ipmx;
+       } else if (mle==4){  /* mle=4 no inter-extrapolation */
-     gsw=sw;
+         lli=log(out[s1][s2]); /* Original formula */
-   }
+       } else{  /* mle=0 back to 1 */
-   return -l;
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- }
+         /*lli=log(out[s1][s2]); */ /* Original formula */
+       } /* End of if */
+       ipmx +=1;
- /*************** function likelione ***********/
+       sw += weight[i];
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+       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]); */
-   /* This routine should help understanding what is done with
+       if(globpr){
-      the selection of individuals/waves and
+         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
-      to check the exact contribution to the likelihood.
+  %11.6f %11.6f %11.6f ", \
-      Plotting could be done.
+                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
-    */
+*weight[i]*lli,out[s1][s2],savm[s1][s2]);
-   int k;
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+           llt +=ll[k]*gipmx/gsw;
-   if(*globpri !=0){ /* Just counts and sums, no printings */
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-     strcpy(fileresilk,"ilk");
+         }
-     strcat(fileresilk,fileres);
+         fprintf(ficresilk," %10.6f\n", -llt);
-     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
+       }
-       printf("Problem with resultfile: %s\n", fileresilk);
+     } /* end of wave */
-       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
+   } /* end of individual */
-     }
+   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
+   if(globpr==0){ /* First time we count the contributions and weights */
-     for(k=1; k<=nlstate; k++)
+     gipmx=ipmx;
-       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
+     gsw=sw;
-     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
+   }
-   }
+   return -l;
+ }
-   *fretone=(*funcone)(p);
-   if(*globpri !=0){
-     fclose(ficresilk);
+ /*************** function likelione ***********/
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-     fflush(fichtm);
+ {
-   }
+   /* This routine should help understanding what is done with
-   return;
+      the selection of individuals/waves and
- }
+      to check the exact contribution to the likelihood.
+      Plotting could be done.
+    */
- /*********** Maximum Likelihood Estimation ***************/
+   int k;
- void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+   if(*globpri !=0){ /* Just counts and sums, no printings */
- {
+     strcpy(fileresilk,"ilk");
-   int i,j, iter;
+     strcat(fileresilk,fileres);
-   double **xi;
+     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
-   double fret;
+       printf("Problem with resultfile: %s\n", fileresilk);
-   double fretone; /* Only one call to likelihood */
+       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
-   /*  char filerespow[FILENAMELENGTH];*/
+     }
-   xi=matrix(1,npar,1,npar);
+     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-   for (i=1;i<=npar;i++)
+     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
-     for (j=1;j<=npar;j++)
+     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
-       xi[i][j]=(i==j ? 1.0 : 0.0);
+     for(k=1; k<=nlstate; k++)
-   printf("Powell\n");  fprintf(ficlog,"Powell\n");
+       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
-   strcpy(filerespow,"pow");
+     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
-   strcat(filerespow,fileres);
+   }
-   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", filerespow);
+   *fretone=(*funcone)(p);
-     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+   if(*globpri !=0){
-   }
+     fclose(ficresilk);
-   fprintf(ficrespow,"# Powell\n# iter -2*LL");
+     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
-   for (i=1;i<=nlstate;i++)
+     fflush(fichtm);
-     for(j=1;j<=nlstate+ndeath;j++)
+   }
-       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   return;
-   fprintf(ficrespow,"\n");
+ }
-   powell(p,xi,npar,ftol,&iter,&fret,func);
+ /*********** Maximum Likelihood Estimation ***************/
-   free_matrix(xi,1,npar,1,npar);
-   fclose(ficrespow);
+ void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-   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));
+   int i,j, iter;
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   double **xi;
+   double fret;
- }
+   double fretone; /* Only one call to likelihood */
+   /*  char filerespow[FILENAMELENGTH];*/
- /**** Computes Hessian and covariance matrix ***/
+   xi=matrix(1,npar,1,npar);
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+   for (i=1;i<=npar;i++)
- {
+     for (j=1;j<=npar;j++)
-   double  **a,**y,*x,pd;
+       xi[i][j]=(i==j ? 1.0 : 0.0);
-   double **hess;
+   printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   int i, j,jk;
+   strcpy(filerespow,"pow");
-   int *indx;
+   strcat(filerespow,fileres);
+   if((ficrespow=fopen(filerespow,"w"))==NULL) {
-   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
+     printf("Problem with resultfile: %s\n", filerespow);
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-   void lubksb(double **a, int npar, int *indx, double b[]) ;
+   }
-   void ludcmp(double **a, int npar, int *indx, double *d) ;
+   fprintf(ficrespow,"# Powell\n# iter -2*LL");
-   double gompertz(double p[]);
+   for (i=1;i<=nlstate;i++)
-   hess=matrix(1,npar,1,npar);
+     for(j=1;j<=nlstate+ndeath;j++)
+       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-   printf("\nCalculation of the hessian matrix. Wait...\n");
+   fprintf(ficrespow,"\n");
-   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
-   for (i=1;i<=npar;i++){
+   powell(p,xi,npar,ftol,&iter,&fret,func);
-     printf("%d",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+   free_matrix(xi,1,npar,1,npar);
+   fclose(ficrespow);
-      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
+   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));
-     /*  printf(" %f ",p[i]);
+   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
-   }
+ }
-   for (i=1;i<=npar;i++) {
+ /**** 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 []))
-       if (j>i) {
+ {
-         printf(".%d%d",i,j);fflush(stdout);
+   double  **a,**y,*x,pd;
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+   double **hess;
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+   int i, j,jk;
+   int *indx;
-         hess[j][i]=hess[i][j];
-         /*printf(" %lf ",hess[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);
-     }
+   void lubksb(double **a, int npar, int *indx, double b[]) ;
-   }
+   void ludcmp(double **a, int npar, int *indx, double *d) ;
-   printf("\n");
+   double gompertz(double p[]);
-   fprintf(ficlog,"\n");
+   hess=matrix(1,npar,1,npar);
-   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+   printf("\nCalculation of the hessian matrix. Wait...\n");
-   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+   for (i=1;i<=npar;i++){
-   a=matrix(1,npar,1,npar);
+     printf("%d",i);fflush(stdout);
-   y=matrix(1,npar,1,npar);
+     fprintf(ficlog,"%d",i);fflush(ficlog);
-   x=vector(1,npar);
-   indx=ivector(1,npar);
+      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-   for (i=1;i<=npar;i++)
-     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+     /*  printf(" %f ",p[i]);
-   ludcmp(a,npar,indx,&pd);
+         printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
+   }
-   for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
+   for (i=1;i<=npar;i++) {
-     x[j]=1;
+     for (j=1;j<=npar;j++)  {
-     lubksb(a,npar,indx,x);
+       if (j>i) {
-     for (i=1;i<=npar;i++){
+         printf(".%d%d",i,j);fflush(stdout);
-       matcov[i][j]=x[i];
+         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
-     }
+         hess[i][j]=hessij(p,delti,i,j,func,npar);
-   }
+         hess[j][i]=hess[i][j];
-   printf("\n#Hessian matrix#\n");
+         /*printf(" %lf ",hess[i][j]);*/
-   fprintf(ficlog,"\n#Hessian matrix#\n");
+       }
-   for (i=1;i<=npar;i++) {
+     }
-     for (j=1;j<=npar;j++) {
+   }
-       printf("%.3e ",hess[i][j]);
+   printf("\n");
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+   fprintf(ficlog,"\n");
-     }
-     printf("\n");
+   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
-     fprintf(ficlog,"\n");
+   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-   }
+   a=matrix(1,npar,1,npar);
-   /* Recompute Inverse */
+   y=matrix(1,npar,1,npar);
-   for (i=1;i<=npar;i++)
+   x=vector(1,npar);
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   indx=ivector(1,npar);
-   ludcmp(a,npar,indx,&pd);
+   for (i=1;i<=npar;i++)
+     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   ludcmp(a,npar,indx,&pd);
    for (j=1;j<=npar;j++) {
      for (i=1;i<=npar;i++) x[i]=0;
      x[j]=1;
      lubksb(a,npar,indx,x);
      for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+       matcov[i][j]=x[i];
-       printf("%.3e ",y[i][j]);
+     }
-       fprintf(ficlog,"%.3e ",y[i][j]);
+   }
-     }
-     printf("\n");
+   printf("\n#Hessian matrix#\n");
-     fprintf(ficlog,"\n");
+   fprintf(ficlog,"\n#Hessian matrix#\n");
-   }
+   for (i=1;i<=npar;i++) {
-   */
+     for (j=1;j<=npar;j++) {
+       printf("%.3e ",hess[i][j]);
-   free_matrix(a,1,npar,1,npar);
+       fprintf(ficlog,"%.3e ",hess[i][j]);
-   free_matrix(y,1,npar,1,npar);
+     }
-   free_vector(x,1,npar);
+     printf("\n");
-   free_ivector(indx,1,npar);
+     fprintf(ficlog,"\n");
-   free_matrix(hess,1,npar,1,npar);
+   }
+   /* Recompute Inverse */
- }
+   for (i=1;i<=npar;i++)
+     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
- /*************** hessian matrix ****************/
+   ludcmp(a,npar,indx,&pd);
- double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+   /*  printf("\n#Hessian matrix recomputed#\n");
-   int i;
-   int l=1, lmax=20;
+   for (j=1;j<=npar;j++) {
-   double k1,k2;
+     for (i=1;i<=npar;i++) x[i]=0;
-   double p2[NPARMAX+1];
+     x[j]=1;
-   double res;
+     lubksb(a,npar,indx,x);
-   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+     for (i=1;i<=npar;i++){
-   double fx;
+       y[i][j]=x[i];
-   int k=0,kmax=10;
+       printf("%.3e ",y[i][j]);
-   double l1;
+       fprintf(ficlog,"%.3e ",y[i][j]);
+     }
-   fx=func(x);
+     printf("\n");
-   for (i=1;i<=npar;i++) p2[i]=x[i];
+     fprintf(ficlog,"\n");
-   for(l=0 ; l <=lmax; l++){
+   }
-     l1=pow(10,l);
+   */
-     delts=delt;
-     for(k=1 ; k <kmax; k=k+1){
+   free_matrix(a,1,npar,1,npar);
-       delt = delta*(l1*k);
+   free_matrix(y,1,npar,1,npar);
-       p2[theta]=x[theta] +delt;
+   free_vector(x,1,npar);
-       k1=func(p2)-fx;
+   free_ivector(indx,1,npar);
-       p2[theta]=x[theta]-delt;
+   free_matrix(hess,1,npar,1,npar);
-       k2=func(p2)-fx;
-       /*res= (k1-2.0*fx+k2)/delt/delt; */
-       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+ }
- #ifdef DEBUG
+ /*************** hessian matrix ****************/
-       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);
+ double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+ {
- #endif
+   int i;
-       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+   int l=1, lmax=20;
-       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+   double k1,k2;
-         k=kmax;
+   double p2[MAXPARM+1]; /* identical to x */
-       }
+   double res;
-       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-         k=kmax; l=lmax*10.;
+   double fx;
-       }
+   int k=0,kmax=10;
-       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+   double l1;
-         delts=delt;
-       }
+   fx=func(x);
-     }
+   for (i=1;i<=npar;i++) p2[i]=x[i];
-   }
+   for(l=0 ; l <=lmax; l++){
-   delti[theta]=delts;
+     l1=pow(10,l);
-   return res;
+     delts=delt;
+     for(k=1 ; k <kmax; k=k+1){
- }
+       delt = delta*(l1*k);
+       p2[theta]=x[theta] +delt;
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+       k1=func(p2)-fx;
- {
+       p2[theta]=x[theta]-delt;
-   int i;
+       k2=func(p2)-fx;
-   int l=1, l1, lmax=20;
+       /*res= (k1-2.0*fx+k2)/delt/delt; */
-   double k1,k2,k3,k4,res,fx;
+       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-   double p2[NPARMAX+1];
-   int k;
+ #ifdef DEBUGHESS
+       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
-   fx=func(x);
+       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 (k=1; k<=2; k++) {
+ #endif
-     for (i=1;i<=npar;i++) p2[i]=x[i];
+       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+         k=kmax;
-     k1=func(p2)-fx;
+       }
+       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+         k=kmax; l=lmax*10.;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+       }
-     k2=func(p2)-fx;
+       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+         delts=delt;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+       }
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     }
-     k3=func(p2)-fx;
+   }
+   delti[theta]=delts;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+   return res;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     k4=func(p2)-fx;
+ }
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
- #ifdef DEBUG
+ double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ {
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+   int i;
- #endif
+   int l=1, l1, lmax=20;
-   }
+   double k1,k2,k3,k4,res,fx;
-   return res;
+   double p2[MAXPARM+1];
- }
+   int k;
- /************** Inverse of matrix **************/
+   fx=func(x);
- void ludcmp(double **a, int n, int *indx, double *d)
+   for (k=1; k<=2; k++) {
- {
+     for (i=1;i<=npar;i++) p2[i]=x[i];
-   int i,imax,j,k;
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   double big,dum,sum,temp;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-   double *vv;
+     k1=func(p2)-fx;
-   vv=vector(1,n);
+     p2[thetai]=x[thetai]+delti[thetai]/k;
-   *d=1.0;
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-   for (i=1;i<=n;i++) {
+     k2=func(p2)-fx;
-     big=0.0;
-     for (j=1;j<=n;j++)
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-       if ((temp=fabs(a[i][j])) > big) big=temp;
+     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     k3=func(p2)-fx;
-     vv[i]=1.0/big;
-   }
+     p2[thetai]=x[thetai]-delti[thetai]/k;
-   for (j=1;j<=n;j++) {
+     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
-     for (i=1;i<j;i++) {
+     k4=func(p2)-fx;
-       sum=a[i][j];
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+ #ifdef DEBUG
-       a[i][j]=sum;
+     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);
-     big=0.0;
+ #endif
-     for (i=j;i<=n;i++) {
+   }
-       sum=a[i][j];
+   return res;
-       for (k=1;k<j;k++)
+ }
-         sum -= a[i][k]*a[k][j];
-       a[i][j]=sum;
+ /************** Inverse of matrix **************/
-       if ( (dum=vv[i]*fabs(sum)) >= big) {
+ void ludcmp(double **a, int n, int *indx, double *d)
-         big=dum;
+ {
-         imax=i;
+   int i,imax,j,k;
-       }
+   double big,dum,sum,temp;
-     }
+   double *vv;
-     if (j != imax) {
-       for (k=1;k<=n;k++) {
+   vv=vector(1,n);
-         dum=a[imax][k];
+   *d=1.0;
-         a[imax][k]=a[j][k];
+   for (i=1;i<=n;i++) {
-         a[j][k]=dum;
+     big=0.0;
-       }
+     for (j=1;j<=n;j++)
-       *d = -(*d);
+       if ((temp=fabs(a[i][j])) > big) big=temp;
-       vv[imax]=vv[j];
+     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
-     }
+     vv[i]=1.0/big;
-     indx[j]=imax;
+   }
-     if (a[j][j] == 0.0) a[j][j]=TINY;
+   for (j=1;j<=n;j++) {
-     if (j != n) {
+     for (i=1;i<j;i++) {
-       dum=1.0/(a[j][j]);
+       sum=a[i][j];
-       for (i=j+1;i<=n;i++) a[i][j] *= dum;
+       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
-     }
+       a[i][j]=sum;
-   }
+     }
-   free_vector(vv,1,n);  /* Doesn't work */
+     big=0.0;
- ;
+     for (i=j;i<=n;i++) {
- }
+       sum=a[i][j];
+       for (k=1;k<j;k++)
- void lubksb(double **a, int n, int *indx, double b[])
+         sum -= a[i][k]*a[k][j];
- {
+       a[i][j]=sum;
-   int i,ii=0,ip,j;
+       if ( (dum=vv[i]*fabs(sum)) >= big) {
-   double sum;
+         big=dum;
+         imax=i;
-   for (i=1;i<=n;i++) {
+       }
-     ip=indx[i];
+     }
-     sum=b[ip];
+     if (j != imax) {
-     b[ip]=b[i];
+       for (k=1;k<=n;k++) {
-     if (ii)
+         dum=a[imax][k];
-       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+         a[imax][k]=a[j][k];
-     else if (sum) ii=i;
+         a[j][k]=dum;
-     b[i]=sum;
+       }
-   }
+       *d = -(*d);
-   for (i=n;i>=1;i--) {
+       vv[imax]=vv[j];
-     sum=b[i];
+     }
-     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+     indx[j]=imax;
-     b[i]=sum/a[i][i];
+     if (a[j][j] == 0.0) a[j][j]=TINY;
-   }
+     if (j != n) {
- }
+       dum=1.0/(a[j][j]);
+       for (i=j+1;i<=n;i++) a[i][j] *= dum;
- void pstamp(FILE *fichier)
+     }
- {
+   }
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   free_vector(vv,1,n);  /* Doesn't work */
- }
+ ;
+ }
- /************ Frequencies ********************/
- 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 lubksb(double **a, int n, int *indx, double b[])
- {  /* Some frequencies */
+ {
+   int i,ii=0,ip,j;
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   double sum;
-   int first;
-   double ***freq; /* Frequencies */
+   for (i=1;i<=n;i++) {
-   double *pp, **prop;
+     ip=indx[i];
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+     sum=b[ip];
-   char fileresp[FILENAMELENGTH];
+     b[ip]=b[i];
+     if (ii)
-   pp=vector(1,nlstate);
+       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+     else if (sum) ii=i;
-   strcpy(fileresp,"p");
+     b[i]=sum;
-   strcat(fileresp,fileres);
+   }
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
+   for (i=n;i>=1;i--) {
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+     sum=b[i];
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
-     exit(0);
+     b[i]=sum/a[i][i];
    }
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+ }
-   j1=0;
+ void pstamp(FILE *fichier)
-   j=cptcoveff;
+ {
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+ }
-   first=1;
+ /************ Frequencies ********************/
-   for(k1=1; k1<=j;k1++){
+ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
-     for(i1=1; i1<=ncodemax[k1];i1++){
+ {  /* Some frequencies */
-       j1++;
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   int i, m, jk, k1,i1, j1, bool, z1,j;
-         scanf("%d", i);*/
+   int first;
-       for (i=-5; i<=nlstate+ndeath; i++)
+   double ***freq; /* Frequencies */
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+   double *pp, **prop;
-           for(m=iagemin; m <= iagemax+3; m++)
+   double pos,posprop, k2, dateintsum=0,k2cpt=0;
-             freq[i][jk][m]=0;
+   char fileresp[FILENAMELENGTH];
-     for (i=1; i<=nlstate; i++)
+   pp=vector(1,nlstate);
-       for(m=iagemin; m <= iagemax+3; m++)
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-         prop[i][m]=0;
+   strcpy(fileresp,"p");
+   strcat(fileresp,fileres);
-       dateintsum=0;
+   if((ficresp=fopen(fileresp,"w"))==NULL) {
-       k2cpt=0;
+     printf("Problem with prevalence resultfile: %s\n", fileresp);
-       for (i=1; i<=imx; i++) {
+     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
-         bool=1;
+     exit(0);
-         if  (cptcovn>0) {
+   }
-           for (z1=1; z1<=cptcoveff; z1++)
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   j1=0;
-               bool=0;
-         }
+   j=cptcoveff;
-         if (bool==1){
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-           for(m=firstpass; m<=lastpass; m++){
-             k2=anint[m][i]+(mint[m][i]/12.);
+   first=1;
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   for(k1=1; k1<=j;k1++){
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+     for(i1=1; i1<=ncodemax[k1];i1++){
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+       j1++;
-               if (m<lastpass) {
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+         scanf("%d", i);*/
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+       for (i=-5; i<=nlstate+ndeath; i++)
-               }
+         for (jk=-5; jk<=nlstate+ndeath; jk++)
+           for(m=iagemin; m <= iagemax+3; m++)
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+             freq[i][jk][m]=0;
-                 dateintsum=dateintsum+k2;
-                 k2cpt++;
+     for (i=1; i<=nlstate; i++)
-               }
+       for(m=iagemin; m <= iagemax+3; m++)
-               /*}*/
+         prop[i][m]=0;
-           }
-         }
+       dateintsum=0;
-       }
+       k2cpt=0;
+       for (i=1; i<=imx; i++) {
-       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         bool=1;
-       pstamp(ficresp);
+         if  (cptcovn>0) {
-       if  (cptcovn>0) {
+           for (z1=1; z1<=cptcoveff; z1++)
-         fprintf(ficresp, "\n#********** Variable ");
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+               bool=0;
-         fprintf(ficresp, "**********\n#");
+         }
-       }
+         if (bool==1){
-       for(i=1; i<=nlstate;i++)
+           for(m=firstpass; m<=lastpass; m++){
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+             k2=anint[m][i]+(mint[m][i]/12.);
-       fprintf(ficresp, "\n");
+             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-       for(i=iagemin; i <= iagemax+3; i++){
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-         if(i==iagemax+3){
+               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-           fprintf(ficlog,"Total");
+               if (m<lastpass) {
-         }else{
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-           if(first==1){
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-             first=0;
+               }
-             printf("See log file for details...\n");
-           }
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-           fprintf(ficlog,"Age %d", i);
+                 dateintsum=dateintsum+k2;
-         }
+                 k2cpt++;
-         for(jk=1; jk <=nlstate ; jk++){
+               }
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+               /*}*/
-             pp[jk] += freq[jk][m][i];
+           }
          }
-         for(jk=1; jk <=nlstate ; jk++){
+       }
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-           if(pp[jk]>=1.e-10){
+       pstamp(ficresp);
-             if(first==1){
+       if  (cptcovn>0) {
-             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         fprintf(ficresp, "\n#********** Variable ");
-             }
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         fprintf(ficresp, "**********\n#");
-           }else{
+       }
-             if(first==1)
+       for(i=1; i<=nlstate;i++)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       fprintf(ficresp, "\n");
-           }
-         }
+       for(i=iagemin; i <= iagemax+3; i++){
+         if(i==iagemax+3){
-         for(jk=1; jk <=nlstate ; jk++){
+           fprintf(ficlog,"Total");
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+         }else{
-             pp[jk] += freq[jk][m][i];
+           if(first==1){
-         }
+             first=0;
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+             printf("See log file for details...\n");
-           pos += pp[jk];
+           }
-           posprop += prop[jk][i];
+           fprintf(ficlog,"Age %d", i);
          }
          for(jk=1; jk <=nlstate ; jk++){
-           if(pos>=1.e-5){
+           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             if(first==1)
+             pp[jk] += freq[jk][m][i];
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         }
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+         for(jk=1; jk <=nlstate ; jk++){
-           }else{
+           for(m=-1, pos=0; m <=0 ; m++)
-             if(first==1)
+             pos += freq[jk][m][i];
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+           if(pp[jk]>=1.e-10){
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+             if(first==1){
-           }
+               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           if( i <= iagemax){
+             }
-             if(pos>=1.e-5){
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+           }else{
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+             if(first==1)
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             }
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             else
+           }
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+         }
-           }
-         }
+         for(jk=1; jk <=nlstate ; jk++){
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+             pp[jk] += freq[jk][m][i];
-           for(m=-1; m <=nlstate+ndeath; m++)
+         }
-             if(freq[jk][m][i] !=0 ) {
+         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
-             if(first==1)
+           pos += pp[jk];
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+           posprop += prop[jk][i];
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+         }
-             }
+         for(jk=1; jk <=nlstate ; jk++){
-         if(i <= iagemax)
+           if(pos>=1.e-5){
-           fprintf(ficresp,"\n");
+             if(first==1)
-         if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-           printf("Others in log...\n");
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-         fprintf(ficlog,"\n");
+           }else{
-       }
+             if(first==1)
-     }
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   }
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-   dateintmean=dateintsum/k2cpt;
+           }
+           if( i <= iagemax){
-   fclose(ficresp);
+             if(pos>=1.e-5){
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
-   free_vector(pp,1,nlstate);
+               /*probs[i][jk][j1]= pp[jk]/pos;*/
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
-   /* End of Freq */
+             }
- }
+             else
+               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
- /************ Prevalence ********************/
+           }
- 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)
+         }
- {
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+         for(jk=-1; jk <=nlstate+ndeath; jk++)
-      in each health status at the date of interview (if between dateprev1 and dateprev2).
+           for(m=-1; m <=nlstate+ndeath; m++)
-      We still use firstpass and lastpass as another selection.
+             if(freq[jk][m][i] !=0 ) {
-   */
+             if(first==1)
+               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
-   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
-   double ***freq; /* Frequencies */
+             }
-   double *pp, **prop;
+         if(i <= iagemax)
-   double pos,posprop;
+           fprintf(ficresp,"\n");
-   double  y2; /* in fractional years */
+         if(first==1)
-   int iagemin, iagemax;
+           printf("Others in log...\n");
+         fprintf(ficlog,"\n");
-   iagemin= (int) agemin;
+       }
-   iagemax= (int) agemax;
+     }
-   /*pp=vector(1,nlstate);*/
+   }
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   dateintmean=dateintsum/k2cpt;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   j1=0;
+   fclose(ficresp);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
-   j=cptcoveff;
+   free_vector(pp,1,nlstate);
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of Freq */
-   for(k1=1; k1<=j;k1++){
+ }
-     for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
+ /************ Prevalence ********************/
+ 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)
-       for (i=1; i<=nlstate; i++)
+ {
-         for(m=iagemin; m <= iagemax+3; m++)
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-           prop[i][m]=0.0;
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
-       for (i=1; i<=imx; i++) { /* Each individual */
+   */
-         bool=1;
-         if  (cptcovn>0) {
+   int i, m, jk, k1, i1, j1, bool, z1,j;
-           for (z1=1; z1<=cptcoveff; z1++)
+   double ***freq; /* Frequencies */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+   double *pp, **prop;
-               bool=0;
+   double pos,posprop;
-         }
+   double  y2; /* in fractional years */
-         if (bool==1) {
+   int iagemin, iagemax;
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+   iagemin= (int) agemin;
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+   iagemax= (int) agemax;
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+   /*pp=vector(1,nlstate);*/
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+   prop=matrix(1,nlstate,iagemin,iagemax+3);
-               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);
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+   j1=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]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+   j=cptcoveff;
-                 prop[s[m][i]][iagemax+3] += weight[i];
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-               }
-             }
+   for(k1=1; k1<=j;k1++){
-           } /* end selection of waves */
+     for(i1=1; i1<=ncodemax[k1];i1++){
-         }
+       j1++;
-       }
-       for(i=iagemin; i <= iagemax+3; i++){
+       for (i=1; i<=nlstate; i++)
+         for(m=iagemin; m <= iagemax+3; m++)
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+           prop[i][m]=0.0;
-           posprop += prop[jk][i];
-         }
+       for (i=1; i<=imx; i++) { /* Each individual */
+         bool=1;
-         for(jk=1; jk <=nlstate ; jk++){
+         if  (cptcovn>0) {
-           if( i <=  iagemax){
+           for (z1=1; z1<=cptcoveff; z1++)
-             if(posprop>=1.e-5){
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+               bool=0;
-             }
+         }
-           }
+         if (bool==1) {
-         }/* end jk */
+           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
-       }/* end i */
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-     } /* end i1 */
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-   } /* end k1 */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+               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);
-   /*free_vector(pp,1,nlstate);*/
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+                 /*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 of prevalence */
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][iagemax+3] += weight[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)
+           } /* end selection of waves */
- {
+         }
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+       }
-      Death is a valid wave (if date is known).
+       for(i=iagemin; i <= iagemax+3; i++){
-      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-      and mw[mi+1][i]. dh depends on stepm.
+           posprop += prop[jk][i];
-      */
+         }
-   int i, mi, m;
+         for(jk=1; jk <=nlstate ; jk++){
-   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+           if( i <=  iagemax){
-      double sum=0., jmean=0.;*/
+             if(posprop>=1.e-5){
-   int first;
+               probs[i][jk][j1]= prop[jk][i]/posprop;
-   int j, k=0,jk, ju, jl;
+             } else
-   double sum=0.;
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
-   first=0;
+           }
-   jmin=1e+5;
+         }/* end jk */
-   jmax=-1;
+       }/* end i */
-   jmean=0.;
+     } /* end i1 */
-   for(i=1; i<=imx; i++){
+   } /* end k1 */
-     mi=0;
-     m=firstpass;
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-     while(s[m][i] <= nlstate){
+   /*free_vector(pp,1,nlstate);*/
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-         mw[++mi][i]=m;
+ }  /* End of prevalence */
-       if(m >=lastpass)
-         break;
+ /************* Waves Concatenation ***************/
-       else
-         m++;
+ 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)
-     }/* end while */
+ {
-     if (s[m][i] > nlstate){
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
-       mi++;     /* Death is another wave */
+      Death is a valid wave (if date is known).
-       /* if(mi==0)  never been interviewed correctly before death */
+      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
-          /* Only death is a correct wave */
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-       mw[mi][i]=m;
+      and mw[mi+1][i]. dh depends on stepm.
-     }
+      */
-     wav[i]=mi;
+   int i, mi, m;
-     if(mi==0){
+   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-       nbwarn++;
+      double sum=0., jmean=0.;*/
-       if(first==0){
+   int first;
-         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+   int j, k=0,jk, ju, jl;
-         first=1;
+   double sum=0.;
-       }
+   first=0;
-       if(first==1){
+   jmin=1e+5;
-         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+   jmax=-1;
-       }
+   jmean=0.;
-     } /* end mi==0 */
+   for(i=1; i<=imx; i++){
-   } /* End individuals */
+     mi=0;
+     m=firstpass;
-   for(i=1; i<=imx; i++){
+     while(s[m][i] <= nlstate){
-     for(mi=1; mi<wav[i];mi++){
+       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
-       if (stepm <=0)
+         mw[++mi][i]=m;
-         dh[mi][i]=1;
+       if(m >=lastpass)
-       else{
+         break;
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+       else
-           if (agedc[i] < 2*AGESUP) {
+         m++;
-             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+     }/* end while */
-             if(j==0) j=1;  /* Survives at least one month after exam */
+     if (s[m][i] > nlstate){
-             else if(j<0){
+       mi++;     /* Death is another wave */
-               nberr++;
+       /* if(mi==0)  never been interviewed correctly before death */
-               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]);
+          /* Only death is a correct wave */
-               j=1; /* Temporary Dangerous patch */
+       mw[mi][i]=m;
-               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+     }
-               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-               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);
+     wav[i]=mi;
-             }
+     if(mi==0){
-             k=k+1;
+       nbwarn++;
-             if (j >= jmax){
+       if(first==0){
-               jmax=j;
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-               ijmax=i;
+         first=1;
-             }
+       }
-             if (j <= jmin){
+       if(first==1){
-               jmin=j;
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
-               ijmin=i;
+       }
-             }
+     } /* end mi==0 */
-             sum=sum+j;
+   } /* End individuals */
-             /*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);*/
+   for(i=1; i<=imx; i++){
-           }
+     for(mi=1; mi<wav[i];mi++){
-         }
+       if (stepm <=0)
-         else{
+         dh[mi][i]=1;
-           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+       else{
- /*        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]); */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+           if (agedc[i] < 2*AGESUP) {
-           k=k+1;
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-           if (j >= jmax) {
+             if(j==0) j=1;  /* Survives at least one month after exam */
-             jmax=j;
+             else if(j<0){
-             ijmax=i;
+               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]);
-           else if (j <= jmin){
+               j=1; /* Temporary Dangerous patch */
-             jmin=j;
+               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);
-             ijmin=i;
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-           }
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+             }
-           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+             k=k+1;
-           if(j<0){
+             if (j >= jmax){
-             nberr++;
+               jmax=j;
-             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]);
+               ijmax=i;
-             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             }
-           }
+             if (j <= jmin){
-           sum=sum+j;
+               jmin=j;
-         }
+               ijmin=i;
-         jk= j/stepm;
+             }
-         jl= j -jk*stepm;
+             sum=sum+j;
-         ju= j -(jk+1)*stepm;
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-           if(jl==0){
+           }
-             dh[mi][i]=jk;
+         }
-             bh[mi][i]=0;
+         else{
-           }else{ /* We want a negative bias in order to only have interpolation ie
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-                   * at the price of an extra matrix product in likelihood */
+ /*        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]); */
-             dh[mi][i]=jk+1;
-             bh[mi][i]=ju;
+           k=k+1;
-           }
+           if (j >= jmax) {
-         }else{
+             jmax=j;
-           if(jl <= -ju){
+             ijmax=i;
-             dh[mi][i]=jk;
+           }
-             bh[mi][i]=jl;       /* bias is positive if real duration
+           else if (j <= jmin){
-                                  * is higher than the multiple of stepm and negative otherwise.
+             jmin=j;
-                                  */
+             ijmin=i;
            }
-           else{
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-             dh[mi][i]=jk+1;
+           /*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]);*/
-             bh[mi][i]=ju;
+           if(j<0){
-           }
+             nberr++;
-           if(dh[mi][i]==0){
+             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]);
-             dh[mi][i]=1; /* At least one step */
+             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]);
-             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);*/
+           sum=sum+j;
-           }
+         }
-         } /* end if mle */
+         jk= j/stepm;
-       }
+         jl= j -jk*stepm;
-     } /* end wave */
+         ju= j -(jk+1)*stepm;
-   }
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-   jmean=sum/k;
+           if(jl==0){
-   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);
+             dh[mi][i]=jk;
-   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);
+             bh[mi][i]=0;
-  }
+           }else{ /* We want a negative bias in order to only have interpolation ie
+                   * to avoid the price of an extra matrix product in likelihood */
- /*********** Tricode ****************************/
+             dh[mi][i]=jk+1;
- void tricode(int *Tvar, int **nbcode, int imx)
+             bh[mi][i]=ju;
- {
+           }
+         }else{
-   int Ndum[20],ij=1, k, j, i, maxncov=19;
+           if(jl <= -ju){
-   int cptcode=0;
+             dh[mi][i]=jk;
-   cptcoveff=0;
+             bh[mi][i]=jl;       /* bias is positive if real duration
+                                  * is higher than the multiple of stepm and negative otherwise.
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+                                  */
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+           }
+           else{
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+             dh[mi][i]=jk+1;
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+             bh[mi][i]=ju;
-                                modality*/
+           }
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+           if(dh[mi][i]==0){
-       Ndum[ij]++; /*store the modality */
+             dh[mi][i]=1; /* At least one step */
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+             bh[mi][i]=ju; /* At least one step */
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+             /*  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);*/
-                                        Tvar[j]. If V=sex and male is 0 and
+           }
-                                        female is 1, then  cptcode=1.*/
+         } /* end if mle */
-     }
+       }
+     } /* end wave */
-     for (i=0; i<=cptcode; i++) {
+   }
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+   jmean=sum/k;
-     }
+   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-     ij=1;
+  }
-     for (i=1; i<=ncodemax[j]; i++) {
-       for (k=0; k<= maxncov; k++) {
+ /*********** Tricode ****************************/
-         if (Ndum[k] != 0) {
+ void tricode(int *Tvar, int **nbcode, int imx)
-           nbcode[Tvar[j]][ij]=k;
+ {
-           /* 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; */
+   /* 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 */
-           ij++;
-         }
+   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-         if (ij > ncodemax[j]) break;
+   int modmaxcovj=0; /* Modality max of covariates j */
-       }
+   cptcoveff=0;
-     }
-   }
+   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
-  for (k=0; k< maxncov; k++) Ndum[k]=0;
+   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
-  for (i=1; i<=ncovmodel-2; i++) {
+     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+                                modality of this covariate Vj*/
-    ij=Tvar[i];
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
-    Ndum[ij]++;
+                                       modality of the nth covariate of individual i. */
-  }
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-  ij=1;
+       if (ij > modmaxcovj) modmaxcovj=ij;
-  for (i=1; i<= maxncov; i++) {
+       /* getting the maximum value of the modality of the covariate
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-      Tvaraff[ij]=i; /*For printing */
+          female is 1, then modmaxcovj=1.*/
-      ij++;
+     }
-    }
-  }
+     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
+       if( Ndum[i] != 0 )
-  cptcoveff=ij-1; /*Number of simple covariates*/
+         ncodemax[j]++;
- }
+       /* Number of modalities of the j th covariate. In fact
+          ncodemax[j]=2 (dichotom. variables only) but it could be more for
- /*********** Health Expectancies ****************/
+          historical reasons */
+     } /* Ndum[-1] number of undefined modalities */
- 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[] )
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
- {
+     ij=1;
-   /* Health expectancies, no variances */
+     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+       for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
-   double age, agelim, hf;
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
-   double ***p3mat;
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
-   double eip;
+                                      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; */
-   pstamp(ficreseij);
+           ij++;
-   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+         }
-   fprintf(ficreseij,"# Age");
+         if (ij > ncodemax[j]) break;
-   for(i=1; i<=nlstate;i++){
+       }
-     for(j=1; j<=nlstate;j++){
+     }
-       fprintf(ficreseij," e%1d%1d ",i,j);
+   }
-     }
-     fprintf(ficreseij," e%1d. ",i);
+  for (k=0; k< maxncov; k++) Ndum[k]=0;
-   }
-   fprintf(ficreseij,"\n");
+  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 */
-   if(estepm < stepm){
+    Ndum[ij]++;
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+  }
-   }
-   else  hstepm=estepm;
+  ij=1;
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+  for (i=1; i<= maxncov; i++) {
-    * This is mainly to measure the difference between two models: for example
+    if((Ndum[i]!=0) && (i<=ncovcol)){
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+      Tvaraff[ij]=i; /*For printing */
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+      ij++;
-    * progression in between and thus overestimating or underestimating according
+    }
-    * to the curvature of the survival function. If, for the same date, we
+  }
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+  ij--;
-    * to compare the new estimate of Life expectancy with the same linear
+  cptcoveff=ij; /*Number of simple covariates*/
-    * hypothesis. A more precise result, taking into account a more precise
+ }
-    * curvature will be obtained if estepm is as small as stepm. */
+ /*********** Health Expectancies ****************/
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-      nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+ {
-      Look at hpijx to understand the reason of that which relies in memory size
+   /* Health expectancies, no variances */
-      and note for a fixed period like estepm months */
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   int nhstepma, nstepma; /* Decreasing with age */
-      survival function given by stepm (the optimization length). Unfortunately it
+   double age, agelim, hf;
-      means that if the survival funtion is printed only each two years of age and if
+   double ***p3mat;
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   double eip;
-      results. So we changed our mind and took the option of the best precision.
-   */
+   pstamp(ficreseij);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+   fprintf(ficreseij,"# Age");
-   agelim=AGESUP;
+   for(i=1; i<=nlstate;i++){
-   /* If stepm=6 months */
+     for(j=1; j<=nlstate;j++){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+       fprintf(ficreseij," e%1d%1d ",i,j);
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+     }
+     fprintf(ficreseij," e%1d. ",i);
- /* nhstepm age range expressed in number of stepm */
+   }
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   fprintf(ficreseij,"\n");
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   /* if (stepm >= YEARM) hstepm=1;*/
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   if(estepm < stepm){
-   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
-   for (age=bage; age<=fage; age ++){
+   else  hstepm=estepm;
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+    * if stepm=24 months pijx are given only every 2 years and by summing them
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+    * progression in between and thus overestimating or underestimating according
+    * to the curvature of the survival function. If, for the same date, we
-     printf("%d|",(int)age);fflush(stdout);
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+    * 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. */
-     /* Computing expectancies */
-     for(i=1; i<=nlstate;i++)
+   /* For example we decided to compute the life expectancy with the smallest unit */
-       for(j=1; j<=nlstate;j++)
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+      nhstepm is the number of hstepm from age to agelim
-           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+      nstepm is the number of stepm from age to agelin.
+      Look at hpijx to understand the reason of that which relies in memory size
-           /*if((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]);*/
+      and note for a fixed period like estepm months */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-         }
+      survival function given by stepm (the optimization length). Unfortunately it
+      means that if the survival funtion is printed only each two years of age and if
-     fprintf(ficreseij,"%3.0f",age );
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-     for(i=1; i<=nlstate;i++){
+      results. So we changed our mind and took the option of the best precision.
-       eip=0;
+   */
-       for(j=1; j<=nlstate;j++){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         eip +=eij[i][j][(int)age];
-         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+   agelim=AGESUP;
-       }
+   /* If stepm=6 months */
-       fprintf(ficreseij,"%9.4f", eip );
+     /* Computed by stepm unit matrices, product of hstepm matrices, stored
-     }
+        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-     fprintf(ficreseij,"\n");
+ /* nhstepm age range expressed in number of stepm */
-   }
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-   printf("\n");
+   /* if (stepm >= YEARM) hstepm=1;*/
-   fprintf(ficlog,"\n");
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- }
+   for (age=bage; age<=fage; age ++){
- 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[] )
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- {
+     /* if (stepm >= YEARM) hstepm=1;*/
-   /* Covariances of health expectancies eij and of total life expectancies according
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-    to initial status i, ei. .
-   */
+     /* If stepm=6 months */
-   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-   double age, agelim, hf;
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-   double ***p3matp, ***p3matm, ***varhe;
-   double **dnewm,**doldm;
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   double *xp, *xm;
-   double **gp, **gm;
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-   double ***gradg, ***trgradg;
-   int theta;
+     printf("%d|",(int)age);fflush(stdout);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   double eip, vip;
+     /* Computing expectancies */
-   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
+     for(i=1; i<=nlstate;i++)
-   xp=vector(1,npar);
+       for(j=1; j<=nlstate;j++)
-   xm=vector(1,npar);
+         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-   dnewm=matrix(1,nlstate*nlstate,1,npar);
+           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
+           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
-   pstamp(ficresstdeij);
-   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+         }
-   fprintf(ficresstdeij,"# Age");
-   for(i=1; i<=nlstate;i++){
+     fprintf(ficreseij,"%3.0f",age );
-     for(j=1; j<=nlstate;j++)
+     for(i=1; i<=nlstate;i++){
-       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+       eip=0;
-     fprintf(ficresstdeij," e%1d. ",i);
+       for(j=1; j<=nlstate;j++){
-   }
+         eip +=eij[i][j][(int)age];
-   fprintf(ficresstdeij,"\n");
+         fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+       }
-   pstamp(ficrescveij);
+       fprintf(ficreseij,"%9.4f", eip );
-   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+     }
-   fprintf(ficrescveij,"# Age");
+     fprintf(ficreseij,"\n");
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++){
+   }
-       cptj= (j-1)*nlstate+i;
+   free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       for(i2=1; i2<=nlstate;i2++)
+   printf("\n");
-         for(j2=1; j2<=nlstate;j2++){
+   fprintf(ficlog,"\n");
-           cptj2= (j2-1)*nlstate+i2;
-           if(cptj2 <= cptj)
+ }
-             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-         }
+ 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[] )
-     }
-   fprintf(ficrescveij,"\n");
+ {
+   /* Covariances of health expectancies eij and of total life expectancies according
-   if(estepm < stepm){
+    to initial status i, ei. .
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   */
-   }
+   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
-   else  hstepm=estepm;
+   int nhstepma, nstepma; /* Decreasing with age */
-   /* We compute the life expectancy from trapezoids spaced every estepm months
+   double age, agelim, hf;
-    * This is mainly to measure the difference between two models: for example
+   double ***p3matp, ***p3matm, ***varhe;
-    * if stepm=24 months pijx are given only every 2 years and by summing them
+   double **dnewm,**doldm;
-    * we are calculating an estimate of the Life Expectancy assuming a linear
+   double *xp, *xm;
-    * progression in between and thus overestimating or underestimating according
+   double **gp, **gm;
-    * to the curvature of the survival function. If, for the same date, we
+   double ***gradg, ***trgradg;
-    * estimate the model with stepm=1 month, we can keep estepm to 24 months
+   int theta;
-    * to compare the new estimate of Life expectancy with the same linear
-    * hypothesis. A more precise result, taking into account a more precise
+   double eip, vip;
-    * curvature will be obtained if estepm is as small as stepm. */
+   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   xp=vector(1,npar);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   xm=vector(1,npar);
-      nhstepm is the number of hstepm from age to agelim
+   dnewm=matrix(1,nlstate*nlstate,1,npar);
-      nstepm is the number of stepm from age to agelin.
+   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-      Look at hpijx to understand the reason of that which relies in memory size
-      and note for a fixed period like estepm months */
+   pstamp(ficresstdeij);
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+   fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
-      survival function given by stepm (the optimization length). Unfortunately it
+   fprintf(ficresstdeij,"# Age");
-      means that if the survival funtion is printed only each two years of age and if
+   for(i=1; i<=nlstate;i++){
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+     for(j=1; j<=nlstate;j++)
-      results. So we changed our mind and took the option of the best precision.
+       fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
-   */
+     fprintf(ficresstdeij," e%1d. ",i);
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+   }
+   fprintf(ficresstdeij,"\n");
-   /* If stepm=6 months */
-   /* nhstepm age range expressed in number of stepm */
+   pstamp(ficrescveij);
-   agelim=AGESUP;
+   fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
-   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+   fprintf(ficrescveij,"# Age");
-   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+   for(i=1; i<=nlstate;i++)
-   /* if (stepm >= YEARM) hstepm=1;*/
+     for(j=1; j<=nlstate;j++){
-   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+       cptj= (j-1)*nlstate+i;
+       for(i2=1; i2<=nlstate;i2++)
-   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(j2=1; j2<=nlstate;j2++){
-   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           cptj2= (j2-1)*nlstate+i2;
-   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+           if(cptj2 <= cptj)
-   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+             fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
-   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+         }
-   gm=matrix(0,nhstepm,1,nlstate*nlstate);
+     }
+   fprintf(ficrescveij,"\n");
-   for (age=bage; age<=fage; age ++){
+   if(estepm < stepm){
-     /* Computed by stepm unit matrices, product of hstepm matrices, stored
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+   }
+   else  hstepm=estepm;
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+   /* We compute the life expectancy from trapezoids spaced every estepm months
+    * This is mainly to measure the difference between two models: for example
-     /* Computing  Variances of health expectancies */
+    * if stepm=24 months pijx are given only every 2 years and by summing them
-     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+    * we are calculating an estimate of the Life Expectancy assuming a linear
-        decrease memory allocation */
+    * progression in between and thus overestimating or underestimating according
-     for(theta=1; theta <=npar; theta++){
+    * to the curvature of the survival function. If, for the same date, we
-       for(i=1; i<=npar; i++){
+    * estimate the model with stepm=1 month, we can keep estepm to 24 months
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+    * to compare the new estimate of Life expectancy with the same linear
-         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+    * hypothesis. A more precise result, taking into account a more precise
-       }
+    * curvature will be obtained if estepm is as small as stepm. */
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+   /* For example we decided to compute the life expectancy with the smallest unit */
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-       for(j=1; j<= nlstate; j++){
+      nhstepm is the number of hstepm from age to agelim
-         for(i=1; i<=nlstate; i++){
+      nstepm is the number of stepm from age to agelin.
-           for(h=0; h<=nhstepm-1; h++){
+      Look at hpijx to understand the reason of that which relies in memory size
-             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+      and note for a fixed period like estepm months */
-             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-           }
+      survival function given by stepm (the optimization length). Unfortunately it
-         }
+      means that if the survival funtion is printed only each two years of age and if
-       }
+      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.
-       for(ij=1; ij<= nlstate*nlstate; ij++)
+   */
-         for(h=0; h<=nhstepm-1; h++){
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
-         }
+   /* If stepm=6 months */
-     }/* End theta */
+   /* nhstepm age range expressed in number of stepm */
+   agelim=AGESUP;
+   nstepm=(int) rint((agelim-bage)*YEARM/stepm);
-     for(h=0; h<=nhstepm-1; h++)
+   /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-       for(j=1; j<=nlstate*nlstate;j++)
+   /* if (stepm >= YEARM) hstepm=1;*/
-         for(theta=1; theta <=npar; theta++)
+   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           trgradg[h][j][theta]=gradg[h][theta][j];
+   p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+   gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
-       for(ji=1;ji<=nlstate*nlstate;ji++)
+   trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-         varhe[ij][ji][(int)age] =0.;
+   gp=matrix(0,nhstepm,1,nlstate*nlstate);
+   gm=matrix(0,nhstepm,1,nlstate*nlstate);
-      printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+   for (age=bage; age<=fage; age ++){
-      for(h=0;h<=nhstepm-1;h++){
+     nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
-       for(k=0;k<=nhstepm-1;k++){
+     /* Typically if 20 years nstepm = 20*12/6=40 stepm */
-         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
+     /* if (stepm >= YEARM) hstepm=1;*/
-         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
+     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
-         for(ij=1;ij<=nlstate*nlstate;ij++)
-           for(ji=1;ji<=nlstate*nlstate;ji++)
+     /* If stepm=6 months */
-             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+     /* Computed by stepm unit matrices, product of hstepma matrices, stored
-       }
+        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     }
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     /* Computing  Variances of health expectancies */
-     for(i=1; i<=nlstate;i++)
+     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
-       for(j=1; j<=nlstate;j++)
+        decrease memory allocation */
-         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+     for(theta=1; theta <=npar; theta++){
-           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
+       for(i=1; i<=npar; i++){
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
+         xm[i] = x[i] - (i==theta ?delti[theta]:0);
+       }
-         }
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-     fprintf(ficresstdeij,"%3.0f",age );
-     for(i=1; i<=nlstate;i++){
+       for(j=1; j<= nlstate; j++){
-       eip=0.;
+         for(i=1; i<=nlstate; i++){
-       vip=0.;
+           for(h=0; h<=nhstepm-1; h++){
-       for(j=1; j<=nlstate;j++){
+             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
-         eip += eij[i][j][(int)age];
+             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
-         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+           }
-           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+         }
-         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+       }
-       }
-       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+       for(ij=1; ij<= nlstate*nlstate; ij++)
-     }
+         for(h=0; h<=nhstepm-1; h++){
-     fprintf(ficresstdeij,"\n");
+           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
+         }
-     fprintf(ficrescveij,"%3.0f",age );
+     }/* End theta */
-     for(i=1; i<=nlstate;i++)
-       for(j=1; j<=nlstate;j++){
-         cptj= (j-1)*nlstate+i;
+     for(h=0; h<=nhstepm-1; h++)
-         for(i2=1; i2<=nlstate;i2++)
+       for(j=1; j<=nlstate*nlstate;j++)
-           for(j2=1; j2<=nlstate;j2++){
+         for(theta=1; theta <=npar; theta++)
-             cptj2= (j2-1)*nlstate+i2;
+           trgradg[h][j][theta]=gradg[h][theta][j];
-             if(cptj2 <= cptj)
-               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-           }
+      for(ij=1;ij<=nlstate*nlstate;ij++)
-       }
+       for(ji=1;ji<=nlstate*nlstate;ji++)
-     fprintf(ficrescveij,"\n");
+         varhe[ij][ji][(int)age] =0.;
-   }
+      printf("%d|",(int)age);fflush(stdout);
-   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+      for(h=0;h<=nhstepm-1;h++){
-   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+       for(k=0;k<=nhstepm-1;k++){
-   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
-   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
-   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         for(ij=1;ij<=nlstate*nlstate;ij++)
-   printf("\n");
+           for(ji=1;ji<=nlstate*nlstate;ji++)
-   fprintf(ficlog,"\n");
+             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
+       }
-   free_vector(xm,1,npar);
+     }
-   free_vector(xp,1,npar);
-   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
+     /* Computing expectancies */
-   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
+     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++){
- /************ Variance ******************/
+           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
- {
+           /* if((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]);*/
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+         }
-   /* double **newm;*/
-   double **dnewm,**doldm;
+     fprintf(ficresstdeij,"%3.0f",age );
-   double **dnewmp,**doldmp;
+     for(i=1; i<=nlstate;i++){
-   int i, j, nhstepm, hstepm, h, nstepm ;
+       eip=0.;
-   int k, cptcode;
+       vip=0.;
-   double *xp;
+       for(j=1; j<=nlstate;j++){
-   double **gp, **gm;  /* for var eij */
+         eip += eij[i][j][(int)age];
-   double ***gradg, ***trgradg; /*for var eij */
+         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
-   double **gradgp, **trgradgp; /* for var p point j */
+           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
-   double *gpp, *gmp; /* for var p point j */
+         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+       }
-   double ***p3mat;
+       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
-   double age,agelim, hf;
+     }
-   double ***mobaverage;
+     fprintf(ficresstdeij,"\n");
-   int theta;
-   char digit[4];
+     fprintf(ficrescveij,"%3.0f",age );
-   char digitp[25];
+     for(i=1; i<=nlstate;i++)
+       for(j=1; j<=nlstate;j++){
-   char fileresprobmorprev[FILENAMELENGTH];
+         cptj= (j-1)*nlstate+i;
+         for(i2=1; i2<=nlstate;i2++)
-   if(popbased==1){
+           for(j2=1; j2<=nlstate;j2++){
-     if(mobilav!=0)
+             cptj2= (j2-1)*nlstate+i2;
-       strcpy(digitp,"-populbased-mobilav-");
+             if(cptj2 <= cptj)
-     else strcpy(digitp,"-populbased-nomobil-");
+               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
-   }
+           }
-   else
+       }
-     strcpy(digitp,"-stablbased-");
+     fprintf(ficrescveij,"\n");
-   if (mobilav!=0) {
+   }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+   free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
-     }
+   free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   }
+   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   printf("\n");
-   strcpy(fileresprobmorprev,"prmorprev");
+   fprintf(ficlog,"\n");
-   sprintf(digit,"%-d",ij);
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+   free_vector(xm,1,npar);
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+   free_vector(xp,1,npar);
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
-   strcat(fileresprobmorprev,fileres);
+   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
+ }
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
+ /************ Variance ******************/
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+ {
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+   /* Variance of health expectancies */
-   pstamp(ficresprobmorprev);
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   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);
+   /* double **newm;*/
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+   double **dnewm,**doldm;
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+   double **dnewmp,**doldmp;
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+   int i, j, nhstepm, hstepm, h, nstepm ;
-     for(i=1; i<=nlstate;i++)
+   int k, cptcode;
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+   double *xp;
-   }
+   double **gp, **gm;  /* for var eij */
-   fprintf(ficresprobmorprev,"\n");
+   double ***gradg, ***trgradg; /*for var eij */
-   fprintf(ficgp,"\n# Routine varevsij");
+   double **gradgp, **trgradgp; /* for var p point j */
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   double *gpp, *gmp; /* for var p point 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");
+   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+   double ***p3mat;
- /*   } */
+   double age,agelim, hf;
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+   double ***mobaverage;
-   pstamp(ficresvij);
+   int theta;
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+   char digit[4];
-   if(popbased==1)
+   char digitp[25];
-     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
-   else
+   char fileresprobmorprev[FILENAMELENGTH];
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresvij,"# Age");
+   if(popbased==1){
-   for(i=1; i<=nlstate;i++)
+     if(mobilav!=0)
-     for(j=1; j<=nlstate;j++)
+       strcpy(digitp,"-populbased-mobilav-");
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+     else strcpy(digitp,"-populbased-nomobil-");
-   fprintf(ficresvij,"\n");
+   }
+   else
-   xp=vector(1,npar);
+     strcpy(digitp,"-stablbased-");
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
+   if (mobilav!=0) {
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+     }
-   gmp=vector(nlstate+1,nlstate+ndeath);
+   }
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   strcpy(fileresprobmorprev,"prmorprev");
-   if(estepm < stepm){
+   sprintf(digit,"%-d",ij);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   }
+   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   else  hstepm=estepm;
+   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   /* For example we decided to compute the life expectancy with the smallest unit */
+   strcat(fileresprobmorprev,fileres);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-      nhstepm is the number of hstepm from age to agelim
+     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-      nstepm is the number of stepm from age to agelin.
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-      Look at hpijx to understand the reason of that which relies in memory size
+   }
-      and note for a fixed period like k years */
+   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   /* 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
+   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-      means that if the survival funtion is printed every two years of age and if
+   pstamp(ficresprobmorprev);
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
+   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);
-      results. So we changed our mind and took the option of the best precision.
+   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   */
+   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+     fprintf(ficresprobmorprev," p.%-d SE",j);
-   agelim = AGESUP;
+     for(i=1; i<=nlstate;i++)
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   }
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+   fprintf(ficresprobmorprev,"\n");
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   fprintf(ficgp,"\n# Routine varevsij");
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     gp=matrix(0,nhstepm,1,nlstate);
+   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");
-     gm=matrix(0,nhstepm,1,nlstate);
+   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+ /*   } */
+   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     for(theta=1; theta <=npar; theta++){
+   pstamp(ficresvij);
-       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   if(popbased==1)
-       }
+     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+   else
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+   fprintf(ficresvij,"# Age");
-       if (popbased==1) {
+   for(i=1; i<=nlstate;i++)
-         if(mobilav ==0){
+     for(j=1; j<=nlstate;j++)
-           for(i=1; i<=nlstate;i++)
+       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-             prlim[i][i]=probs[(int)age][i][ij];
+   fprintf(ficresvij,"\n");
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
+   xp=vector(1,npar);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+   dnewm=matrix(1,nlstate,1,npar);
-         }
+   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=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
+   gpp=vector(nlstate+1,nlstate+ndeath);
-             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
+   gmp=vector(nlstate+1,nlstate+ndeath);
-         }
+   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-       }
-       /* This for computing probability of death (h=1 means
+   if(estepm < stepm){
-          computed over hstepm matrices product = hstepm*stepm months)
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-          as a weighted average of prlim.
+   }
-       */
+   else  hstepm=estepm;
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+   /* For example we decided to compute the life expectancy with the smallest unit */
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
+   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
+      nhstepm is the number of hstepm from age to agelim
-       }
+      nstepm is the number of stepm from age to agelin.
-       /* end probability of death */
+      Look at function hpijx to understand why (it is linked to memory size questions) */
+   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
-       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+      survival function given by stepm (the optimization length). Unfortunately it
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+      means that if the survival funtion is printed every two years of age and if
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+      results. So we changed our mind and took the option of the best precision.
+   */
-       if (popbased==1) {
+   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         if(mobilav ==0){
+   agelim = AGESUP;
-           for(i=1; i<=nlstate;i++)
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-             prlim[i][i]=probs[(int)age][i][ij];
+     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-         }else{ /* mobilav */
+     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-           for(i=1; i<=nlstate;i++)
+     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-         }
+     gp=matrix(0,nhstepm,1,nlstate);
-       }
+     gm=matrix(0,nhstepm,1,nlstate);
-       for(j=1; j<= nlstate; j++){
-         for(h=0; h<=nhstepm; h++){
+     for(theta=1; theta <=npar; theta++){
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-         }
+       }
-       }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       /* This for computing probability of death (h=1 means
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
+       if (popbased==1) {
-       */
+         if(mobilav ==0){
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+           for(i=1; i<=nlstate;i++)
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+             prlim[i][i]=probs[(int)age][i][ij];
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+         }else{ /* mobilav */
-       }
+           for(i=1; i<=nlstate;i++)
-       /* end probability of death */
+             prlim[i][i]=mobaverage[(int)age][i][ij];
+         }
-       for(j=1; j<= nlstate; j++) /* vareij */
+       }
-         for(h=0; h<=nhstepm; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+       for(j=1; j<= nlstate; j++){
-         }
+         for(h=0; h<=nhstepm; h++){
+           for(i=1, gp[h][j]=0.;i<=nlstate;i++)
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+             gp[h][j] += prlim[i][i]*p3mat[i][j][h];
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+         }
        }
+       /* This for computing probability of death (h=1 means
-     } /* End theta */
+          computed over hstepm matrices product = hstepm*stepm months)
+          as a weighted average of prlim.
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+       */
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     for(h=0; h<=nhstepm; h++) /* veij */
+         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-       for(j=1; j<=nlstate;j++)
+           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-         for(theta=1; theta <=npar; theta++)
+       }
-           trgradg[h][j][theta]=gradg[h][theta][j];
+       /* end probability of death */
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
-       for(theta=1; theta <=npar; theta++)
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-         trgradgp[j][theta]=gradgp[theta][j];
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+       if (popbased==1) {
-     for(i=1;i<=nlstate;i++)
+         if(mobilav ==0){
-       for(j=1;j<=nlstate;j++)
+           for(i=1; i<=nlstate;i++)
-         vareij[i][j][(int)age] =0.;
+             prlim[i][i]=probs[(int)age][i][ij];
+         }else{ /* mobilav */
-     for(h=0;h<=nhstepm;h++){
+           for(i=1; i<=nlstate;i++)
-       for(k=0;k<=nhstepm;k++){
+             prlim[i][i]=mobaverage[(int)age][i][ij];
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+         }
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+       }
-         for(i=1;i<=nlstate;i++)
-           for(j=1;j<=nlstate;j++)
+       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+         for(h=0; h<=nhstepm; h++){
-       }
+           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
-     }
+             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+         }
-     /* pptj */
+       }
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+       /* This for computing probability of death (h=1 means
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+          computed over hstepm matrices product = hstepm*stepm months)
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+          as a weighted average of prlim.
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+       */
-         varppt[j][i]=doldmp[j][i];
+       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-     /* end ppptj */
+         for(i=1,gmp[j]=0.; i<= nlstate; i++)
-     /*  x centered again */
+          gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+       }
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+       /* end probability of death */
-     if (popbased==1) {
+       for(j=1; j<= nlstate; j++) /* vareij */
-       if(mobilav ==0){
+         for(h=0; h<=nhstepm; h++){
-         for(i=1; i<=nlstate;i++)
+           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-           prlim[i][i]=probs[(int)age][i][ij];
+         }
-       }else{ /* mobilav */
-         for(i=1; i<=nlstate;i++)
+       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }
-     }
+     } /* End theta */
-     /* This for computing probability of death (h=1 means
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-        as a weighted average of prlim.
-     */
+     for(h=0; h<=nhstepm; h++) /* veij */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+       for(j=1; j<=nlstate;j++)
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+         for(theta=1; theta <=npar; theta++)
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
+           trgradg[h][j][theta]=gradg[h][theta][j];
-     }
-     /* end probability of death */
+     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+       for(theta=1; theta <=npar; theta++)
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+         trgradgp[j][theta]=gradgp[theta][j];
-     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++){
+     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+     for(i=1;i<=nlstate;i++)
-       }
+       for(j=1;j<=nlstate;j++)
-     }
+         vareij[i][j][(int)age] =0.;
-     fprintf(ficresprobmorprev,"\n");
+     for(h=0;h<=nhstepm;h++){
-     fprintf(ficresvij,"%.0f ",age );
+       for(k=0;k<=nhstepm;k++){
-     for(i=1; i<=nlstate;i++)
+         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-       for(j=1; j<=nlstate;j++){
+         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+         for(i=1;i<=nlstate;i++)
-       }
+           for(j=1;j<=nlstate;j++)
-     fprintf(ficresvij,"\n");
+             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-     free_matrix(gp,0,nhstepm,1,nlstate);
+       }
-     free_matrix(gm,0,nhstepm,1,nlstate);
+     }
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+     /* pptj */
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
-   } /* End age */
+     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++)
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
+       for(i=nlstate+1;i<=nlstate+ndeath;i++)
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+         varppt[j][i]=doldmp[j][i];
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+     /* end ppptj */
-   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+     /*  x centered again */
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
- /*   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); */
+     if (popbased==1) {
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+       if(mobilav ==0){
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
+         for(i=1; i<=nlstate;i++)
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
+           prlim[i][i]=probs[(int)age][i][ij];
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
+       }else{ /* mobilav */
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+         for(i=1; i<=nlstate;i++)
-   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);
+           prlim[i][i]=mobaverage[(int)age][i][ij];
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+       }
- */
+     }
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+     /* This for computing probability of death (h=1 means
+        computed over hstepm (estepm) matrices product = hstepm*stepm months)
-   free_vector(xp,1,npar);
+        as a weighted average of prlim.
-   free_matrix(doldm,1,nlstate,1,nlstate);
+     */
-   free_matrix(dnewm,1,nlstate,1,npar);
+     for(j=nlstate+1;j<=nlstate+ndeath;j++){
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+     }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     /* end probability of death */
-   fclose(ficresprobmorprev);
-   fflush(ficgp);
+     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-   fflush(fichtm);
+     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- }  /* end varevsij */
+       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+       for(i=1; i<=nlstate;i++){
- /************ Variance of prevlim ******************/
+         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+       }
- {
+     }
-   /* Variance of prevalence limit */
+     fprintf(ficresprobmorprev,"\n");
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
+     fprintf(ficresvij,"%.0f ",age );
-   double **dnewm,**doldm;
+     for(i=1; i<=nlstate;i++)
-   int i, j, nhstepm, hstepm;
+       for(j=1; j<=nlstate;j++){
-   int k, cptcode;
+         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-   double *xp;
+       }
-   double *gp, *gm;
+     fprintf(ficresvij,"\n");
-   double **gradg, **trgradg;
+     free_matrix(gp,0,nhstepm,1,nlstate);
-   double age,agelim;
+     free_matrix(gm,0,nhstepm,1,nlstate);
-   int theta;
+     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-   pstamp(ficresvpl);
+     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   } /* End age */
-   fprintf(ficresvpl,"# Age");
+   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   for(i=1; i<=nlstate;i++)
+   free_vector(gmp,nlstate+1,nlstate+ndeath);
-       fprintf(ficresvpl," %1d-%1d",i,i);
+   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   fprintf(ficresvpl,"\n");
+   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+   fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
-   xp=vector(1,npar);
+   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   dnewm=matrix(1,nlstate,1,npar);
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-   doldm=matrix(1,nlstate,1,nlstate);
+ /*   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); */
-   hstepm=1*YEARM; /* Every year of age */
+ /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
-   agelim = AGESUP;
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
-     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-     if (stepm >= YEARM) hstepm=1;
+   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);
-     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+   /*  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);
-     gradg=matrix(1,npar,1,nlstate);
+ */
-     gp=vector(1,nlstate);
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-     gm=vector(1,nlstate);
+   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-     for(theta=1; theta <=npar; theta++){
+   free_vector(xp,1,npar);
-       for(i=1; i<=npar; i++){ /* Computes gradient */
+   free_matrix(doldm,1,nlstate,1,nlstate);
-         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+   free_matrix(dnewm,1,nlstate,1,npar);
-       }
+   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-       for(i=1;i<=nlstate;i++)
+   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-         gp[i] = prlim[i][i];
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresprobmorprev);
-       for(i=1; i<=npar; i++) /* Computes gradient */
+   fflush(ficgp);
-         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+   fflush(fichtm);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ }  /* end varevsij */
-       for(i=1;i<=nlstate;i++)
-         gm[i] = prlim[i][i];
+ /************ Variance of prevlim ******************/
+ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
-       for(i=1;i<=nlstate;i++)
+ {
-         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+   /* Variance of prevalence limit */
-     } /* End theta */
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   double **newm;
-     trgradg =matrix(1,nlstate,1,npar);
+   double **dnewm,**doldm;
+   int i, j, nhstepm, hstepm;
-     for(j=1; j<=nlstate;j++)
+   int k, cptcode;
-       for(theta=1; theta <=npar; theta++)
+   double *xp;
-         trgradg[j][theta]=gradg[theta][j];
+   double *gp, *gm;
+   double **gradg, **trgradg;
-     for(i=1;i<=nlstate;i++)
+   double age,agelim;
-       varpl[i][(int)age] =0.;
+   int theta;
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+   pstamp(ficresvpl);
-     for(i=1;i<=nlstate;i++)
+   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+   fprintf(ficresvpl,"# Age");
+   for(i=1; i<=nlstate;i++)
-     fprintf(ficresvpl,"%.0f ",age );
+       fprintf(ficresvpl," %1d-%1d",i,i);
-     for(i=1; i<=nlstate;i++)
+   fprintf(ficresvpl,"\n");
-       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-     fprintf(ficresvpl,"\n");
+   xp=vector(1,npar);
-     free_vector(gp,1,nlstate);
+   dnewm=matrix(1,nlstate,1,npar);
-     free_vector(gm,1,nlstate);
+   doldm=matrix(1,nlstate,1,nlstate);
-     free_matrix(gradg,1,npar,1,nlstate);
-     free_matrix(trgradg,1,nlstate,1,npar);
+   hstepm=1*YEARM; /* Every year of age */
-   } /* End age */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGESUP;
-   free_vector(xp,1,npar);
+   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-   free_matrix(doldm,1,nlstate,1,npar);
+     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
- }
+     gradg=matrix(1,npar,1,nlstate);
+     gp=vector(1,nlstate);
- /************ Variance of one-step probabilities  ******************/
+     gm=vector(1,nlstate);
- 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(theta=1; theta <=npar; theta++){
-   int i, j=0,  i1, k1, l1, t, tj;
+       for(i=1; i<=npar; i++){ /* Computes gradient */
-   int k2, l2, j1,  z1;
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
-   int k=0,l, cptcode;
+       }
-   int first=1, first1;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+       for(i=1;i<=nlstate;i++)
-   double **dnewm,**doldm;
+         gp[i] = prlim[i][i];
-   double *xp;
-   double *gp, *gm;
+       for(i=1; i<=npar; i++) /* Computes gradient */
-   double **gradg, **trgradg;
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
-   double **mu;
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-   double age,agelim, cov[NCOVMAX];
+       for(i=1;i<=nlstate;i++)
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+         gm[i] = prlim[i][i];
-   int theta;
-   char fileresprob[FILENAMELENGTH];
+       for(i=1;i<=nlstate;i++)
-   char fileresprobcov[FILENAMELENGTH];
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
-   char fileresprobcor[FILENAMELENGTH];
+     } /* End theta */
-   double ***varpij;
+     trgradg =matrix(1,nlstate,1,npar);
-   strcpy(fileresprob,"prob");
+     for(j=1; j<=nlstate;j++)
-   strcat(fileresprob,fileres);
+       for(theta=1; theta <=npar; theta++)
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+         trgradg[j][theta]=gradg[theta][j];
-     printf("Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+     for(i=1;i<=nlstate;i++)
-   }
+       varpl[i][(int)age] =0.;
-   strcpy(fileresprobcov,"probcov");
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
-   strcat(fileresprobcov,fileres);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+     for(i=1;i<=nlstate;i++)
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   }
+     fprintf(ficresvpl,"%.0f ",age );
-   strcpy(fileresprobcor,"probcor");
+     for(i=1; i<=nlstate;i++)
-   strcat(fileresprobcor,fileres);
+       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+     fprintf(ficresvpl,"\n");
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+     free_vector(gp,1,nlstate);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+     free_vector(gm,1,nlstate);
-   }
+     free_matrix(gradg,1,npar,1,nlstate);
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+     free_matrix(trgradg,1,nlstate,1,npar);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   } /* End age */
-   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);
+   free_vector(xp,1,npar);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   free_matrix(doldm,1,nlstate,1,npar);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+   free_matrix(dnewm,1,nlstate,1,nlstate);
-   pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+ }
-   fprintf(ficresprob,"# Age");
-   pstamp(ficresprobcov);
+ /************ Variance of one-step probabilities  ******************/
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+ 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(ficresprobcov,"# Age");
+ {
-   pstamp(ficresprobcor);
+   int i, j=0,  i1, k1, l1, t, tj;
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+   int k2, l2, j1,  z1;
-   fprintf(ficresprobcor,"# Age");
+   int k=0,l, cptcode;
+   int first=1, first1;
+   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   for(i=1; i<=nlstate;i++)
+   double **dnewm,**doldm;
-     for(j=1; j<=(nlstate+ndeath);j++){
+   double *xp;
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+   double *gp, *gm;
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+   double **gradg, **trgradg;
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+   double **mu;
-     }
+   double age,agelim, cov[NCOVMAX];
-  /* fprintf(ficresprob,"\n");
+   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   fprintf(ficresprobcov,"\n");
+   int theta;
-   fprintf(ficresprobcor,"\n");
+   char fileresprob[FILENAMELENGTH];
-  */
+   char fileresprobcov[FILENAMELENGTH];
-  xp=vector(1,npar);
+   char fileresprobcor[FILENAMELENGTH];
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   double ***varpij;
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+   strcpy(fileresprob,"prob");
-   first=1;
+   strcat(fileresprob,fileres);
-   fprintf(ficgp,"\n# Routine varprob");
+   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+     printf("Problem with resultfile: %s\n", fileresprob);
-   fprintf(fichtm,"\n");
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+   }
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   strcpy(fileresprobcov,"probcov");
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   strcat(fileresprobcov,fileres);
-   file %s<br>\n",optionfilehtmcov);
+   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+     printf("Problem with resultfile: %s\n", fileresprobcov);
- and drawn. It helps understanding how is the covariance between two incidences.\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+   }
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+   strcpy(fileresprobcor,"probcor");
- It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+   strcat(fileresprobcor,fileres);
- would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
- standard deviations wide on each axis. <br>\
+     printf("Problem with resultfile: %s\n", fileresprobcor);
-  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+   }
- To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
+   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   cov[1]=1;
+   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   tj=cptcoveff;
+   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   j1=0;
+   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   for(t=1; t<=tj;t++){
+   pstamp(ficresprob);
-     for(i1=1; i1<=ncodemax[t];i1++){
+   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-       j1++;
+   fprintf(ficresprob,"# Age");
-       if  (cptcovn>0) {
+   pstamp(ficresprobcov);
-         fprintf(ficresprob, "\n#********** Variable ");
+   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   fprintf(ficresprobcov,"# Age");
-         fprintf(ficresprob, "**********\n#\n");
+   pstamp(ficresprobcor);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   fprintf(ficresprobcor,"# Age");
-         fprintf(ficresprobcov, "**********\n#\n");
-         fprintf(ficgp, "\n#********** Variable ");
+   for(i=1; i<=nlstate;i++)
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+     for(j=1; j<=(nlstate+ndeath);j++){
-         fprintf(ficgp, "**********\n#\n");
+       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+       fprintf(ficresprobcor," p%1d-%1d ",i,j);
-         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(ficresprob,"\n");
-         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+   fprintf(ficresprobcov,"\n");
+   fprintf(ficresprobcor,"\n");
-         fprintf(ficresprobcor, "\n#********** Variable ");
+  */
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+   xp=vector(1,npar);
-         fprintf(ficresprobcor, "**********\n#");
+   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       }
+   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-       for (age=bage; age<=fage; age ++){
+   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-         cov[2]=age;
+   first=1;
-         for (k=1; k<=cptcovn;k++) {
+   fprintf(ficgp,"\n# Routine varprob");
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-         }
+   fprintf(fichtm,"\n");
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         for (k=1; k<=cptcovprod;k++)
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   file %s<br>\n",optionfilehtmcov);
-         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ and drawn. It helps understanding how is the covariance between two incidences.\
-         gp=vector(1,(nlstate)*(nlstate+ndeath));
+  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-         gm=vector(1,(nlstate)*(nlstate+ndeath));
+   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+ It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-         for(theta=1; theta <=npar; theta++){
+ would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-           for(i=1; i<=npar; i++)
+ standard deviations wide on each axis. <br>\
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+ To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-           k=0;
+   cov[1]=1;
-           for(i=1; i<= (nlstate); i++){
+   tj=cptcoveff;
-             for(j=1; j<=(nlstate+ndeath);j++){
+   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-               k=k+1;
+   j1=0;
-               gp[k]=pmmij[i][j];
+   for(t=1; t<=tj;t++){
-             }
+     for(i1=1; i1<=ncodemax[t];i1++){
-           }
+       j1++;
+       if  (cptcovn>0) {
-           for(i=1; i<=npar; i++)
+         fprintf(ficresprob, "\n#********** Variable ");
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresprob, "**********\n#\n");
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+         fprintf(ficresprobcov, "\n#********** Variable ");
-           k=0;
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-           for(i=1; i<=(nlstate); i++){
+         fprintf(ficresprobcov, "**********\n#\n");
-             for(j=1; j<=(nlstate+ndeath);j++){
-               k=k+1;
+         fprintf(ficgp, "\n#********** Variable ");
-               gm[k]=pmmij[i][j];
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-             }
+         fprintf(ficgp, "**********\n#\n");
-           }
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+         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\">");
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+         fprintf(ficresprobcor, "\n#********** Variable ");
-           for(theta=1; theta <=npar; theta++)
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-             trgradg[j][theta]=gradg[theta][j];
+         fprintf(ficresprobcor, "**********\n#");
+       }
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+       for (age=bage; age<=fage; age ++){
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+         cov[2]=age;
-         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+         for (k=1; k<=cptcovn;k++) {
-         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
-         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+         }
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
+         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]]];
-         k=0;
-         for(i=1; i<=(nlstate); i++){
+         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-           for(j=1; j<=(nlstate+ndeath);j++){
+         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-             k=k+1;
+         gp=vector(1,(nlstate)*(nlstate+ndeath));
-             mu[k][(int) age]=pmmij[i][j];
+         gm=vector(1,(nlstate)*(nlstate+ndeath));
-           }
-         }
+         for(theta=1; theta <=npar; theta++){
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+           for(i=1; i<=npar; i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-             varpij[i][j][(int)age] = doldm[i][j];
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           k=0;
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+           for(i=1; i<= (nlstate); i++){
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+             for(j=1; j<=(nlstate+ndeath);j++){
-           }*/
+               k=k+1;
+               gp[k]=pmmij[i][j];
-         fprintf(ficresprob,"\n%d ",(int)age);
+             }
-         fprintf(ficresprobcov,"\n%d ",(int)age);
+           }
-         fprintf(ficresprobcor,"\n%d ",(int)age);
+           for(i=1; i<=npar; i++)
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+           k=0;
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+           for(i=1; i<=(nlstate); i++){
-         }
+             for(j=1; j<=(nlstate+ndeath);j++){
-         i=0;
+               k=k+1;
-         for (k=1; k<=(nlstate);k++){
+               gm[k]=pmmij[i][j];
-           for (l=1; l<=(nlstate+ndeath);l++){
+             }
-             i=i++;
+           }
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
-             for (j=1; j<=i;j++){
+             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-               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]));
-             }
+         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-           }
+           for(theta=1; theta <=npar; theta++)
-         }/* end of loop for state */
+             trgradg[j][theta]=gradg[theta][j];
-       } /* end of loop for age */
+         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-       /* Confidence intervalle of pij  */
+         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-       /*
+         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         fprintf(ficgp,"\nset noparametric;unset label");
+         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+         pmij(pmmij,cov,ncovmodel,x,nlstate);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+         k=0;
-       */
+         for(i=1; i<=(nlstate); i++){
+           for(j=1; j<=(nlstate+ndeath);j++){
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+             k=k+1;
-       first1=1;
+             mu[k][(int) age]=pmmij[i][j];
-       for (k2=1; k2<=(nlstate);k2++){
+           }
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
+         }
-           if(l2==k2) continue;
+         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           j=(k2-1)*(nlstate+ndeath)+l2;
+           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-           for (k1=1; k1<=(nlstate);k1++){
+             varpij[i][j][(int)age] = doldm[i][j];
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
+         /*printf("\n%d ",(int)age);
-               i=(k1-1)*(nlstate+ndeath)+l1;
+           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-               if(i<=j) continue;
+           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-               for (age=bage; age<=fage; age ++){
+           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                 if ((int)age %5==0){
+           }*/
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+         fprintf(ficresprob,"\n%d ",(int)age);
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+         fprintf(ficresprobcov,"\n%d ",(int)age);
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
+         fprintf(ficresprobcor,"\n%d ",(int)age);
-                   mu2=mu[j][(int) age]/stepm*YEARM;
-                   c12=cv12/sqrt(v1*v2);
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                   /* Computing eigen value of matrix of covariance */
+           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-                   /* Eigen vectors */
+           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+         }
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+         i=0;
-                   v21=(lc1-v1)/cv12*v11;
+         for (k=1; k<=(nlstate);k++){
-                   v12=-v21;
+           for (l=1; l<=(nlstate+ndeath);l++){
-                   v22=v11;
+             i=i++;
-                   tnalp=v21/v11;
+             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-                   if(first1==1){
+             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-                     first1=0;
+             for (j=1; j<=i;j++){
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+               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(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*/
+           }
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+         }/* end of loop for state */
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+       } /* end of loop for age */
-                   if(first==1){
-                     first=0;
+       /* Confidence intervalle of pij  */
-                     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);
+         fprintf(ficgp,"\nunset parametric;unset label");
-                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+         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);
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+       */
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+       first1=1;
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+       for (k2=1; k2<=(nlstate);k2++){
-                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+         for (l2=1; l2<=(nlstate+ndeath);l2++){
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+           if(l2==k2) continue;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+           j=(k2-1)*(nlstate+ndeath)+l2;
-                   }else{
+           for (k1=1; k1<=(nlstate);k1++){
-                     first=0;
+             for (l1=1; l1<=(nlstate+ndeath);l1++){
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+               if(l1==k1) continue;
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+               i=(k1-1)*(nlstate+ndeath)+l1;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+               if(i<=j) continue;
-                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+               for (age=bage; age<=fage; age ++){
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+                 if ((int)age %5==0){
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   }/* if first */
+                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                 } /* age mod 5 */
+                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-               } /* end loop age */
+                   mu1=mu[i][(int) age]/stepm*YEARM ;
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                   mu2=mu[j][(int) age]/stepm*YEARM;
-               first=1;
+                   c12=cv12/sqrt(v1*v2);
-             } /*l12 */
+                   /* Computing eigen value of matrix of covariance */
-           } /* k12 */
+                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-         } /*l1 */
+                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-       }/* k1 */
+                   if ((lc2 <0) || (lc1 <0) ){
-     } /* loop covariates */
+                     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);
-   }
+                     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);
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+                     lc1=fabs(lc1);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+                     lc2=fabs(lc2);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+                   }
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_vector(xp,1,npar);
+                   /* Eigen vectors */
-   fclose(ficresprob);
+                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
-   fclose(ficresprobcov);
+                   /*v21=sqrt(1.-v11*v11); *//* error */
-   fclose(ficresprobcor);
+                   v21=(lc1-v1)/cv12*v11;
-   fflush(ficgp);
+                   v12=-v21;
-   fflush(fichtmcov);
+                   v22=v11;
- }
+                   tnalp=v21/v11;
+                   if(first1==1){
+                     first1=0;
- /******************* Printing html file ***********/
+                     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);
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+                   }
-                   int lastpass, int stepm, int weightopt, char model[],\
+                   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);
-                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+                   /*printf(fignu*/
-                   int popforecast, int estepm ,\
+                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
-                   double jprev1, double mprev1,double anprev1, \
+                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
-                   double jprev2, double mprev2,double anprev2){
+                   if(first==1){
-   int jj1, k1, i1, cpt;
+                     first=0;
+                     fprintf(ficgp,"\nset parametric;unset label");
-    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+                     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);
-    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- </ul>");
+                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
+  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+ %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
-    fprintf(fichtm,"\
+                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-    fprintf(fichtm,"\
+                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
-    fprintf(fichtm,"\
+                     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",\
-  - (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): \
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-    <a href=\"%s\">%s</a> <br>\n",
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+                   }else{
-    fprintf(fichtm,"\
+                     first=0;
-  - Population projections by age and states: \
+                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
+                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
-  m=cptcoveff;
+                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+                   }/* if first */
+                 } /* age mod 5 */
-  jj1=0;
+               } /* end loop age */
-  for(k1=1; k1<=m;k1++){
+               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
-    for(i1=1; i1<=ncodemax[k1];i1++){
+               first=1;
-      jj1++;
+             } /*l12 */
-      if (cptcovn > 0) {
+           } /* k12 */
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         } /*l1 */
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+       }/* k1 */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+     } /* loop covariates */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+   }
-      }
+   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-      /* Pij */
+   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
-      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> \
+   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-      /* Quasi-incidences */
+   free_vector(xp,1,npar);
-      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
+   fclose(ficresprob);
-  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> \
+   fclose(ficresprobcov);
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+   fclose(ficresprobcor);
-        /* Period (stable) prevalence in each health state */
+   fflush(ficgp);
-        for(cpt=1; cpt<nlstate;cpt++){
+   fflush(fichtmcov);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+ }
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-        }
-      for(cpt=1; cpt<=nlstate;cpt++) {
+ /******************* Printing html file ***********/
-         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> \
+ void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+                   int lastpass, int stepm, int weightopt, char model[],\
-      }
+                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-    } /* end i1 */
+                   int popforecast, int estepm ,\
-  }/* End k1 */
+                   double jprev1, double mprev1,double anprev1, \
-  fprintf(fichtm,"</ul>");
+                   double jprev2, double mprev2,double anprev2){
+   int jj1, k1, i1, cpt;
-  fprintf(fichtm,"\
+    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
- \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
+    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+ </ul>");
+    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
-  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+    fprintf(fichtm,"\
-  fprintf(fichtm,"\
+  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+    fprintf(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): \
-  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n",
-    <a href=\"%s\">%s</a> <br>\n</li>",
+            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+    fprintf(fichtm,"\
-  fprintf(fichtm,"\
+  - Population projections by age and states: \
-  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
-    <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  m=cptcoveff;
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  fprintf(fichtm,"\
-  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
+  jj1=0;
-          subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+  for(k1=1; k1<=m;k1++){
-  fprintf(fichtm,"\
+    for(i1=1; i1<=ncodemax[k1];i1++){
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+      jj1++;
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+      if (cptcovn > 0) {
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
- /*  if(popforecast==1) fprintf(fichtm,"\n */
+        for (cpt=1; cpt<=cptcoveff;cpt++)
- /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
- /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
- /*      <br>",fileres,fileres,fileres,fileres); */
+      }
- /*  else  */
+      /* Pij */
- /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
+      fprintf(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> \
-  fflush(fichtm);
+ <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+      /* Quasi-incidences */
+      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
-  m=cptcoveff;
+  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> \
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+ <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+        /* Period (stable) prevalence in each health state */
-  jj1=0;
+        for(cpt=1; cpt<nlstate;cpt++){
-  for(k1=1; k1<=m;k1++){
+          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
-    for(i1=1; i1<=ncodemax[k1];i1++){
+ <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
-      jj1++;
+        }
-      if (cptcovn > 0) {
+      for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+         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 (cpt=1; cpt<=cptcoveff;cpt++)
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+      }
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+    } /* end i1 */
-      }
+  }/* End k1 */
-      for(cpt=1; cpt<=nlstate;cpt++) {
+  fprintf(fichtm,"</ul>");
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+  fprintf(fichtm,"\
-      }
+ \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
- health expectancies in states (1) and (2): %s%d.png<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-    } /* end i1 */
+          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
-  }/* End k1 */
+  fprintf(fichtm,"\
-  fprintf(fichtm,"</ul>");
+  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-  fflush(fichtm);
+          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
- }
+  fprintf(fichtm,"\
- /******************* Gnuplot file **************/
+  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+  fprintf(fichtm,"\
-   char dirfileres[132],optfileres[132];
+  - 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): \
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+    <a href=\"%s\">%s</a> <br>\n</li>",
-   int ng;
+            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
- /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
+  fprintf(fichtm,"\
- /*     printf("Problem with file %s",optionfilegnuplot); */
+  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
- /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
+    <a href=\"%s\">%s</a> <br>\n</li>",
- /*   } */
+            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+  fprintf(fichtm,"\
-   /*#ifdef windows */
+  - 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",
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
+          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
-     /*#endif */
+  fprintf(fichtm,"\
-   m=pow(2,cptcoveff);
+  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
+          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
-   strcpy(dirfileres,optionfilefiname);
+  fprintf(fichtm,"\
-   strcpy(optfileres,"vpl");
+  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-  /* 1eme*/
+          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
-    for (k1=1; k1<= m ; k1 ++) {
+ /*  if(popforecast==1) fprintf(fichtm,"\n */
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+ /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+ /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+ /*      <br>",fileres,fileres,fileres,fileres); */
- set ylabel \"Probability\" \n\
+ /*  else  */
- set ter png small\n\
+ /*    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); */
- set size 0.65,0.65\n\
+  fflush(fichtm);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-      for (i=1; i<= nlstate ; i ++) {
+  m=cptcoveff;
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
-      }
+  jj1=0;
-      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+  for(k1=1; k1<=m;k1++){
-      for (i=1; i<= nlstate ; i ++) {
+    for(i1=1; i1<=ncodemax[k1];i1++){
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+      jj1++;
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      if (cptcovn > 0) {
-      }
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+        for (cpt=1; cpt<=cptcoveff;cpt++)
-      for (i=1; i<= nlstate ; i ++) {
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+      }
-      }
+      for(cpt=1; cpt<=nlstate;cpt++) {
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-    }
+ prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
-   }
+ <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
-   /*2 eme*/
+      }
+      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-   for (k1=1; k1<= m ; k1 ++) {
+ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+ true period expectancies (those weighted with period prevalences are also\
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+  drawn in addition to the population based expectancies computed using\
+  observed and cahotic prevalences: %s%d.png<br>\
-     for (i=1; i<= nlstate+1 ; i ++) {
+ <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
-       k=2*i;
+    } /* end i1 */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+  }/* End k1 */
-       for (j=1; j<= nlstate+1 ; j ++) {
+  fprintf(fichtm,"</ul>");
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  fflush(fichtm);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
-       }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+ /******************* Gnuplot file **************/
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+ void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-       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 ++) {
+   char dirfileres[132],optfileres[132];
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   int ng=0;
-       }
+ /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-       fprintf(ficgp,"\" t\"\" w l 0,");
+ /*     printf("Problem with file %s",optionfilegnuplot); */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+ /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-       for (j=1; j<= nlstate+1 ; j ++) {
+ /*   } */
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+   /*#ifdef windows */
-       }
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+     /*#endif */
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+   m=pow(2,cptcoveff);
-     }
-   }
+   strcpy(dirfileres,optionfilefiname);
+   strcpy(optfileres,"vpl");
-   /*3eme*/
+  /* 1eme*/
+   for (cpt=1; cpt<= nlstate ; cpt ++) {
-   for (k1=1; k1<= m ; k1 ++) {
+    for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
+      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
-       /*       k=2+nlstate*(2*cpt-2); */
+      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
-       k=2+(nlstate+1)*(cpt-1);
+      fprintf(ficgp,"set xlabel \"Age\" \n\
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+ set ylabel \"Probability\" \n\
-       fprintf(ficgp,"set ter png small\n\
+ set ter png small\n\
  set size 0.65,0.65\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+      for (i=1; i<= nlstate ; i ++) {
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+        else        fprintf(ficgp," \%%*lf (\%%*lf)");
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+      }
-         fprintf(ficgp,"\" t \"e%d1\" w l",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);
+      for (i=1; i<= nlstate ; i ++) {
-       */
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       for (i=1; i< nlstate ; i ++) {
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+      }
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      for (i=1; i<= nlstate ; i ++) {
-       }
+        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+        else fprintf(ficgp," \%%*lf (\%%*lf)");
-     }
+      }
-   }
+      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+    }
-   /* CV preval stable (period) */
+   }
-   for (k1=1; k1<= m ; k1 ++) {
+   /*2 eme*/
-     for (cpt=1; cpt<=nlstate ; cpt ++) {
-       k=3;
+   for (k1=1; k1<= m ; k1 ++) {
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
- set ter png small\nset size 0.65,0.65\n\
- unset log y\n\
+     for (i=1; i<= nlstate+1 ; i ++) {
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+       k=2*i;
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-       for (i=1; i< nlstate ; i ++)
+       for (j=1; j<= nlstate+1 ; j ++) {
-         fprintf(ficgp,"+$%d",k+i+1);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-       l=3+(nlstate+ndeath)*cpt;
+       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-       for (i=1; i< nlstate ; i ++) {
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
-         l=3+(nlstate+ndeath)*cpt;
+       for (j=1; j<= nlstate+1 ; j ++) {
-         fprintf(ficgp,"+$%d",l+i+1);
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-       }
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+       }
-     }
+       fprintf(ficgp,"\" t\"\" w l 0,");
-   }
+       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+       for (j=1; j<= nlstate+1 ; j ++) {
-   /* proba elementaires */
+         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-   for(i=1,jk=1; i <=nlstate; i++){
+         else fprintf(ficgp," \%%*lf (\%%*lf)");
-     for(k=1; k <=(nlstate+ndeath); k++){
+       }
-       if (k != i) {
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
-         for(j=1; j <=ncovmodel; j++){
+       else fprintf(ficgp,"\" t\"\" w l 0,");
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+     }
-           jk++;
+   }
-           fprintf(ficgp,"\n");
-         }
+   /*3eme*/
-       }
-     }
+   for (k1=1; k1<= m ; k1 ++) {
-    }
+     for (cpt=1; cpt<= nlstate ; cpt ++) {
+       /*       k=2+nlstate*(2*cpt-2); */
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+       k=2+(nlstate+1)*(cpt-1);
-      for(jk=1; jk <=m; jk++) {
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+       fprintf(ficgp,"set ter png small\n\
-        if (ng==2)
+ set size 0.65,0.65\n\
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
-        else
+       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-        i=1;
+         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-        for(k2=1; k2<=nlstate; k2++) {
+         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-          k3=i;
+         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-          for(k=1; k<=(nlstate+ndeath); k++) {
-            if (k != k2){
+       */
-              if(ng==2)
+       for (i=1; i< nlstate ; i ++) {
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
-              else
+         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
+       }
-              for(j=3; j <=ncovmodel; j++) {
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
-                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++;
-                }
+   /* CV preval stable (period) */
-                else
+   for (k1=1; k1<= m ; k1 ++) {
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     for (cpt=1; cpt<=nlstate ; cpt ++) {
-              }
+       k=3;
-              fprintf(ficgp,")/(1");
+       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-              for(k1=1; k1 <=nlstate; k1++){
+ set ter png small\nset size 0.65,0.65\n\
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ unset log y\n\
-                ij=1;
+ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-                for(j=3; j <=ncovmodel; j++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+       for (i=1; i< nlstate ; i ++)
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+         fprintf(ficgp,"+$%d",k+i+1);
-                    ij++;
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-                  }
-                  else
+       l=3+(nlstate+ndeath)*cpt;
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
-                }
+       for (i=1; i< nlstate ; i ++) {
-                fprintf(ficgp,")");
+         l=3+(nlstate+ndeath)*cpt;
-              }
+         fprintf(ficgp,"+$%d",l+i+1);
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+       }
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
-              i=i+ncovmodel;
+     }
-            }
+   }
-          } /* end k */
-        } /* end k2 */
+   /* proba elementaires */
-      } /* end jk */
+   for(i=1,jk=1; i <=nlstate; i++){
-    } /* end ng */
+     for(k=1; k <=(nlstate+ndeath); k++){
-    fflush(ficgp);
+       if (k != i) {
- }  /* end gnuplot */
+         for(j=1; j <=ncovmodel; j++){
+           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           jk++;
- /*************** Moving average **************/
+           fprintf(ficgp,"\n");
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+         }
+       }
-   int i, cpt, cptcod;
+     }
-   int modcovmax =1;
+    }
-   int mobilavrange, mob;
-   double age;
+    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+      for(jk=1; jk <=m; jk++) {
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
+        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
-                            a covariate has 2 modalities */
+        if (ng==2)
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+        else
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+          fprintf(ficgp,"\nset title \"Probability\"\n");
-     if(mobilav==1) mobilavrange=5; /* default */
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-     else mobilavrange=mobilav;
+        i=1;
-     for (age=bage; age<=fage; age++)
+        for(k2=1; k2<=nlstate; k2++) {
-       for (i=1; i<=nlstate;i++)
+          k3=i;
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
+          for(k=1; k<=(nlstate+ndeath); k++) {
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+            if (k != k2){
-     /* We keep the original values on the extreme ages bage, fage and for
+              if(ng==2)
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-        we use a 5 terms etc. until the borders are no more concerned.
+              else
-     */
+                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+              ij=1;
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+              for(j=3; j <=ncovmodel; j++) {
-         for (i=1; i<=nlstate;i++){
+                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+                  ij++;
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                else
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-               }
+              }
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+              fprintf(ficgp,")/(1");
-           }
-         }
+              for(k1=1; k1 <=nlstate; k1++){
-       }/* end age */
+                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-     }/* end mob */
+                ij=1;
-   }else return -1;
+                for(j=3; j <=ncovmodel; j++){
-   return 0;
+                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- }/* End movingaverage */
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    ij++;
+                  }
- /************** Forecasting ******************/
+                  else
- prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-   /* proj1, year, month, day of starting projection
+                }
-      agemin, agemax range of age
+                fprintf(ficgp,")");
-      dateprev1 dateprev2 range of dates during which prevalence is computed
+              }
-      anproj2 year of en of projection (same day and month as proj1).
+              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-   */
+              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
+              i=i+ncovmodel;
-   int *popage;
+            }
-   double agec; /* generic age */
+          } /* end k */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+        } /* end k2 */
-   double *popeffectif,*popcount;
+      } /* end jk */
-   double ***p3mat;
+    } /* end ng */
-   double ***mobaverage;
+    fflush(ficgp);
-   char fileresf[FILENAMELENGTH];
+ }  /* end gnuplot */
-   agelim=AGESUP;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /*************** Moving average **************/
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-   strcpy(fileresf,"f");
-   strcat(fileresf,fileres);
+   int i, cpt, cptcod;
-   if((ficresf=fopen(fileresf,"w"))==NULL) {
+   int modcovmax =1;
-     printf("Problem with forecast resultfile: %s\n", fileresf);
+   int mobilavrange, mob;
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+   double age;
-   }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+                            a covariate has 2 modalities */
+   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-   if (mobilav!=0) {
+     if(mobilav==1) mobilavrange=5; /* default */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     else mobilavrange=mobilav;
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+     for (age=bage; age<=fage; age++)
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       for (i=1; i<=nlstate;i++)
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-     }
+           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
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+        we use a 5 terms etc. until the borders are no more concerned.
-   if (stepm<=12) stepsize=1;
+     */
-   if(estepm < stepm){
+     for (mob=3;mob <=mobilavrange;mob=mob+2){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-   }
+         for (i=1; i<=nlstate;i++){
-   else  hstepm=estepm;
+           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
-   hstepm=hstepm/stepm;
+               for (cpt=1;cpt<=(mob-1)/2;cpt++){
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
-                                fractional in yp1 */
+                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-   anprojmean=yp;
+               }
-   yp2=modf((yp1*12),&yp);
+             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-   mprojmean=yp;
+           }
-   yp1=modf((yp2*30.5),&yp);
+         }
-   jprojmean=yp;
+       }/* end age */
-   if(jprojmean==0) jprojmean=1;
+     }/* end mob */
-   if(mprojmean==0) jprojmean=1;
+   }else return -1;
+   return 0;
-   i1=cptcoveff;
+ }/* End movingaverage */
-   if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+ /************** Forecasting ******************/
+ prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   /* proj1, year, month, day of starting projection
+      agemin, agemax range of age
- /*            if (h==(int)(YEARM*yearp)){ */
+      dateprev1 dateprev2 range of dates during which prevalence is computed
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+      anproj2 year of en of projection (same day and month as proj1).
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   */
-       k=k+1;
+   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
-       fprintf(ficresf,"\n#******");
+   int *popage;
-       for(j=1;j<=cptcoveff;j++) {
+   double agec; /* generic age */
-         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]]);
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
-       }
+   double *popeffectif,*popcount;
-       fprintf(ficresf,"******\n");
+   double ***p3mat;
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
+   double ***mobaverage;
-       for(j=1; j<=nlstate+ndeath;j++){
+   char fileresf[FILENAMELENGTH];
-         for(i=1; i<=nlstate;i++)
-           fprintf(ficresf," p%d%d",i,j);
+   agelim=AGESUP;
-         fprintf(ficresf," p.%d",j);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-       }
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+   strcpy(fileresf,"f");
-         fprintf(ficresf,"\n");
+   strcat(fileresf,fileres);
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+   if((ficresf=fopen(fileresf,"w"))==NULL) {
+     printf("Problem with forecast resultfile: %s\n", fileresf);
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+   }
-           nhstepm = nhstepm/hstepm;
+   printf("Computing forecasting: result on file '%s' \n", fileresf);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-           oldm=oldms;savm=savms;
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-           for (h=0; h<=nhstepm; h++){
+   if (mobilav!=0) {
-             if (h*hstepm/YEARM*stepm ==yearp) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               fprintf(ficresf,"\n");
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-               for(j=1;j<=cptcoveff;j++)
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+     }
-             }
+   }
-             for(j=1; j<=nlstate+ndeath;j++) {
-               ppij=0.;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-               for(i=1; i<=nlstate;i++) {
+   if (stepm<=12) stepsize=1;
-                 if (mobilav==1)
+   if(estepm < stepm){
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+     printf ("Problem %d lower than %d\n",estepm, stepm);
-                 else {
+   }
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+   else  hstepm=estepm;
-                 }
-                 if (h*hstepm/YEARM*stepm== yearp) {
+   hstepm=hstepm/stepm;
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-                 }
+                                fractional in yp1 */
-               } /* end i */
+   anprojmean=yp;
-               if (h*hstepm/YEARM*stepm==yearp) {
+   yp2=modf((yp1*12),&yp);
-                 fprintf(ficresf," %.3f", ppij);
+   mprojmean=yp;
-               }
+   yp1=modf((yp2*30.5),&yp);
-             }/* end j */
+   jprojmean=yp;
-           } /* end h */
+   if(jprojmean==0) jprojmean=1;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+   if(mprojmean==0) jprojmean=1;
-         } /* end agec */
-       } /* end yearp */
+   i1=cptcoveff;
-     } /* end cptcod */
+   if (cptcovn < 1){i1=1;}
-   } /* end  cptcov */
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fprintf(ficresf,"#****** Routine prevforecast **\n");
-   fclose(ficresf);
- }
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
- /************** Forecasting *****not tested NB*************/
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- 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){
+       k=k+1;
+       fprintf(ficresf,"\n#******");
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+       for(j=1;j<=cptcoveff;j++) {
-   int *popage;
+         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]]);
-   double calagedatem, agelim, kk1, kk2;
+       }
-   double *popeffectif,*popcount;
+       fprintf(ficresf,"******\n");
-   double ***p3mat,***tabpop,***tabpopprev;
+       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
-   double ***mobaverage;
+       for(j=1; j<=nlstate+ndeath;j++){
-   char filerespop[FILENAMELENGTH];
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresf," p%d%d",i,j);
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+         fprintf(ficresf," p.%d",j);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       }
-   agelim=AGESUP;
+       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+         fprintf(ficresf,"\n");
+         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+         for (agec=fage; agec>=(ageminpar-1); agec--){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-   strcpy(filerespop,"pop");
+           nhstepm = nhstepm/hstepm;
-   strcat(filerespop,fileres);
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+           oldm=oldms;savm=savms;
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-   }
+           for (h=0; h<=nhstepm; h++){
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+             if (h*hstepm/YEARM*stepm ==yearp) {
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+               fprintf(ficresf,"\n");
+               for(j=1;j<=cptcoveff;j++)
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-   if (mobilav!=0) {
+             }
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             for(j=1; j<=nlstate+ndeath;j++) {
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+               ppij=0.;
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+               for(i=1; i<=nlstate;i++) {
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                 if (mobilav==1)
-     }
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-   }
+                 else {
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+                 }
-   if (stepm<=12) stepsize=1;
+                 if (h*hstepm/YEARM*stepm== yearp) {
+                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
-   agelim=AGESUP;
+                 }
+               } /* end i */
-   hstepm=1;
+               if (h*hstepm/YEARM*stepm==yearp) {
-   hstepm=hstepm/stepm;
+                 fprintf(ficresf," %.3f", ppij);
+               }
-   if (popforecast==1) {
+             }/* end j */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+           } /* end h */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+         } /* end agec */
-     }
+       } /* end yearp */
-     popage=ivector(0,AGESUP);
+     } /* end cptcod */
-     popeffectif=vector(0,AGESUP);
+   } /* end  cptcov */
-     popcount=vector(0,AGESUP);
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     i=1;
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+   fclose(ficresf);
+ }
-     imx=i;
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ /************** Forecasting *****not tested NB*************/
-   }
+ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   int *popage;
-       k=k+1;
+   double calagedatem, agelim, kk1, kk2;
-       fprintf(ficrespop,"\n#******");
+   double *popeffectif,*popcount;
-       for(j=1;j<=cptcoveff;j++) {
+   double ***p3mat,***tabpop,***tabpopprev;
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+   double ***mobaverage;
-       }
+   char filerespop[FILENAMELENGTH];
-       fprintf(ficrespop,"******\n");
-       fprintf(ficrespop,"# Age");
+   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+   agelim=AGESUP;
+   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-       for (cpt=0; cpt<=0;cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+   strcpy(filerespop,"pop");
-           nhstepm = nhstepm/hstepm;
+   strcat(filerespop,fileres);
+   if((ficrespop=fopen(filerespop,"w"))==NULL) {
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     printf("Problem with forecast resultfile: %s\n", filerespop);
-           oldm=oldms;savm=savms;
+     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+   }
+   printf("Computing forecasting: result on file '%s' \n", filerespop);
-           for (h=0; h<=nhstepm; h++){
+   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
+   if (mobilav!=0) {
-               kk1=0.;kk2=0;
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-               for(i=1; i<=nlstate;i++) {
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
-                 if (mobilav==1)
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-                 else {
+     }
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+   }
-                 }
-               }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
-               if (h==(int)(calagedatem+12*cpt)){
+   if (stepm<=12) stepsize=1;
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-                   /*fprintf(ficrespop," %.3f", kk1);
+   agelim=AGESUP;
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
+   hstepm=1;
-             }
+   hstepm=hstepm/stepm;
-             for(i=1; i<=nlstate;i++){
-               kk1=0.;
+   if (popforecast==1) {
-                 for(j=1; j<=nlstate;j++){
+     if((ficpop=fopen(popfile,"r"))==NULL) {
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+       printf("Problem with population file : %s\n",popfile);exit(0);
-                 }
+       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+     }
-             }
+     popage=ivector(0,AGESUP);
+     popeffectif=vector(0,AGESUP);
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+     popcount=vector(0,AGESUP);
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-           }
+     i=1;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-         }
-       }
+     imx=i;
+     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-   /******/
+   }
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+       k=k+1;
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+       fprintf(ficrespop,"\n#******");
-           nhstepm = nhstepm/hstepm;
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       }
-           oldm=oldms;savm=savms;
+       fprintf(ficrespop,"******\n");
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fprintf(ficrespop,"# Age");
-           for (h=0; h<=nhstepm; h++){
+       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+       if (popforecast==1)  fprintf(ficrespop," [Population]");
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
+       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);
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-               }
+           nhstepm = nhstepm/hstepm;
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-             }
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           }
+           oldm=oldms;savm=savms;
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-         }
-       }
+           for (h=0; h<=nhstepm; h++){
-    }
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-   }
+               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+             }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             for(j=1; j<=nlstate+ndeath;j++) {
+               kk1=0.;kk2=0;
-   if (popforecast==1) {
+               for(i=1; i<=nlstate;i++) {
-     free_ivector(popage,0,AGESUP);
+                 if (mobilav==1)
-     free_vector(popeffectif,0,AGESUP);
+                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-     free_vector(popcount,0,AGESUP);
+                 else {
-   }
+                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                 }
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+               }
-   fclose(ficrespop);
+               if (h==(int)(calagedatem+12*cpt)){
- } /* End of popforecast */
+                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+                   /*fprintf(ficrespop," %.3f", kk1);
- int fileappend(FILE *fichier, char *optionfich)
+                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
- {
+               }
-   if((fichier=fopen(optionfich,"a"))==NULL) {
+             }
-     printf("Problem with file: %s\n", optionfich);
+             for(i=1; i<=nlstate;i++){
-     fprintf(ficlog,"Problem with file: %s\n", optionfich);
+               kk1=0.;
-     return (0);
+                 for(j=1; j<=nlstate;j++){
-   }
+                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-   fflush(fichier);
+                 }
-   return (1);
+                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
- }
+             }
+             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
- /**************** function prwizard **********************/
+               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
- void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
+           }
- {
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         }
-   /* Wizard to print covariance matrix template */
+       }
-   char ca[32], cb[32], cc[32];
+   /******/
-   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
-   int numlinepar;
+       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-   for(i=1; i <=nlstate; i++){
+           nhstepm = nhstepm/hstepm;
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       if(j==i) continue;
+           oldm=oldms;savm=savms;
-       jj++;
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-       /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           for (h=0; h<=nhstepm; h++){
-       printf("%1d%1d",i,j);
+             if (h==(int) (calagedatem+YEARM*cpt)) {
-       fprintf(ficparo,"%1d%1d",i,j);
+               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-       for(k=1; k<=ncovmodel;k++){
+             }
-         /*        printf(" %lf",param[i][j][k]); */
+             for(j=1; j<=nlstate+ndeath;j++) {
-         /*        fprintf(ficparo," %lf",param[i][j][k]); */
+               kk1=0.;kk2=0;
-         printf(" 0.");
+               for(i=1; i<=nlstate;i++) {
-         fprintf(ficparo," 0.");
+                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
-       }
+               }
-       printf("\n");
+               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
-       fprintf(ficparo,"\n");
+             }
-     }
+           }
-   }
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   printf("# Scales (for hessian or gradient estimation)\n");
+         }
-   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
+       }
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+    }
-   for(i=1; i <=nlstate; i++){
+   }
-     jj=0;
-     for(j=1; j <=nlstate+ndeath; j++){
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if(j==i) continue;
-       jj++;
+   if (popforecast==1) {
-       fprintf(ficparo,"%1d%1d",i,j);
+     free_ivector(popage,0,AGESUP);
-       printf("%1d%1d",i,j);
+     free_vector(popeffectif,0,AGESUP);
-       fflush(stdout);
+     free_vector(popcount,0,AGESUP);
-       for(k=1; k<=ncovmodel;k++){
+   }
-         /*      printf(" %le",delti3[i][j][k]); */
+   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
+   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-         printf(" 0.");
+   fclose(ficrespop);
-         fprintf(ficparo," 0.");
+ } /* End of popforecast */
-       }
-       numlinepar++;
+ int fileappend(FILE *fichier, char *optionfich)
-       printf("\n");
+ {
-       fprintf(ficparo,"\n");
+   if((fichier=fopen(optionfich,"a"))==NULL) {
-     }
+     printf("Problem with file: %s\n", optionfich);
-   }
+     fprintf(ficlog,"Problem with file: %s\n", optionfich);
-   printf("# Covariance matrix\n");
+     return (0);
- /* # 121 Var(a12)\n\ */
+   }
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
+   fflush(fichier);
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+   return (1);
- /* # 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\ */
+ /**************** function prwizard **********************/
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+ void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
-   fflush(stdout);
+ {
-   fprintf(ficparo,"# Covariance matrix\n");
-   /* # 121 Var(a12)\n\ */
+   /* Wizard to print covariance matrix template */
-   /* # 122 Cov(b12,a12) Var(b12)\n\ */
-   /* #   ...\n\ */
+   char ca[32], cb[32], cc[32];
-   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
+   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
+   int numlinepar;
-   for(itimes=1;itimes<=2;itimes++){
-     jj=0;
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     for(i=1; i <=nlstate; i++){
+   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-       for(j=1; j <=nlstate+ndeath; j++){
+   for(i=1; i <=nlstate; i++){
-         if(j==i) continue;
+     jj=0;
-         for(k=1; k<=ncovmodel;k++){
+     for(j=1; j <=nlstate+ndeath; j++){
-           jj++;
+       if(j==i) continue;
-           ca[0]= k+'a'-1;ca[1]='\0';
+       jj++;
-           if(itimes==1){
+       /*ca[0]= k+'a'-1;ca[1]='\0';*/
-             printf("#%1d%1d%d",i,j,k);
+       printf("%1d%1d",i,j);
-             fprintf(ficparo,"#%1d%1d%d",i,j,k);
+       fprintf(ficparo,"%1d%1d",i,j);
-           }else{
+       for(k=1; k<=ncovmodel;k++){
-             printf("%1d%1d%d",i,j,k);
+         /*        printf(" %lf",param[i][j][k]); */
-             fprintf(ficparo,"%1d%1d%d",i,j,k);
+         /*        fprintf(ficparo," %lf",param[i][j][k]); */
-             /*  printf(" %.5le",matcov[i][j]); */
+         printf(" 0.");
-           }
+         fprintf(ficparo," 0.");
-           ll=0;
+       }
-           for(li=1;li <=nlstate; li++){
+       printf("\n");
-             for(lj=1;lj <=nlstate+ndeath; lj++){
+       fprintf(ficparo,"\n");
-               if(lj==li) continue;
+     }
-               for(lk=1;lk<=ncovmodel;lk++){
+   }
-                 ll++;
+   printf("# Scales (for hessian or gradient estimation)\n");
-                 if(ll<=jj){
+   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
-                   cb[0]= lk +'a'-1;cb[1]='\0';
+   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-                   if(ll<jj){
+   for(i=1; i <=nlstate; i++){
-                     if(itimes==1){
+     jj=0;
-                       printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+     for(j=1; j <=nlstate+ndeath; j++){
-                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+       if(j==i) continue;
-                     }else{
+       jj++;
-                       printf(" 0.");
+       fprintf(ficparo,"%1d%1d",i,j);
-                       fprintf(ficparo," 0.");
+       printf("%1d%1d",i,j);
-                     }
+       fflush(stdout);
-                   }else{
+       for(k=1; k<=ncovmodel;k++){
-                     if(itimes==1){
+         /*      printf(" %le",delti3[i][j][k]); */
-                       printf(" Var(%s%1d%1d)",ca,i,j);
+         /*      fprintf(ficparo," %le",delti3[i][j][k]); */
-                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
+         printf(" 0.");
-                     }else{
+         fprintf(ficparo," 0.");
-                       printf(" 0.");
+       }
-                       fprintf(ficparo," 0.");
+       numlinepar++;
-                     }
+       printf("\n");
-                   }
+       fprintf(ficparo,"\n");
-                 }
+     }
-               } /* end lk */
+   }
-             } /* end lj */
+   printf("# Covariance matrix\n");
-           } /* end li */
+ /* # 121 Var(a12)\n\ */
-           printf("\n");
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */
-           fprintf(ficparo,"\n");
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-           numlinepar++;
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-         } /* end k*/
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-       } /*end j */
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     } /* end i */
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-   } /* end itimes */
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+   fflush(stdout);
- } /* end of prwizard */
+   fprintf(ficparo,"# Covariance matrix\n");
- /******************* Gompertz Likelihood ******************************/
+   /* # 121 Var(a12)\n\ */
- double gompertz(double x[])
+   /* # 122 Cov(b12,a12) Var(b12)\n\ */
- {
+   /* #   ...\n\ */
-   double A,B,L=0.0,sump=0.,num=0.;
+   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
-   int i,n=0; /* n is the size of the sample */
+   for(itimes=1;itimes<=2;itimes++){
-   for (i=0;i<=imx-1 ; i++) {
+     jj=0;
-     sump=sump+weight[i];
+     for(i=1; i <=nlstate; i++){
-     /*    sump=sump+1;*/
+       for(j=1; j <=nlstate+ndeath; j++){
-     num=num+1;
+         if(j==i) continue;
-   }
+         for(k=1; k<=ncovmodel;k++){
+           jj++;
+           ca[0]= k+'a'-1;ca[1]='\0';
-   /* for (i=0; i<=imx; i++)
+           if(itimes==1){
-      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("#%1d%1d%d",i,j,k);
+             fprintf(ficparo,"#%1d%1d%d",i,j,k);
-   for (i=1;i<=imx ; i++)
+           }else{
-     {
+             printf("%1d%1d%d",i,j,k);
-       if (cens[i] == 1 && wav[i]>1)
+             fprintf(ficparo,"%1d%1d%d",i,j,k);
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+             /*  printf(" %.5le",matcov[i][j]); */
+           }
-       if (cens[i] == 0 && wav[i]>1)
+           ll=0;
-         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+           for(li=1;li <=nlstate; li++){
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+             for(lj=1;lj <=nlstate+ndeath; lj++){
+               if(lj==li) continue;
-       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+               for(lk=1;lk<=ncovmodel;lk++){
-       if (wav[i] > 1 ) { /* ??? */
+                 ll++;
-         L=L+A*weight[i];
+                 if(ll<=jj){
-         /*      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]);*/
+                   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);
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+                       fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                     }else{
-   return -2*L*num/sump;
+                       printf(" 0.");
- }
+                       fprintf(ficparo," 0.");
+                     }
- /******************* Printing html file ***********/
+                   }else{
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+                     if(itimes==1){
-                   int lastpass, int stepm, int weightopt, char model[],\
+                       printf(" Var(%s%1d%1d)",ca,i,j);
-                   int imx,  double p[],double **matcov,double agemortsup){
+                       fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
-   int i,k;
+                     }else{
+                       printf(" 0.");
-   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
+                       fprintf(ficparo," 0.");
-   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
+                     }
-   for (i=1;i<=2;i++)
+                   }
-     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+                 }
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+               } /* end lk */
-   fprintf(fichtm,"</ul>");
+             } /* end lj */
+           } /* end li */
- fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
+           printf("\n");
+           fprintf(ficparo,"\n");
-  fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
+           numlinepar++;
+         } /* end k*/
-  for (k=agegomp;k<(agemortsup-2);k++)
+       } /*end j */
-    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]);
+     } /* end i */
+   } /* end itimes */
-   fflush(fichtm);
+ } /* end of prwizard */
- }
+ /******************* Gompertz Likelihood ******************************/
+ double gompertz(double x[])
- /******************* Gnuplot file **************/
+ {
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+   double A,B,L=0.0,sump=0.,num=0.;
+   int i,n=0; /* n is the size of the sample */
-   char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+   for (i=0;i<=imx-1 ; i++) {
-   int ng;
+     sump=sump+weight[i];
+     /*    sump=sump+1;*/
+     num=num+1;
-   /*#ifdef windows */
+   }
-   fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   strcpy(dirfileres,optionfilefiname);
-   strcpy(optfileres,"vpl");
+   for (i=1;i<=imx ; i++)
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+     {
-   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
+       if (cens[i] == 1 && wav[i]>1)
-   fprintf(ficgp, "set ter png small\n set log y\n");
+         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-   fprintf(ficgp, "set size 0.65,0.65\n");
-   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
+       if (cens[i] == 0 && wav[i]>1)
+         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
- }
+              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+       if (wav[i] > 1 ) { /* ??? */
+         L=L+A*weight[i];
+         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
- /***********************************************/
+       }
- /**************** Main Program *****************/
+     }
- /***********************************************/
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
- int main(int argc, char *argv[])
- {
+   return -2*L*num/sump;
-   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
+ }
-   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-   int linei, month, year,iout;
+ #ifdef GSL
-   int jj, ll, li, lj, lk, imk;
+ /******************* Gompertz_f Likelihood ******************************/
-   int numlinepar=0; /* Current linenumber of parameter file */
+ double gompertz_f(const gsl_vector *v, void *params)
-   int itimes;
+ {
-   int NDIM=2;
+   double A,B,LL=0.0,sump=0.,num=0.;
+   double *x= (double *) v->data;
-   char ca[32], cb[32], cc[32];
+   int i,n=0; /* n is the size of the sample */
-   char dummy[]="                         ";
-   /*  FILE *fichtm; *//* Html File */
+   for (i=0;i<=imx-1 ; i++) {
-   /* FILE *ficgp;*/ /*Gnuplot File */
+     sump=sump+weight[i];
-   struct stat info;
+     /*    sump=sump+1;*/
-   double agedeb, agefin,hf;
+     num=num+1;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   }
-   double fret;
-   double **xi,tmp,delta;
+   /* for (i=0; i<=imx; i++)
+      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   double dum; /* Dummy variable */
+   printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
-   double ***p3mat;
+   for (i=1;i<=imx ; i++)
-   double ***mobaverage;
+     {
-   int *indx;
+       if (cens[i] == 1 && wav[i]>1)
-   char line[MAXLINE], linepar[MAXLINE];
+         A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
-   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-   char pathr[MAXLINE], pathimach[MAXLINE];
+       if (cens[i] == 0 && wav[i]>1)
-   char **bp, *tok, *val; /* pathtot */
+         A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
-   int firstobs=1, lastobs=10;
+              +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
-   int sdeb, sfin; /* Status at beginning and end */
-   int c,  h , cpt,l;
+       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-   int ju,jl, mi;
+       if (wav[i] > 1 ) { /* ??? */
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+         LL=LL+A*weight[i];
-   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
+         /*      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]);*/
-   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+       }
-   int mobilav=0,popforecast=0;
+     }
-   int hstepm, nhstepm;
-   int agemortsup;
+  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-   float  sumlpop=0.;
+   printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
-   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
+   return -2*LL*num/sump;
+ }
-   double bage, fage, age, agelim, agebase;
+ #endif
-   double ftolpl=FTOL;
-   double **prlim;
+ /******************* Printing html file ***********/
-   double *severity;
+ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
-   double ***param; /* Matrix of parameters */
+                   int lastpass, int stepm, int weightopt, char model[],\
-   double  *p;
+                   int imx,  double p[],double **matcov,double agemortsup){
-   double **matcov; /* Matrix of covariance */
+   int i,k;
-   double ***delti3; /* Scale */
-   double *delti; /* Scale */
+   fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
-   double ***eij, ***vareij;
+   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
-   double **varpl; /* Variances of prevalence limits by age */
+   for (i=1;i<=2;i++)
-   double *epj, vepp;
+     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]));
-   double kk1, kk2;
+   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   fprintf(fichtm,"</ul>");
-   double **ximort;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+ fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-   int *dcwave;
+  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>");
-   char z[1]="c", occ;
+  for (k=agegomp;k<(agemortsup-2);k++)
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+    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]);
-   char  *strt, strtend[80];
-   char *stratrunc;
-   int lstra;
+   fflush(fichtm);
+ }
-   long total_usecs;
+ /******************* Gnuplot file **************/
- /*   setlocale (LC_ALL, ""); */
+ void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
- /*   bindtextdomain (PACKAGE, LOCALEDIR); */
- /*   textdomain (PACKAGE); */
+   char dirfileres[132],optfileres[132];
- /*   setlocale (LC_CTYPE, ""); */
+   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- /*   setlocale (LC_MESSAGES, ""); */
+   int ng;
-   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   (void) gettimeofday(&start_time,&tzp);
+   /*#ifdef windows */
-   curr_time=start_time;
+   fprintf(ficgp,"cd \"%s\" \n",pathc);
-   tm = *localtime(&start_time.tv_sec);
+     /*#endif */
-   tmg = *gmtime(&start_time.tv_sec);
-   strcpy(strstart,asctime(&tm));
+   strcpy(dirfileres,optionfilefiname);
- /*  printf("Localtime (at start)=%s",strstart); */
+   strcpy(optfileres,"vpl");
- /*  tp.tv_sec = tp.tv_sec +86400; */
+   fprintf(ficgp,"set out \"graphmort.png\"\n ");
- /*  tm = *localtime(&start_time.tv_sec); */
+   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
- /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
+   fprintf(ficgp, "set ter png small\n set log y\n");
- /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
+   fprintf(ficgp, "set size 0.65,0.65\n");
- /*   tmg.tm_hour=tmg.tm_hour + 1; */
+   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
- /*   tp.tv_sec = mktime(&tmg); */
- /*   strt=asctime(&tmg); */
+ }
- /*   printf("Time(after) =%s",strstart);  */
- /*  (void) time (&time_value);
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
- *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
+ {
- *  tm = *localtime(&time_value);
- *  strstart=asctime(&tm);
+   /*-------- data file ----------*/
- *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
+   FILE *fic;
- */
+   char dummy[]="                         ";
+   int i, j, n;
-   nberr=0; /* Number of errors and warnings */
+   int linei, month, year,iout;
-   nbwarn=0;
+   char line[MAXLINE], linetmp[MAXLINE];
-   getcwd(pathcd, size);
+   char stra[80], strb[80];
+   char *stratrunc;
-   printf("\n%s\n%s",version,fullversion);
+   int lstra;
-   if(argc <=1){
-     printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+   if((fic=fopen(datafile,"r"))==NULL)    {
-     i=strlen(pathr);
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
-     if(pathr[i-1]=='\n')
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
-       pathr[i-1]='\0';
+   }
-    for (tok = pathr; tok != NULL; ){
-       printf("Pathr |%s|\n",pathr);
+   i=1;
-       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+   linei=0;
-       printf("val= |%s| pathr=%s\n",val,pathr);
+   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
-       strcpy (pathtot, val);
+     linei=linei+1;
-       if(pathr[0] == '\0') break; /* Dirty */
+     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
-     }
+       if(line[j] == '\t')
-   }
+         line[j] = ' ';
-   else{
+     }
-     strcpy(pathtot,argv[1]);
+     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
-   }
+       ;
-   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
+     };
-   /*cygwin_split_path(pathtot,path,optionfile);
+     line[j+1]=0;  /* Trims blanks at end of line */
-     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+     if(line[0]=='#'){
-   /* cutv(path,optionfile,pathtot,'\\');*/
+       fprintf(ficlog,"Comment line\n%s\n",line);
+       printf("Comment line\n%s\n",line);
-   /* Split argv[0], imach program to get pathimach */
+       continue;
-   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
+     }
-   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
-   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+     for (j=0; line[j]!='\0';j++){
-  /*   strcpy(pathimach,argv[0]); */
+       line[j]=linetmp[j];
-   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
+     }
-   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-   chdir(path); /* Can be a relative path */
+     for (j=maxwav;j>=1;j--){
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+       cutv(stra, strb,line,' ');
-     printf("Current directory %s!\n",pathcd);
+       if(strb[0]=='.') { /* Missing status */
-   strcpy(command,"mkdir ");
+         lval=-1;
-   strcat(command,optionfilefiname);
+       }else{
-   if((outcmd=system(command)) != 0){
+         errno=0;
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+         lval=strtol(strb,&endptr,10);
-     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-     /* fclose(ficlog); */
+         if( strb[0]=='\0' || (*endptr != '\0')){
- /*     exit(1); */
+           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);
- /*   if((imk=mkdir(optionfilefiname))<0){ */
+           return 1;
- /*     perror("mkdir"); */
+         }
- /*   } */
+       }
+       s[j][i]=lval;
-   /*-------- arguments in the command line --------*/
+       strcpy(line,stra);
-   /* Log file */
+       cutv(stra, strb,line,' ');
-   strcat(filelog, optionfilefiname);
+       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   strcat(filelog,".log");    /* */
+       }
-   if((ficlog=fopen(filelog,"w"))==NULL)    {
+       else  if(iout=sscanf(strb,"%s.") != 0){
-     printf("Problem with logfile %s\n",filelog);
+         month=99;
-     goto end;
+         year=9999;
-   }
+       }else{
-   fprintf(ficlog,"Log filename:%s\n",filelog);
+         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);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+         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);
-   fprintf(ficlog,"\nEnter the parameter file name: \n");
+         return 1;
-   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
+       }
-  path=%s \n\
+       anint[j][i]= (double) year;
-  optionfile=%s\n\
+       mint[j][i]= (double)month;
-  optionfilext=%s\n\
+       strcpy(line,stra);
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+     } /* ENd Waves */
-   printf("Local time (at start):%s",strstart);
+     cutv(stra, strb,line,' ');
-   fprintf(ficlog,"Local time (at start): %s",strstart);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-   fflush(ficlog);
+     }
- /*   (void) gettimeofday(&curr_time,&tzp); */
+     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+       month=99;
+       year=9999;
-   /* */
+     }else{
-   strcpy(fileres,"r");
+       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);
-   strcat(fileres, optionfilefiname);
+         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);
-   strcat(fileres,".txt");    /* Other files have txt extension */
+         return 1;
+     }
-   /*---------arguments file --------*/
+     andc[i]=(double) year;
+     moisdc[i]=(double) month;
-   if((ficpar=fopen(optionfile,"r"))==NULL)    {
+     strcpy(line,stra);
-     printf("Problem with optionfile %s\n",optionfile);
-     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+     cutv(stra, strb,line,' ');
-     fflush(ficlog);
+     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
-     goto end;
+     }
-   }
+     else  if(iout=sscanf(strb,"%s.") != 0){
+       month=99;
+       year=9999;
+     }else{
-   strcpy(filereso,"o");
+       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);
-   strcat(filereso,fileres);
+       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);
-   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
+         return 1;
-     printf("Problem with Output resultfile: %s\n", filereso);
+     }
-     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+     if (year==9999) {
-     fflush(ficlog);
+       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);
-     goto end;
+       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);
-   }
+         return 1;
-   /* Reads comments: lines beginning with '#' */
+     }
-   numlinepar=0;
+     annais[i]=(double)(year);
-   while((c=getc(ficpar))=='#' && c!= EOF){
+     moisnais[i]=(double)(month);
-     ungetc(c,ficpar);
+     strcpy(line,stra);
-     fgets(line, MAXLINE, ficpar);
-     numlinepar++;
+     cutv(stra, strb,line,' ');
-     puts(line);
+     errno=0;
-     fputs(line,ficparo);
+     dval=strtod(strb,&endptr);
-     fputs(line,ficlog);
+     if( strb[0]=='\0' || (*endptr != '\0')){
-   }
+       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
-   ungetc(c,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);
+       fflush(ficlog);
-   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);
+       return 1;
-   numlinepar++;
+     }
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+     weight[i]=dval;
-   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);
+     strcpy(line,stra);
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-   fflush(ficlog);
+     for (j=ncovcol;j>=1;j--){
-   while((c=getc(ficpar))=='#' && c!= EOF){
+       cutv(stra, strb,line,' ');
-     ungetc(c,ficpar);
+       if(strb[0]=='.') { /* Missing status */
-     fgets(line, MAXLINE, ficpar);
+         lval=-1;
-     numlinepar++;
+       }else{
-     puts(line);
+         errno=0;
-     fputs(line,ficparo);
+         lval=strtol(strb,&endptr,10);
-     fputs(line,ficlog);
+         if( strb[0]=='\0' || (*endptr != '\0')){
-   }
+           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);
-   ungetc(c,ficpar);
+           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);
+           return 1;
+         }
-   covar=matrix(0,NCOVMAX,1,n);
+       }
-   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
+       if(lval <-1 || lval >1){
-   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+  For example, for multinomial values like 1, 2 and 3,\n \
-   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
+  build V1=0 V2=0 for the reference value (1),\n \
+         V1=1 V2=0 for (2) \n \
-   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-   delti=delti3[1][1];
+  output of IMaCh is often meaningless.\n \
-   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+  Exiting.\n",lval,linei, i,line,j);
-   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+         fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+  For example, for multinomial values like 1, 2 and 3,\n \
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+  build V1=0 V2=0 for the reference value (1),\n \
-     fclose (ficparo);
+         V1=1 V2=0 for (2) \n \
-     fclose (ficlog);
+  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-     goto end;
+  output of IMaCh is often meaningless.\n \
-     exit(0);
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-   }
+         return 1;
-   else if(mle==-3) {
+       }
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+       covar[j][i]=(double)(lval);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+       strcpy(line,stra);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     }
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     lstra=strlen(stra);
-     matcov=matrix(1,npar,1,npar);
-   }
+     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
-   else{
+       stratrunc = &(stra[lstra-9]);
-     /* Read guess parameters */
+       num[i]=atol(stratrunc);
-     /* Reads comments: lines beginning with '#' */
+     }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     else
-       ungetc(c,ficpar);
+       num[i]=atol(stra);
-       fgets(line, MAXLINE, ficpar);
+     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
-       numlinepar++;
+       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;}*/
-       puts(line);
-       fputs(line,ficparo);
+     i=i+1;
-       fputs(line,ficlog);
+   } /* End loop reading  data */
-     }
-     ungetc(c,ficpar);
+   *imax=i-1; /* Number of individuals */
+   fclose(fic);
-     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-     for(i=1; i <=nlstate; i++){
+   return (0);
-       j=0;
+   endread:
-       for(jj=1; jj <=nlstate+ndeath; jj++){
+     printf("Exiting readdata: ");
-         if(jj==i) continue;
+     fclose(fic);
-         j++;
+     return (1);
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1 != i) && (j1 != j)){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
- It might be a problem of design; if ncovcol and the model are correct\n \
+ }
- run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           exit(1);
+ int decodemodel ( char model[], int lastobs)
-         }
+ {
-         fprintf(ficparo,"%1d%1d",i1,j1);
+   int i, j, k;
-         if(mle==1)
+   int i1, j1, k1, k2;
-           printf("%1d%1d",i,j);
+   char modelsav[80];
-         fprintf(ficlog,"%1d%1d",i,j);
+    char stra[80], strb[80], strc[80], strd[80],stre[80];
-         for(k=1; k<=ncovmodel;k++){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+   if (strlen(model) >1){ /* If there is at least 1 covariate */
-           if(mle==1){
+     j=0, j1=0, k1=1, k2=1;
-             printf(" %lf",param[i][j][k]);
+     j=nbocc(model,'+'); /* j=Number of '+' */
-             fprintf(ficlog," %lf",param[i][j][k]);
+     j1=nbocc(model,'*'); /* j1=Number of '*' */
-           }
+     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
-           else
+                   but the covariates which are product must be computed and stored. */
-             fprintf(ficlog," %lf",param[i][j][k]);
+     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
-           fprintf(ficparo," %lf",param[i][j][k]);
-         }
+     strcpy(modelsav,model);
-         fscanf(ficpar,"\n");
+     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
-         numlinepar++;
+       printf("Error. Non available option model=%s ",model);
-         if(mle==1)
+       fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
-           printf("\n");
+       return 1;
-         fprintf(ficlog,"\n");
+     }
-         fprintf(ficparo,"\n");
-       }
+     /* This loop fills the array Tvar from the string 'model'.*/
-     }
+     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
-     fflush(ficlog);
+     /*    modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
+         i=1 Tvar[1]=3 Tage[1]=1
-     p=param[1][1];
+         i=2 Tvar[2]=2
+         i=3 Tvar[3]=1
-     /* Reads comments: lines beginning with '#' */
+         i=4 Tvar[4]= 4
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         i=5 Tvar[5]
-       ungetc(c,ficpar);
+       for (k=1; k<=cptcovn;k++) {
-       fgets(line, MAXLINE, ficpar);
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-       numlinepar++;
+      */
-       puts(line);
+     for(k=1; k<=(j+1);k++){
-       fputs(line,ficparo);
+       cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+'
-       fputs(line,ficlog);
+                                      modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
-     }
+                                     */
-     ungetc(c,ficpar);
+       /* if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);*/ /* and analyzes it */
+       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-     for(i=1; i <=nlstate; i++){
+       /*scanf("%d",i);*/
-       for(j=1; j <=nlstate+ndeath-1; j++){
+       if (strchr(strb,'*')) {  /* Model includes a product V3*age+V2+V1+V4 strb=V3*age */
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-         if ((i1-i)*(j1-j)!=0){
+         if (strcmp(strc,"age")==0) { /* Vn*age */
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           cptcovprod--;
-           exit(1);
+           cutv(strb,stre,strd,'V'); /* stre="V3" */
-         }
+           Tvar[k]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
-         printf("%1d%1d",i,j);
+           cptcovage++; /* Sums the number of covariates which include age as a product */
-         fprintf(ficparo,"%1d%1d",i1,j1);
+           Tage[cptcovage]=k;  /* Tage[1] =2 */
-         fprintf(ficlog,"%1d%1d",i1,j1);
+           /*printf("stre=%s ", stre);*/
-         for(k=1; k<=ncovmodel;k++){
+         }
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+         else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           printf(" %le",delti3[i][j][k]);
+           cptcovprod--;
-           fprintf(ficparo," %le",delti3[i][j][k]);
+           cutv(strb,stre,strc,'V');
-           fprintf(ficlog," %le",delti3[i][j][k]);
+           Tvar[k]=atoi(stre);
-         }
+           cptcovage++;
-         fscanf(ficpar,"\n");
+           Tage[cptcovage]=k;
-         numlinepar++;
+         }
-         printf("\n");
+         else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
-         fprintf(ficparo,"\n");
+           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-         fprintf(ficlog,"\n");
+           Tvar[k]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar.
-       }
+                                   If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
-     }
+           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
-     fflush(ficlog);
+           Tprod[k1]=k;  /* Tprod[1]  */
+           Tvard[k1][1]=atoi(strc); /* m*/
-     delti=delti3[1][1];
+           Tvard[k1][2]=atoi(stre); /* n */
+           Tvar[cptcovn+k2]=Tvard[k1][1];
+           Tvar[cptcovn+k2+1]=Tvard[k1][2];
-     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
+           for (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
+                                      and is stored at ncovol+k1 */
-     /* Reads comments: lines beginning with '#' */
+             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-     while((c=getc(ficpar))=='#' && c!= EOF){
+           k1++;
-       ungetc(c,ficpar);
+           k2=k2+2;
-       fgets(line, MAXLINE, ficpar);
+         }
-       numlinepar++;
+       }
-       puts(line);
+       else { /* no more sum */
-       fputs(line,ficparo);
+         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-       fputs(line,ficlog);
+        /*  scanf("%d",i);*/
-     }
+         cutv(strd,strc,strb,'V');
-     ungetc(c,ficpar);
+         Tvar[i]=atoi(strc);
+       }
-     matcov=matrix(1,npar,1,npar);
+       strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
-     for(i=1; i <=npar; i++){
+       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-       fscanf(ficpar,"%s",&str);
+         scanf("%d",i);*/
-       if(mle==1)
+     } /* end of loop + */
-         printf("%s",str);
+   } /* end model */
-       fprintf(ficlog,"%s",str);
-       fprintf(ficparo,"%s",str);
+   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-       for(j=1; j <=i; j++){
+     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-         fscanf(ficpar," %le",&matcov[i][j]);
-         if(mle==1){
+   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-           printf(" %.5le",matcov[i][j]);
+   printf("cptcovprod=%d ", cptcovprod);
-         }
+   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-         fprintf(ficlog," %.5le",matcov[i][j]);
-         fprintf(ficparo," %.5le",matcov[i][j]);
+   scanf("%d ",i);*/
-       }
-       fscanf(ficpar,"\n");
-       numlinepar++;
+   return (0);
-       if(mle==1)
+   endread:
-         printf("\n");
+     printf("Exiting decodemodel: ");
-       fprintf(ficlog,"\n");
+     return (1);
-       fprintf(ficparo,"\n");
+ }
-     }
-     for(i=1; i <=npar; i++)
+ calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
-       for(j=i+1;j<=npar;j++)
+ {
-         matcov[i][j]=matcov[j][i];
+   int i, m;
-     if(mle==1)
+   for (i=1; i<=imx; i++) {
-       printf("\n");
+     for(m=2; (m<= maxwav); m++) {
-     fprintf(ficlog,"\n");
+       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+         anint[m][i]=9999;
-     fflush(ficlog);
+         s[m][i]=-1;
+       }
-     /*-------- Rewriting parameter file ----------*/
+       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-     strcpy(rfileres,"r");    /* "Rparameterfile */
+         *nberr++;
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+         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);
-     strcat(rfileres,".");    /* */
+         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);
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+         s[m][i]=-1;
-     if((ficres =fopen(rfileres,"w"))==NULL) {
+       }
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+         *nberr++;
-     }
+         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
-     fprintf(ficres,"#%s\n",version);
+         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
-   }    /* End of mle != -3 */
+         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+       }
-   /*-------- data file ----------*/
+     }
-   if((fic=fopen(datafile,"r"))==NULL)    {
+   }
-     printf("Problem while opening datafile: %s\n", datafile);goto end;
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
+   for (i=1; i<=imx; i++)  {
-   }
+     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     for(m=firstpass; (m<= lastpass); m++){
-   n= lastobs;
+       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
-   severity = vector(1,maxwav);
+         if (s[m][i] >= nlstate+1) {
-   outcome=imatrix(1,maxwav+1,1,n);
+           if(agedc[i]>0)
-   num=lvector(1,n);
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
-   moisnais=vector(1,n);
+               agev[m][i]=agedc[i];
-   annais=vector(1,n);
+           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
-   moisdc=vector(1,n);
+             else {
-   andc=vector(1,n);
+               if ((int)andc[i]!=9999){
-   agedc=vector(1,n);
+                 nbwarn++;
-   cod=ivector(1,n);
+                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
-   weight=vector(1,n);
+                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+                 agev[m][i]=-1;
-   mint=matrix(1,maxwav,1,n);
+               }
-   anint=matrix(1,maxwav,1,n);
+             }
-   s=imatrix(1,maxwav+1,1,n);
+         }
-   tab=ivector(1,NCOVMAX);
+         else if(s[m][i] !=9){ /* Standard case, age in fractional
-   ncodemax=ivector(1,8);
+                                  years but with the precision of a month */
+           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-   i=1;
+           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
-   linei=0;
+             agev[m][i]=1;
-   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+           else if(agev[m][i] < *agemin){
-     linei=linei+1;
+             *agemin=agev[m][i];
-     for(j=strlen(line); j>=0;j--){  /* Untabifies line */
+             printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
-       if(line[j] == '\t')
+           }
-         line[j] = ' ';
+           else if(agev[m][i] >*agemax){
-     }
+             *agemax=agev[m][i];
-     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
-       ;
+           }
-     };
+           /*agev[m][i]=anint[m][i]-annais[i];*/
-     line[j+1]=0;  /* Trims blanks at end of line */
+           /*     agev[m][i] = age[i]+2*m;*/
-     if(line[0]=='#'){
+         }
-       fprintf(ficlog,"Comment line\n%s\n",line);
+         else { /* =9 */
-       printf("Comment line\n%s\n",line);
+           agev[m][i]=1;
-       continue;
+           s[m][i]=-1;
-     }
+         }
+       }
-     for (j=maxwav;j>=1;j--){
+       else /*= 0 Unknown */
-       cutv(stra, strb,line,' ');
+         agev[m][i]=1;
-       errno=0;
+     }
-       lval=strtol(strb,&endptr,10);
-       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+   }
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   for (i=1; i<=imx; 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);
+     for(m=firstpass; (m<=lastpass); m++){
-         exit(1);
+       if (s[m][i] > (nlstate+ndeath)) {
-       }
+         *nberr++;
-       s[j][i]=lval;
+         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
-       strcpy(line,stra);
+         return 1;
-       cutv(stra, strb,line,' ');
+       }
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     }
-       }
+   }
-       else  if(iout=sscanf(strb,"%s.") != 0){
-         month=99;
+   /*for (i=1; i<=imx; i++){
-         year=9999;
+   for (m=firstpass; (m<lastpass); m++){
-       }else{
+      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][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);
+ }
-         exit(1);
-       }
+ }*/
-       anint[j][i]= (double) year;
-       mint[j][i]= (double)month;
-       strcpy(line,stra);
+   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     } /* ENd Waves */
+   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-     cutv(stra, strb,line,' ');
+   return (0);
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+   endread:
-     }
+     printf("Exiting calandcheckages: ");
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+     return (1);
-       month=99;
+ }
-       year=9999;
-     }else{
-       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+ /***********************************************/
-       exit(1);
+ /**************** Main Program *****************/
-     }
+ /***********************************************/
-     andc[i]=(double) year;
-     moisdc[i]=(double) month;
+ int main(int argc, char *argv[])
-     strcpy(line,stra);
+ {
+ #ifdef GSL
-     cutv(stra, strb,line,' ');
+   const gsl_multimin_fminimizer_type *T;
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+   size_t iteri = 0, it;
-     }
+   int rval = GSL_CONTINUE;
-     else  if(iout=sscanf(strb,"%s.") != 0){
+   int status = GSL_SUCCESS;
-       month=99;
+   double ssval;
-       year=9999;
+ #endif
-     }else{
+   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-       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);
+   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
-       exit(1);
+   int linei, month, year,iout;
-     }
+   int jj, ll, li, lj, lk, imk;
-     annais[i]=(double)(year);
+   int numlinepar=0; /* Current linenumber of parameter file */
-     moisnais[i]=(double)(month);
+   int itimes;
-     strcpy(line,stra);
+   int NDIM=2;
+   int vpopbased=0;
-     cutv(stra, strb,line,' ');
-     errno=0;
+   char ca[32], cb[32], cc[32];
-     dval=strtod(strb,&endptr);
+   /*  FILE *fichtm; *//* Html File */
-     if( strb[0]=='\0' || (*endptr != '\0')){
+   /* FILE *ficgp;*/ /*Gnuplot File */
-       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
+   struct stat info;
-       exit(1);
+   double agedeb, agefin,hf;
-     }
+   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-     weight[i]=dval;
-     strcpy(line,stra);
+   double fret;
+   double **xi,tmp,delta;
-     for (j=ncovcol;j>=1;j--){
-       cutv(stra, strb,line,' ');
+   double dum; /* Dummy variable */
-       errno=0;
+   double ***p3mat;
-       lval=strtol(strb,&endptr,10);
+   double ***mobaverage;
-       if( strb[0]=='\0' || (*endptr != '\0')){
+   int *indx;
-         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);
+   char line[MAXLINE], linepar[MAXLINE];
-         exit(1);
+   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
-       }
+   char pathr[MAXLINE], pathimach[MAXLINE];
-       if(lval <-1 || lval >1){
+   char **bp, *tok, *val; /* pathtot */
-         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+   int firstobs=1, lastobs=10;
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+   int sdeb, sfin; /* Status at beginning and end */
-  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+   int c,  h , cpt,l;
-  For example, for multinomial values like 1, 2 and 3,\n \
+   int ju,jl, mi;
-  build V1=0 V2=0 for the reference value (1),\n \
+   int i1,j1, jk,aa,bb, stepsize, ij;
-         V1=1 V2=0 for (2) \n \
+   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
-  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-  output of IMaCh is often meaningless.\n \
+   int mobilav=0,popforecast=0;
-  Exiting.\n",lval,linei, i,line,j);
+   int hstepm, nhstepm;
-         exit(1);
+   int agemortsup;
-       }
+   float  sumlpop=0.;
-       covar[j][i]=(double)(lval);
+   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
-       strcpy(line,stra);
+   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-     }
-     lstra=strlen(stra);
+   double bage, fage, age, agelim, agebase;
+   double ftolpl=FTOL;
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+   double **prlim;
-       stratrunc = &(stra[lstra-9]);
+   double ***param; /* Matrix of parameters */
-       num[i]=atol(stratrunc);
+   double  *p;
-     }
+   double **matcov; /* Matrix of covariance */
-     else
+   double ***delti3; /* Scale */
-       num[i]=atol(stra);
+   double *delti; /* Scale */
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+   double ***eij, ***vareij;
-       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;}*/
+   double **varpl; /* Variances of prevalence limits by age */
+   double *epj, vepp;
-     i=i+1;
+   double kk1, kk2;
-   } /* End loop reading  data */
+   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
-   fclose(fic);
+   double **ximort;
-   /* printf("ii=%d", ij);
+   char *alph[]={"a","a","b","c","d","e"}, str[4];
-      scanf("%d",i);*/
+   int *dcwave;
-   imx=i-1; /* Number of individuals */
+   char z[1]="c", occ;
-   /* for (i=1; i<=imx; i++){
-     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+   /*char  *strt;*/
-     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+   char strtend[80];
-     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
-     }*/
+   long total_usecs;
-    /*  for (i=1; i<=imx; i++){
-      if (s[4][i]==9)  s[4][i]=-1;
+ /*   setlocale (LC_ALL, ""); */
-      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]));}*/
+ /*   bindtextdomain (PACKAGE, LOCALEDIR); */
+ /*   textdomain (PACKAGE); */
-   /* for (i=1; i<=imx; i++) */
+ /*   setlocale (LC_CTYPE, ""); */
+ /*   setlocale (LC_MESSAGES, ""); */
-    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
-      else weight[i]=1;*/
+   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+   (void) gettimeofday(&start_time,&tzp);
-   /* Calculation of the number of parameters from char model */
+   curr_time=start_time;
-   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+   tm = *localtime(&start_time.tv_sec);
-   Tprod=ivector(1,15);
+   tmg = *gmtime(&start_time.tv_sec);
-   Tvaraff=ivector(1,15);
+   strcpy(strstart,asctime(&tm));
-   Tvard=imatrix(1,15,1,2);
-   Tage=ivector(1,15);
+ /*  printf("Localtime (at start)=%s",strstart); */
+ /*  tp.tv_sec = tp.tv_sec +86400; */
-   if (strlen(model) >1){ /* If there is at least 1 covariate */
+ /*  tm = *localtime(&start_time.tv_sec); */
-     j=0, j1=0, k1=1, k2=1;
+ /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
-     j=nbocc(model,'+'); /* j=Number of '+' */
+ /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
+ /*   tmg.tm_hour=tmg.tm_hour + 1; */
-     cptcovn=j+1;
+ /*   tp.tv_sec = mktime(&tmg); */
-     cptcovprod=j1; /*Number of products */
+ /*   strt=asctime(&tmg); */
+ /*   printf("Time(after) =%s",strstart);  */
-     strcpy(modelsav,model);
+ /*  (void) time (&time_value);
-     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+ *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
-       printf("Error. Non available option model=%s ",model);
+ *  tm = *localtime(&time_value);
-       fprintf(ficlog,"Error. Non available option model=%s ",model);
+ *  strstart=asctime(&tm);
-       goto end;
+ *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-     }
+ */
-     /* This loop fills the array Tvar from the string 'model'.*/
+   nberr=0; /* Number of errors and warnings */
+   nbwarn=0;
-     for(i=(j+1); i>=1;i--){
+   getcwd(pathcd, size);
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+   printf("\n%s\n%s",version,fullversion);
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+   if(argc <=1){
-       /*scanf("%d",i);*/
+     printf("\nEnter the parameter file name: ");
-       if (strchr(strb,'*')) {  /* Model includes a product */
+     fgets(pathr,FILENAMELENGTH,stdin);
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
+     i=strlen(pathr);
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+     if(pathr[i-1]=='\n')
-           cptcovprod--;
+       pathr[i-1]='\0';
-           cutv(strb,stre,strd,'V');
+    for (tok = pathr; tok != NULL; ){
-           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+       printf("Pathr |%s|\n",pathr);
-           cptcovage++;
+       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
-             Tage[cptcovage]=i;
+       printf("val= |%s| pathr=%s\n",val,pathr);
-             /*printf("stre=%s ", stre);*/
+       strcpy (pathtot, val);
-         }
+       if(pathr[0] == '\0') break; /* Dirty */
-         else if (strcmp(strd,"age")==0) { /* or age*Vn */
+     }
-           cptcovprod--;
+   }
-           cutv(strb,stre,strc,'V');
+   else{
-           Tvar[i]=atoi(stre);
+     strcpy(pathtot,argv[1]);
-           cptcovage++;
+   }
-           Tage[cptcovage]=i;
+   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
-         }
+   /*cygwin_split_path(pathtot,path,optionfile);
-         else {  /* Age is not in the model */
+     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+   /* cutv(path,optionfile,pathtot,'\\');*/
-           Tvar[i]=ncovcol+k1;
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+   /* Split argv[0], imach program to get pathimach */
-           Tprod[k1]=i;
+   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
-           Tvard[k1][1]=atoi(strc); /* m*/
+   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           Tvard[k1][2]=atoi(stre); /* n */
+   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
-           Tvar[cptcovn+k2]=Tvard[k1][1];
+  /*   strcpy(pathimach,argv[0]); */
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];
+   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
-           for (k=1; k<=lastobs;k++)
+   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-           k1++;
+   chdir(path); /* Can be a relative path */
-           k2=k2+2;
+   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
-         }
+     printf("Current directory %s!\n",pathcd);
-       }
+   strcpy(command,"mkdir ");
-       else { /* no more sum */
+   strcat(command,optionfilefiname);
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+   if((outcmd=system(command)) != 0){
-        /*  scanf("%d",i);*/
+     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
-       cutv(strd,strc,strb,'V');
+     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
-       Tvar[i]=atoi(strc);
+     /* fclose(ficlog); */
-       }
+ /*     exit(1); */
-       strcpy(modelsav,stra);
+   }
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ /*   if((imk=mkdir(optionfilefiname))<0){ */
-         scanf("%d",i);*/
+ /*     perror("mkdir"); */
-     } /* end of loop + */
+ /*   } */
-   } /* end model */
+   /*-------- arguments in the command line --------*/
-   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
-     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+   /* Log file */
+   strcat(filelog, optionfilefiname);
-   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+   strcat(filelog,".log");    /* */
-   printf("cptcovprod=%d ", cptcovprod);
+   if((ficlog=fopen(filelog,"w"))==NULL)    {
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+     printf("Problem with logfile %s\n",filelog);
+     goto end;
-   scanf("%d ",i);*/
+   }
+   fprintf(ficlog,"Log filename:%s\n",filelog);
-     /*  if(mle==1){*/
+   fprintf(ficlog,"\n%s\n%s",version,fullversion);
-   if (weightopt != 1) { /* Maximisation without weights*/
+   fprintf(ficlog,"\nEnter the parameter file name: \n");
-     for(i=1;i<=n;i++) weight[i]=1.0;
+   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
-   }
+  path=%s \n\
-     /*-calculation of age at interview from date of interview and age at death -*/
+  optionfile=%s\n\
-   agev=matrix(1,maxwav,1,imx);
+  optionfilext=%s\n\
+  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-   for (i=1; i<=imx; i++) {
-     for(m=2; (m<= maxwav); m++) {
+   printf("Local time (at start):%s",strstart);
-       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+   fprintf(ficlog,"Local time (at start): %s",strstart);
-         anint[m][i]=9999;
+   fflush(ficlog);
-         s[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)); */
-       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         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);
+   strcpy(fileres,"r");
-         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);
+   strcat(fileres, optionfilefiname);
-         s[m][i]=-1;
+   strcat(fileres,".txt");    /* Other files have txt extension */
-       }
-       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+   /*---------arguments file --------*/
-         nberr++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+   if((ficpar=fopen(optionfile,"r"))==NULL)    {
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+     printf("Problem with optionfile %s\n",optionfile);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
-       }
+     fflush(ficlog);
-     }
+     goto end;
    }
-   for (i=1; i<=imx; i++)  {
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
-     for(m=firstpass; (m<= lastpass); m++){
+   strcpy(filereso,"o");
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+   strcat(filereso,fileres);
-         if (s[m][i] >= nlstate+1) {
+   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
-           if(agedc[i]>0)
+     printf("Problem with Output resultfile: %s\n", filereso);
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
-               agev[m][i]=agedc[i];
+     fflush(ficlog);
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+     goto end;
-             else {
+   }
-               if ((int)andc[i]!=9999){
-                 nbwarn++;
+   /* Reads comments: lines beginning with '#' */
-                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);
+   numlinepar=0;
-                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
+   while((c=getc(ficpar))=='#' && c!= EOF){
-                 agev[m][i]=-1;
+     ungetc(c,ficpar);
-               }
+     fgets(line, MAXLINE, ficpar);
-             }
+     numlinepar++;
-         }
+     puts(line);
-         else if(s[m][i] !=9){ /* Standard case, age in fractional
+     fputs(line,ficparo);
-                                  years but with the precision of a month */
+     fputs(line,ficlog);
-           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)
+   ungetc(c,ficpar);
-             agev[m][i]=1;
-           else if(agev[m][i] <agemin){
+   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);
-             agemin=agev[m][i];
+   numlinepar++;
-             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
-           }
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
-           else if(agev[m][i] >agemax){
+   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);
-             agemax=agev[m][i];
+   fflush(ficlog);
-             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+   while((c=getc(ficpar))=='#' && c!= EOF){
-           }
+     ungetc(c,ficpar);
-           /*agev[m][i]=anint[m][i]-annais[i];*/
+     fgets(line, MAXLINE, ficpar);
-           /*     agev[m][i] = age[i]+2*m;*/
+     numlinepar++;
-         }
+     puts(line);
-         else { /* =9 */
+     fputs(line,ficparo);
-           agev[m][i]=1;
+     fputs(line,ficlog);
-           s[m][i]=-1;
+   }
-         }
+   ungetc(c,ficpar);
-       }
-       else /*= 0 Unknown */
-         agev[m][i]=1;
+   covar=matrix(0,NCOVMAX,1,n);
-     }
+   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
-   }
+      v1+v2*age+v2*v3 makes cptcovn = 3
-   for (i=1; i<=imx; i++)  {
+   */
-     for(m=firstpass; (m<=lastpass); m++){
+   if (strlen(model)>1)
-       if (s[m][i] > (nlstate+ndeath)) {
+     cptcovn=nbocc(model,'+')+1;
-         nberr++;
+   /* ncovprod */
-         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);
+   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
-         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);
+   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-         goto end;
+   nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
-       }
+   npar= nforce*ncovmodel; /* Number of parameters like aij*/
-     }
+   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
-   }
+     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
+     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
-   /*for (i=1; i<=imx; i++){
+     fflush(stdout);
-   for (m=firstpass; (m<lastpass); m++){
+     fclose (ficlog);
-      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+     goto end;
- }
+   }
+   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
- }*/
+   delti=delti3[1][1];
+   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
+   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
-   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-   agegomp=(int)agemin;
+     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-   free_vector(severity,1,maxwav);
+     fclose (ficparo);
-   free_imatrix(outcome,1,maxwav+1,1,n);
+     fclose (ficlog);
-   free_vector(moisnais,1,n);
+     goto end;
-   free_vector(annais,1,n);
+     exit(0);
-   /* free_matrix(mint,1,maxwav,1,n);
+   }
-      free_matrix(anint,1,maxwav,1,n);*/
+   else if(mle==-3) {
-   free_vector(moisdc,1,n);
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-   free_vector(andc,1,n);
+     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-   wav=ivector(1,imx);
+     matcov=matrix(1,npar,1,npar);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   }
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   else{
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+     /* Read guess parameters */
+     /* Reads comments: lines beginning with '#' */
-   /* Concatenates waves */
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+       numlinepar++;
+       puts(line);
-   Tcode=ivector(1,100);
+       fputs(line,ficparo);
-   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+       fputs(line,ficlog);
-   ncodemax[1]=1;
+     }
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+     ungetc(c,ficpar);
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
-                                  the estimations*/
+     for(i=1; i <=nlstate; i++){
-   h=0;
+       j=0;
-   m=pow(2,cptcoveff);
+       for(jj=1; jj <=nlstate+ndeath; jj++){
+         if(jj==i) continue;
-   for(k=1;k<=cptcoveff; k++){
+         j++;
-     for(i=1; i <=(m/pow(2,k));i++){
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-       for(j=1; j <= ncodemax[k]; j++){
+         if ((i1 != i) && (j1 != j)){
-         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-           h++;
+ It might be a problem of design; if ncovcol and the model are correct\n \
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+ run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+           exit(1);
          }
-       }
+         fprintf(ficparo,"%1d%1d",i1,j1);
-     }
+         if(mle==1)
-   }
+           printf("%1d%1d",i,j);
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+         fprintf(ficlog,"%1d%1d",i,j);
-      codtab[1][2]=1;codtab[2][2]=2; */
+         for(k=1; k<=ncovmodel;k++){
-   /* for(i=1; i <=m ;i++){
+           fscanf(ficpar," %lf",&param[i][j][k]);
-      for(k=1; k <=cptcovn; k++){
+           if(mle==1){
-      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+             printf(" %lf",param[i][j][k]);
-      }
+             fprintf(ficlog," %lf",param[i][j][k]);
-      printf("\n");
+           }
-      }
+           else
-      scanf("%d",i);*/
+             fprintf(ficlog," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
-   /*------------ gnuplot -------------*/
+         }
-   strcpy(optionfilegnuplot,optionfilefiname);
+         fscanf(ficpar,"\n");
-   if(mle==-3)
+         numlinepar++;
-     strcat(optionfilegnuplot,"-mort");
+         if(mle==1)
-   strcat(optionfilegnuplot,".gp");
+           printf("\n");
+         fprintf(ficlog,"\n");
-   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+         fprintf(ficparo,"\n");
-     printf("Problem with file %s",optionfilegnuplot);
+       }
-   }
+     }
-   else{
+     fflush(ficlog);
-     fprintf(ficgp,"\n# %s\n", version);
-     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     p=param[1][1];
-     fprintf(ficgp,"set missing 'NaNq'\n");
-   }
+     /* Reads comments: lines beginning with '#' */
-   /*  fclose(ficgp);*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   /*--------- index.htm --------*/
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
+       numlinepar++;
-   if(mle==-3)
+       puts(line);
-     strcat(optionfilehtm,"-mort");
+       fputs(line,ficparo);
-   strcat(optionfilehtm,".htm");
+       fputs(line,ficlog);
-   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+     }
-     printf("Problem with %s \n",optionfilehtm), exit(0);
+     ungetc(c,ficpar);
-   }
+     for(i=1; i <=nlstate; i++){
-   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+       for(j=1; j <=nlstate+ndeath-1; j++){
-   strcat(optionfilehtmcov,"-cov.htm");
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
+         if ((i1-i)*(j1-j)!=0){
-     printf("Problem with %s \n",optionfilehtmcov), exit(0);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-   }
+           exit(1);
-   else{
+         }
-   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+         printf("%1d%1d",i,j);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+         fprintf(ficparo,"%1d%1d",i1,j1);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+         fprintf(ficlog,"%1d%1d",i1,j1);
-           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+         for(k=1; k<=ncovmodel;k++){
-   }
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+           fprintf(ficparo," %le",delti3[i][j][k]);
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+           fprintf(ficlog," %le",delti3[i][j][k]);
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+         }
- \n\
+         fscanf(ficpar,"\n");
- <hr  size=\"2\" color=\"#EC5E5E\">\
+         numlinepar++;
-  <ul><li><h4>Parameter files</h4>\n\
+         printf("\n");
-  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
+         fprintf(ficparo,"\n");
-  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
+         fprintf(ficlog,"\n");
-  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
+       }
-  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
+     }
-  - Date and time at start: %s</ul>\n",\
+     fflush(ficlog);
-           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
+     delti=delti3[1][1];
-           fileres,fileres,\
-           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-   fflush(fichtm);
+     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-   strcpy(pathr,path);
+     /* Reads comments: lines beginning with '#' */
-   strcat(pathr,optionfilefiname);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-   chdir(optionfilefiname); /* Move to directory named optionfile */
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-   /* Calculates basic frequencies. Computes observed prevalence at single age
+       numlinepar++;
-      and prints on file fileres'p'. */
+       puts(line);
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
-   fprintf(fichtm,"\n");
+     }
-   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\
- Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
+     matcov=matrix(1,npar,1,npar);
-           imx,agemin,agemax,jmin,jmax,jmean);
+     for(i=1; i <=npar; i++)
-   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+     for(i=1; i <=npar; i++){
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+       fscanf(ficpar,"%s",&str);
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+       if(mle==1)
+         printf("%s",str);
+       fprintf(ficlog,"%s",str);
-   /* For Powell, parameters are in a vector p[] starting at p[1]
+       fprintf(ficparo,"%s",str);
-      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+       for(j=1; j <=i; j++){
-   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+         fscanf(ficpar," %le",&matcov[i][j]);
+         if(mle==1){
-   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+           printf(" %.5le",matcov[i][j]);
+         }
-   if (mle==-3){
+         fprintf(ficlog," %.5le",matcov[i][j]);
-     ximort=matrix(1,NDIM,1,NDIM);
+         fprintf(ficparo," %.5le",matcov[i][j]);
-     cens=ivector(1,n);
+       }
-     ageexmed=vector(1,n);
+       fscanf(ficpar,"\n");
-     agecens=vector(1,n);
+       numlinepar++;
-     dcwave=ivector(1,n);
+       if(mle==1)
+         printf("\n");
-     for (i=1; i<=imx; i++){
+       fprintf(ficlog,"\n");
-       dcwave[i]=-1;
+       fprintf(ficparo,"\n");
-       for (m=firstpass; m<=lastpass; m++)
+     }
-         if (s[m][i]>nlstate) {
+     for(i=1; i <=npar; i++)
-           dcwave[i]=m;
+       for(j=i+1;j<=npar;j++)
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+         matcov[i][j]=matcov[j][i];
-           break;
-         }
+     if(mle==1)
-     }
+       printf("\n");
+     fprintf(ficlog,"\n");
-     for (i=1; i<=imx; i++) {
-       if (wav[i]>0){
+     fflush(ficlog);
-         ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];
+     /*-------- Rewriting parameter file ----------*/
-         agecens[i]=1.;
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-         if (ageexmed[i]> 1 && wav[i] > 0){
+     strcat(rfileres,".");    /* */
-           agecens[i]=agev[mw[j][i]][i];
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-           cens[i]= 1;
+     if((ficres =fopen(rfileres,"w"))==NULL) {
-         }else if (ageexmed[i]< 1)
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-           cens[i]= -1;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+     }
-           cens[i]=0 ;
+     fprintf(ficres,"#%s\n",version);
-       }
+   }    /* End of mle != -3 */
-       else cens[i]=-1;
-     }
+   n= lastobs;
-     for (i=1;i<=NDIM;i++) {
+   num=lvector(1,n);
-       for (j=1;j<=NDIM;j++)
+   moisnais=vector(1,n);
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+   annais=vector(1,n);
-     }
+   moisdc=vector(1,n);
+   andc=vector(1,n);
-     p[1]=0.0268; p[NDIM]=0.083;
+   agedc=vector(1,n);
-     /*printf("%lf %lf", p[1], p[2]);*/
+   cod=ivector(1,n);
+   weight=vector(1,n);
+   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
-     printf("Powell\n");  fprintf(ficlog,"Powell\n");
+   mint=matrix(1,maxwav,1,n);
-     strcpy(filerespow,"pow-mort");
+   anint=matrix(1,maxwav,1,n);
-     strcat(filerespow,fileres);
+   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
-     if((ficrespow=fopen(filerespow,"w"))==NULL) {
+   tab=ivector(1,NCOVMAX);
-       printf("Problem with resultfile: %s\n", filerespow);
+   ncodemax=ivector(1,8);
-       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-     }
+   /* Reads data from file datafile */
-     fprintf(ficrespow,"# Powell\n# iter -2*LL");
+   if (readdata(datafile, firstobs, lastobs, &imx)==1)
-     /*  for (i=1;i<=nlstate;i++)
+     goto end;
-         for(j=1;j<=nlstate+ndeath;j++)
-         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+   /* Calculation of the number of parameters from char model */
-     */
+   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
-     fprintf(ficrespow,"\n");
+   Tprod=ivector(1,15);
+   Tvaraff=ivector(1,15);
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+   Tvard=imatrix(1,15,1,2);
-     fclose(ficrespow);
+   Tage=ivector(1,15);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+   if(decodemodel(model, lastobs) == 1)
+     goto end;
-     for(i=1; i <=NDIM; i++)
-       for(j=i+1;j<=NDIM;j++)
+     /*  if(mle==1){*/
-         matcov[i][j]=matcov[j][i];
+   if (weightopt != 1) { /* Maximisation without weights*/
+     for(i=1;i<=n;i++) weight[i]=1.0;
-     printf("\nCovariance matrix\n ");
+   }
-     for(i=1; i <=NDIM; i++) {
-       for(j=1;j<=NDIM;j++){
+     /*-calculation of age at interview from date of interview and age at death -*/
-         printf("%f ",matcov[i][j]);
+   agev=matrix(1,maxwav,1,imx);
-       }
-       printf("\n ");
+   if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
-     }
+     goto end;
-     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++)
+   agegomp=(int)agemin;
-       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+   free_vector(moisnais,1,n);
+   free_vector(annais,1,n);
-     lsurv=vector(1,AGESUP);
+   /* free_matrix(mint,1,maxwav,1,n);
-     lpop=vector(1,AGESUP);
+      free_matrix(anint,1,maxwav,1,n);*/
-     tpop=vector(1,AGESUP);
+   free_vector(moisdc,1,n);
-     lsurv[agegomp]=100000;
+   free_vector(andc,1,n);
-     for (k=agegomp;k<=AGESUP;k++) {
-       agemortsup=k;
+   wav=ivector(1,imx);
-       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
+   dh=imatrix(1,lastpass-firstpass+1,1,imx);
-     }
+   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   mw=imatrix(1,lastpass-firstpass+1,1,imx);
-     for (k=agegomp;k<agemortsup;k++)
-       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
+   /* Concatenates waves */
+   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-     for (k=agegomp;k<agemortsup;k++){
-       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-       sumlpop=sumlpop+lpop[k];
-     }
+   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+   ncodemax[1]=1;
-     tpop[agegomp]=sumlpop;
+   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-     for (k=agegomp;k<(agemortsup-3);k++){
-       /*  tpop[k+1]=2;*/
+   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
-       tpop[k+1]=tpop[k]-lpop[k];
+                                  the estimations*/
-     }
+   h=0;
+   m=pow(2,cptcoveff);
-     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
+   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     for (k=agegomp;k<(agemortsup-2);k++)
+     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 */
-       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]);
+       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
+         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 */
+           h++;
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+           if (h>m) {
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+             h=1;
+             codtab[h][k]=j;
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+             codtab[h][Tvar[k]]=j;
-                      stepm, weightopt,\
+           }
-                      model,imx,p,matcov,agemortsup);
+           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]]);
+         }
-     free_vector(lsurv,1,AGESUP);
+       }
-     free_vector(lpop,1,AGESUP);
+     }
-     free_vector(tpop,1,AGESUP);
+   }
-   } /* Endof if mle==-3 */
+   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      codtab[1][2]=1;codtab[2][2]=2; */
-   else{ /* For mle >=1 */
+   /* for(i=1; i <=m ;i++){
+      for(k=1; k <=cptcovn; k++){
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
-     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+      }
-     for (k=1; k<=npar;k++)
+      printf("\n");
-       printf(" %d %8.5f",k,p[k]);
+      }
-     printf("\n");
+      scanf("%d",i);*/
-     globpr=1; /* to print the contributions */
-     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+   /*------------ gnuplot -------------*/
-     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
+   strcpy(optionfilegnuplot,optionfilefiname);
-     for (k=1; k<=npar;k++)
+   if(mle==-3)
-       printf(" %d %8.5f",k,p[k]);
+     strcat(optionfilegnuplot,"-mort");
-     printf("\n");
+   strcat(optionfilegnuplot,".gp");
-     if(mle>=1){ /* Could be 1 or 2 */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-     }
+     printf("Problem with file %s",optionfilegnuplot);
+   }
-     /*--------- results files --------------*/
+   else{
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"# %s\n", optionfilegnuplot);
+     fprintf(ficgp,"set missing 'NaNq'\n");
-     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   }
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /*  fclose(ficgp);*/
-     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   /*--------- index.htm --------*/
-     for(i=1,jk=1; i <=nlstate; i++){
-       for(k=1; k <=(nlstate+ndeath); k++){
+   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
-         if (k != i) {
+   if(mle==-3)
-           printf("%d%d ",i,k);
+     strcat(optionfilehtm,"-mort");
-           fprintf(ficlog,"%d%d ",i,k);
+   strcat(optionfilehtm,".htm");
-           fprintf(ficres,"%1d%1d ",i,k);
+   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-           for(j=1; j <=ncovmodel; j++){
+     printf("Problem with %s \n",optionfilehtm);
-             printf("%lf ",p[jk]);
+     exit(0);
-             fprintf(ficlog,"%lf ",p[jk]);
+   }
-             fprintf(ficres,"%lf ",p[jk]);
-             jk++;
+   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
-           }
+   strcat(optionfilehtmcov,"-cov.htm");
-           printf("\n");
+   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
-           fprintf(ficlog,"\n");
+     printf("Problem with %s \n",optionfilehtmcov), exit(0);
-           fprintf(ficres,"\n");
+   }
-         }
+   else{
-       }
+   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\
-     if(mle!=0){
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
-       /* Computing hessian and covariance matrix */
+           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
-       ftolhess=ftol; /* Usually correct */
+   }
-       hesscov(matcov, p, npar, delti, ftolhess, func);
-     }
+   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
-     printf("# Scales (for hessian or gradient estimation)\n");
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ \n\
-     for(i=1,jk=1; i <=nlstate; i++){
+ <hr  size=\"2\" color=\"#EC5E5E\">\
-       for(j=1; j <=nlstate+ndeath; j++){
+  <ul><li><h4>Parameter files</h4>\n\
-         if (j!=i) {
+  - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
-           fprintf(ficres,"%1d%1d",i,j);
+  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
-           printf("%1d%1d",i,j);
+  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
-           fprintf(ficlog,"%1d%1d",i,j);
+  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
-           for(k=1; k<=ncovmodel;k++){
+  - Date and time at start: %s</ul>\n",\
-             printf(" %.5e",delti[jk]);
+           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
-             fprintf(ficlog," %.5e",delti[jk]);
+           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
-             fprintf(ficres," %.5e",delti[jk]);
+           fileres,fileres,\
-             jk++;
+           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
-           }
+   fflush(fichtm);
-           printf("\n");
-           fprintf(ficlog,"\n");
+   strcpy(pathr,path);
-           fprintf(ficres,"\n");
+   strcat(pathr,optionfilefiname);
-         }
+   chdir(optionfilefiname); /* Move to directory named optionfile */
-       }
-     }
+   /* Calculates basic frequencies. Computes observed prevalence at single age
+      and prints on file fileres'p'. */
-     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");
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-     if(mle>=1)
-       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+   fprintf(fichtm,"\n");
-     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-     /* # 121 Var(a12)\n\ */
+ Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-     /* # 122 Cov(b12,a12) Var(b12)\n\ */
+ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
+           imx,agemin,agemax,jmin,jmax,jmean);
-     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
+     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
+     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
+     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-     /* Just to have a covariance matrix which will be more understandable
+   /* For Powell, parameters are in a vector p[] starting at p[1]
-        even is we still don't want to manage dictionary of variables
+      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
-     */
+   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-     for(itimes=1;itimes<=2;itimes++){
-       jj=0;
+   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-       for(i=1; i <=nlstate; i++){
-         for(j=1; j <=nlstate+ndeath; j++){
+   if (mle==-3){
-           if(j==i) continue;
+     ximort=matrix(1,NDIM,1,NDIM);
-           for(k=1; k<=ncovmodel;k++){
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-             jj++;
+     cens=ivector(1,n);
-             ca[0]= k+'a'-1;ca[1]='\0';
+     ageexmed=vector(1,n);
-             if(itimes==1){
+     agecens=vector(1,n);
-               if(mle>=1)
+     dcwave=ivector(1,n);
-                 printf("#%1d%1d%d",i,j,k);
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+     for (i=1; i<=imx; i++){
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+       dcwave[i]=-1;
-             }else{
+       for (m=firstpass; m<=lastpass; m++)
-               if(mle>=1)
+         if (s[m][i]>nlstate) {
-                 printf("%1d%1d%d",i,j,k);
+           dcwave[i]=m;
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+           break;
-             }
+         }
-             ll=0;
+     }
-             for(li=1;li <=nlstate; li++){
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+     for (i=1; i<=imx; i++) {
-                 if(lj==li) continue;
+       if (wav[i]>0){
-                 for(lk=1;lk<=ncovmodel;lk++){
+         ageexmed[i]=agev[mw[1][i]][i];
-                   ll++;
+         j=wav[i];
-                   if(ll<=jj){
+         agecens[i]=1.;
-                     cb[0]= lk +'a'-1;cb[1]='\0';
-                     if(ll<jj){
+         if (ageexmed[i]> 1 && wav[i] > 0){
-                       if(itimes==1){
+           agecens[i]=agev[mw[j][i]][i];
-                         if(mle>=1)
+           cens[i]= 1;
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         }else if (ageexmed[i]< 1)
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+           cens[i]= -1;
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-                       }else{
+           cens[i]=0 ;
-                         if(mle>=1)
+       }
-                           printf(" %.5e",matcov[jj][ll]);
+       else cens[i]=-1;
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+     }
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+     for (i=1;i<=NDIM;i++) {
-                     }else{
+       for (j=1;j<=NDIM;j++)
-                       if(itimes==1){
+         ximort[i][j]=(i == j ? 1.0 : 0.0);
-                         if(mle>=1)
+     }
-                           printf(" Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+     p[1]=0.0268; p[NDIM]=0.083;
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+     /*printf("%lf %lf", p[1], p[2]);*/
-                       }else{
-                         if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+ #ifdef GSL
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+ #elsedef
-                       }
+     printf("Powell\n");  fprintf(ficlog,"Powell\n");
-                     }
+ #endif
-                   }
+     strcpy(filerespow,"pow-mort");
-                 } /* end lk */
+     strcat(filerespow,fileres);
-               } /* end lj */
+     if((ficrespow=fopen(filerespow,"w"))==NULL) {
-             } /* end li */
+       printf("Problem with resultfile: %s\n", filerespow);
-             if(mle>=1)
+       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
-               printf("\n");
+     }
-             fprintf(ficlog,"\n");
+ #ifdef GSL
-             fprintf(ficres,"\n");
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
-             numlinepar++;
+ #elsedef
-           } /* end k*/
+     fprintf(ficrespow,"# Powell\n# iter -2*LL");
-         } /*end j */
+ #endif
-       } /* end i */
+     /*  for (i=1;i<=nlstate;i++)
-     } /* end itimes */
+         for(j=1;j<=nlstate+ndeath;j++)
+         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
-     fflush(ficlog);
+     */
-     fflush(ficres);
+     fprintf(ficrespow,"\n");
+ #ifdef GSL
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /* gsl starts here */
-       ungetc(c,ficpar);
+     T = gsl_multimin_fminimizer_nmsimplex;
-       fgets(line, MAXLINE, ficpar);
+     gsl_multimin_fminimizer *sfm = NULL;
-       puts(line);
+     gsl_vector *ss, *x;
-       fputs(line,ficparo);
+     gsl_multimin_function minex_func;
-     }
-     ungetc(c,ficpar);
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
-     estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (ss == NULL){
-     if (estepm==0 || estepm < stepm) estepm=stepm;
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
-     if (fage <= 2) {
+     }
-       bage = ageminpar;
+     /* Set all step sizes to 1 */
-       fage = agemaxpar;
+     gsl_vector_set_all (ss, 0.001);
-     }
+     /* Starting point */
-     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);
+     x = gsl_vector_alloc (NDIM);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     if (x == NULL){
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       gsl_vector_free(ss);
-       ungetc(c,ficpar);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
-       fgets(line, MAXLINE, ficpar);
+     }
-       puts(line);
-       fputs(line,ficparo);
+     /* Initialize method and iterate */
-     }
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
-     ungetc(c,ficpar);
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
-     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);
+     gsl_vector_set(x, 0, p[1]);
-     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);
+     gsl_vector_set(x, 1, p[2]);
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+     minex_func.f = &gompertz_f;
-     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);
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
-       fgets(line, MAXLINE, ficpar);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
-       puts(line);
-       fputs(line,ficparo);
+     printf("Iterations beginning .....\n\n");
-     }
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
-     ungetc(c,ficpar);
+     iteri=0;
+     while (rval == GSL_CONTINUE){
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
+       iteri++;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
+       status = gsl_multimin_fminimizer_iterate(sfm);
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
+       if (status) printf("error: %s\n", gsl_strerror (status));
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+       fflush(0);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+       if (status)
-     while((c=getc(ficpar))=='#' && c!= EOF){
+         break;
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
-       puts(line);
+       ssval = gsl_multimin_fminimizer_size (sfm);
-       fputs(line,ficparo);
-     }
+       if (rval == GSL_SUCCESS)
-     ungetc(c,ficpar);
+         printf ("converged to a local maximum at\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("%5d ", iteri);
-     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);
+       for (it = 0; it < NDIM; it++){
-     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);
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       }
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
-     /* day and month of proj2 are not used but only year anproj2.*/
+     }
+     printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
-     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
+     gsl_vector_free(x); /* initial values */
-     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+     gsl_vector_free(ss); /* inital step size */
+     for (it=0; it<NDIM; it++){
-     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+       p[it+1]=gsl_vector_get(sfm->x,it);
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+       fprintf(ficrespow," %.12lf", p[it]);
+     }
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ #endif
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+ #ifdef POWELL
+      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
-    /*------------ free_vector  -------------*/
+ #endif
-    /*  chdir(path); */
+     fclose(ficrespow);
-     free_ivector(wav,1,imx);
+     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     for(i=1; i <=NDIM; i++)
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+       for(j=i+1;j<=NDIM;j++)
-     free_lvector(num,1,n);
+         matcov[i][j]=matcov[j][i];
-     free_vector(agedc,1,n);
-     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     printf("\nCovariance matrix\n ");
-     /*free_matrix(covar,1,NCOVMAX,1,n);*/
+     for(i=1; i <=NDIM; i++) {
-     fclose(ficparo);
+       for(j=1;j<=NDIM;j++){
-     fclose(ficres);
+         printf("%f ",matcov[i][j]);
+       }
+       printf("\n ");
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     }
-     strcpy(filerespl,"pl");
+     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-     strcat(filerespl,fileres);
+     for (i=1;i<=NDIM;i++)
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
+       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+     lsurv=vector(1,AGESUP);
-     }
+     lpop=vector(1,AGESUP);
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     tpop=vector(1,AGESUP);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     lsurv[agegomp]=100000;
-     pstamp(ficrespl);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     for (k=agegomp;k<=AGESUP;k++) {
-     fprintf(ficrespl,"#Age ");
+       agemortsup=k;
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+       if (p[1]*exp(p[2]*(k-agegomp))>1) break;
-     fprintf(ficrespl,"\n");
+     }
-     prlim=matrix(1,nlstate,1,nlstate);
+     for (k=agegomp;k<agemortsup;k++)
+       lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-     agebase=ageminpar;
-     agelim=agemaxpar;
+     for (k=agegomp;k<agemortsup;k++){
-     ftolpl=1.e-10;
+       lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
-     i1=cptcoveff;
+       sumlpop=sumlpop+lpop[k];
-     if (cptcovn < 1){i1=1;}
+     }
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     tpop[agegomp]=sumlpop;
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     for (k=agegomp;k<(agemortsup-3);k++){
-         k=k+1;
+       /*  tpop[k+1]=2;*/
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+       tpop[k+1]=tpop[k]-lpop[k];
-         fprintf(ficrespl,"\n#******");
+     }
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
-         for(j=1;j<=cptcoveff;j++) {
+     printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for (k=agegomp;k<(agemortsup-2);k++)
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       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]);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficrespl,"******\n");
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-         printf("******\n");
+     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-         fprintf(ficlog,"******\n");
+     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
-         for (age=agebase; age<=agelim; age++){
+                      stepm, weightopt,\
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+                      model,imx,p,matcov,agemortsup);
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
+     free_vector(lsurv,1,AGESUP);
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     free_vector(lpop,1,AGESUP);
-           for(i=1; i<=nlstate;i++)
+     free_vector(tpop,1,AGESUP);
-             fprintf(ficrespl," %.5f", prlim[i][i]);
+ #ifdef GSL
-           fprintf(ficrespl,"\n");
+     free_ivector(cens,1,n);
-         }
+     free_vector(agecens,1,n);
-       }
+     free_ivector(dcwave,1,n);
-     }
+     free_matrix(ximort,1,NDIM,1,NDIM);
-     fclose(ficrespl);
+ #endif
+   } /* Endof if mle==-3 */
-     /*------------- h Pij x at various ages ------------*/
+   else{ /* For mle >=1 */
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+     globpr=0;/* debug */
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+     for (k=1; k<=npar;k++)
-     }
+       printf(" %d %8.5f",k,p[k]);
-     printf("Computing pij: result on file '%s' \n", filerespij);
+     printf("\n");
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     globpr=1; /* to print the contributions */
+     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
-     /*if (stepm<=24) stepsize=2;*/
+     for (k=1; k<=npar;k++)
+       printf(" %d %8.5f",k,p[k]);
-     agelim=AGESUP;
+     printf("\n");
-     hstepm=stepsize*YEARM; /* Every year of age */
+     if(mle>=1){ /* Could be 1 or 2 */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
+     /*--------- results files --------------*/
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-         fprintf(ficrespij,"\n#****** ");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-         for(j=1;j<=cptcoveff;j++)
+     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     for(i=1,jk=1; i <=nlstate; i++){
-         fprintf(ficrespij,"******\n");
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+           printf("%d%d ",i,k);
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+           fprintf(ficlog,"%d%d ",i,k);
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+           fprintf(ficres,"%1d%1d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
+             printf("%lf ",p[jk]);
+             fprintf(ficlog,"%lf ",p[jk]);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+             fprintf(ficres,"%lf ",p[jk]);
-           oldm=oldms;savm=savms;
+             jk++;
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+           }
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+           printf("\n");
-           for(i=1; i<=nlstate;i++)
+           fprintf(ficlog,"\n");
-             for(j=1; j<=nlstate+ndeath;j++)
+           fprintf(ficres,"\n");
-               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 );
+     if(mle!=0){
-             for(i=1; i<=nlstate;i++)
+       /* Computing hessian and covariance matrix */
-               for(j=1; j<=nlstate+ndeath;j++)
+       ftolhess=ftol; /* Usually correct */
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+       hesscov(matcov, p, npar, delti, ftolhess, func);
-             fprintf(ficrespij,"\n");
+     }
-           }
+     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     printf("# Scales (for hessian or gradient estimation)\n");
-           fprintf(ficrespij,"\n");
+     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
-         }
+     for(i=1,jk=1; i <=nlstate; i++){
-       }
+       for(j=1; j <=nlstate+ndeath; j++){
-     }
+         if (j!=i) {
+           fprintf(ficres,"%1d%1d",i,j);
-     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+           printf("%1d%1d",i,j);
+           fprintf(ficlog,"%1d%1d",i,j);
-     fclose(ficrespij);
+           for(k=1; k<=ncovmodel;k++){
+             printf(" %.5e",delti[jk]);
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+             fprintf(ficlog," %.5e",delti[jk]);
-     for(i=1;i<=AGESUP;i++)
+             fprintf(ficres," %.5e",delti[jk]);
-       for(j=1;j<=NCOVMAX;j++)
+             jk++;
-         for(k=1;k<=NCOVMAX;k++)
+           }
-           probs[i][j][k]=0.;
+           printf("\n");
+           fprintf(ficlog,"\n");
-     /*---------- Forecasting ------------------*/
+           fprintf(ficres,"\n");
-     /*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);*/
+     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-       /*      }  */
+     if(mle>=1)
-       /*      else{ */
+       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");
-       /*        erreur=108; */
+     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");
-       /*        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); */
+     /* # 121 Var(a12)\n\ */
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     /* # 122 Cov(b12,a12) Var(b12)\n\ */
-       /*      } */
+     /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-     }
+     /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
+     /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
+     /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-     /*---------- Health expectancies and variances ------------*/
+     /* # 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" */
-     strcpy(filerest,"t");
-     strcat(filerest,fileres);
-     if((ficrest=fopen(filerest,"w"))==NULL) {
+     /* Just to have a covariance matrix which will be more understandable
-       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+        even is we still don't want to manage dictionary of variables
-       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+     */
-     }
+     for(itimes=1;itimes<=2;itimes++){
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       jj=0;
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+       for(i=1; i <=nlstate; i++){
+         for(j=1; j <=nlstate+ndeath; j++){
+           if(j==i) continue;
-     strcpy(filerese,"e");
+           for(k=1; k<=ncovmodel;k++){
-     strcat(filerese,fileres);
+             jj++;
-     if((ficreseij=fopen(filerese,"w"))==NULL) {
+             ca[0]= k+'a'-1;ca[1]='\0';
-       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+             if(itimes==1){
-       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+               if(mle>=1)
-     }
+                 printf("#%1d%1d%d",i,j,k);
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+               fprintf(ficlog,"#%1d%1d%d",i,j,k);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+               fprintf(ficres,"#%1d%1d%d",i,j,k);
+             }else{
-     strcpy(fileresstde,"stde");
+               if(mle>=1)
-     strcat(fileresstde,fileres);
+                 printf("%1d%1d%d",i,j,k);
-     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+               fprintf(ficlog,"%1d%1d%d",i,j,k);
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+               fprintf(ficres,"%1d%1d%d",i,j,k);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+             }
-     }
+             ll=0;
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+             for(li=1;li <=nlstate; li++){
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+               for(lj=1;lj <=nlstate+ndeath; lj++){
+                 if(lj==li) continue;
-     strcpy(filerescve,"cve");
+                 for(lk=1;lk<=ncovmodel;lk++){
-     strcat(filerescve,fileres);
+                   ll++;
-     if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+                   if(ll<=jj){
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+                     cb[0]= lk +'a'-1;cb[1]='\0';
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+                     if(ll<jj){
-     }
+                       if(itimes==1){
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+                         if(mle>=1)
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+                           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(fileresv,"v");
+                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-     strcat(fileresv,fileres);
+                       }else{
-     if((ficresvij=fopen(fileresv,"w"))==NULL) {
+                         if(mle>=1)
-       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+                           printf(" %.5e",matcov[jj][ll]);
-       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-     }
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+                       }
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+                     }else{
+                       if(itimes==1){
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+                         if(mle>=1)
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+                           printf(" Var(%s%1d%1d)",ca,i,j);
-     /*  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",\
+                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
+                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
-     */
+                       }else{
+                         if(mle>=1)
-     if (mobilav!=0) {
+                           printf(" %.5e",matcov[jj][ll]);
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+                         fprintf(ficlog," %.5e",matcov[jj][ll]);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+                         fprintf(ficres," %.5e",matcov[jj][ll]);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                       }
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                     }
-       }
+                   }
-     }
+                 } /* end lk */
+               } /* end lj */
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+             } /* end li */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+             if(mle>=1)
-         k=k+1;
+               printf("\n");
-         fprintf(ficrest,"\n#****** ");
+             fprintf(ficlog,"\n");
-         for(j=1;j<=cptcoveff;j++)
+             fprintf(ficres,"\n");
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+             numlinepar++;
-         fprintf(ficrest,"******\n");
+           } /* end k*/
+         } /*end j */
-         fprintf(ficreseij,"\n#****** ");
+       } /* end i */
-         fprintf(ficresstdeij,"\n#****** ");
+     } /* end itimes */
-         fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+     fflush(ficlog);
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     fflush(ficres);
-           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]]);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         }
+       ungetc(c,ficpar);
-         fprintf(ficreseij,"******\n");
+       fgets(line, MAXLINE, ficpar);
-         fprintf(ficresstdeij,"******\n");
+       puts(line);
-         fprintf(ficrescveij,"******\n");
+       fputs(line,ficparo);
+     }
-         fprintf(ficresvij,"\n#****** ");
+     ungetc(c,ficpar);
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+     estepm=0;
-         fprintf(ficresvij,"******\n");
+     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if (estepm==0 || estepm < stepm) estepm=stepm;
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     if (fage <= 2) {
-         oldm=oldms;savm=savms;
+       bage = ageminpar;
-         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       fage = agemaxpar;
-         cvevsij(fileres, 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);
+     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-         oldm=oldms;savm=savms;
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-         if(popbased==1){
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
+     while((c=getc(ficpar))=='#' && c!= EOF){
-         }
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
-         pstamp(ficrest);
+       puts(line);
-         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
+       fputs(line,ficparo);
-         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+     }
-         fprintf(ficrest,"\n");
+     ungetc(c,ficpar);
-         epj=vector(1,nlstate+1);
+     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);
-         for(age=bage; age <=fage ;age++){
+     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);
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+     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);
-           if (popbased==1) {
+     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-             if(mobilav ==0){
+     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);
-               for(i=1; i<=nlstate;i++)
-                 prlim[i][i]=probs[(int)age][i][k];
+     while((c=getc(ficpar))=='#' && c!= EOF){
-             }else{ /* mobilav */
+       ungetc(c,ficpar);
-               for(i=1; i<=nlstate;i++)
+       fgets(line, MAXLINE, ficpar);
-                 prlim[i][i]=mobaverage[(int)age][i][k];
+       puts(line);
-             }
+       fputs(line,ficparo);
-           }
+     }
+     ungetc(c,ficpar);
-           fprintf(ficrest," %4.0f",age);
-           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-             }
+     fscanf(ficpar,"pop_based=%d\n",&popbased);
-             epj[nlstate+1] +=epj[j];
+     fprintf(ficparo,"pop_based=%d\n",popbased);
-           }
+     fprintf(ficres,"pop_based=%d\n",popbased);
-           for(i=1, vepp=0.;i <=nlstate;i++)
+     while((c=getc(ficpar))=='#' && c!= EOF){
-             for(j=1;j <=nlstate;j++)
+       ungetc(c,ficpar);
-               vepp += vareij[i][j][(int)age];
+       fgets(line, MAXLINE, ficpar);
-           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+       puts(line);
-           for(j=1;j <=nlstate;j++){
+       fputs(line,ficparo);
-             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+     }
-           }
+     ungetc(c,ficpar);
-           fprintf(ficrest,"\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);
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     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);
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+     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);
-         free_vector(epj,1,nlstate+1);
+     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-       }
+     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
-     }
+     /* day and month of proj2 are not used but only year anproj2.*/
-     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);
+     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
-     free_matrix(mint,1,maxwav,1,n);
+     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-     free_ivector(cod,1,n);
-     free_ivector(tab,1,NCOVMAX);
+     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     fclose(ficreseij);
+     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
+     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
-     fclose(ficresvij);
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
-     fclose(ficrest);
+                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-     fclose(ficpar);
+    /*------------ free_vector  -------------*/
-     /*------- Variance of period (stable) prevalence------*/
+    /*  chdir(path); */
-     strcpy(fileresvpl,"vpl");
+     free_ivector(wav,1,imx);
-     strcat(fileresvpl,fileres);
+     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
+     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
-       exit(0);
+     free_lvector(num,1,n);
-     }
+     free_vector(agedc,1,n);
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     /*free_matrix(covar,0,NCOVMAX,1,n);*/
+     /*free_matrix(covar,1,NCOVMAX,1,n);*/
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     fclose(ficparo);
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     fclose(ficres);
-         k=k+1;
-         fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvpl,"******\n");
+     strcpy(filerespl,"pl");
+     strcat(filerespl,fileres);
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-         oldm=oldms;savm=savms;
+       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+     }
-       }
+     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     }
+     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+     pstamp(ficrespl);
-     fclose(ficresvpl);
+     fprintf(ficrespl,"# Period (stable) prevalence \n");
+     fprintf(ficrespl,"#Age ");
-     /*---------- End : free ----------------*/
+     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     fprintf(ficrespl,"\n");
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     prlim=matrix(1,nlstate,1,nlstate);
-   }  /* mle==-3 arrives here for freeing */
-   free_matrix(prlim,1,nlstate,1,nlstate);
+     agebase=ageminpar;
-     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+     agelim=agemaxpar;
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     ftolpl=1.e-10;
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     i1=cptcoveff;
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+     if (cptcovn < 1){i1=1;}
-     free_matrix(covar,0,NCOVMAX,1,n);
-     free_matrix(matcov,1,npar,1,npar);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-     /*free_vector(delti,1,npar);*/
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         k=k+1;
-     free_matrix(agev,1,maxwav,1,imx);
+         /* to clean */
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+         printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
+         fprintf(ficrespl,"\n#******");
-     free_ivector(ncodemax,1,8);
+         printf("\n#******");
-     free_ivector(Tvar,1,15);
+         fprintf(ficlog,"\n#******");
-     free_ivector(Tprod,1,15);
+         for(j=1;j<=cptcoveff;j++) {
-     free_ivector(Tvaraff,1,15);
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     free_ivector(Tage,1,15);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     free_ivector(Tcode,1,100);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         }
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+         fprintf(ficrespl,"******\n");
-     free_imatrix(codtab,1,100,1,10);
+         printf("******\n");
-   fflush(fichtm);
+         fprintf(ficlog,"******\n");
-   fflush(ficgp);
+         for (age=agebase; age<=agelim; age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-   if((nberr >0) || (nbwarn>0)){
+           fprintf(ficrespl,"%.0f ",age );
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+           for(j=1;j<=cptcoveff;j++)
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   }else{
+           for(i=1; i<=nlstate;i++)
-     printf("End of Imach\n");
+             fprintf(ficrespl," %.5f", prlim[i][i]);
-     fprintf(ficlog,"End of Imach\n");
+           fprintf(ficrespl,"\n");
-   }
+         }
-   printf("See log file on %s\n",filelog);
+       }
-   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
+     }
-   (void) gettimeofday(&end_time,&tzp);
+     fclose(ficrespl);
-   tm = *localtime(&end_time.tv_sec);
-   tmg = *gmtime(&end_time.tv_sec);
+     /*------------- h Pij x at various ages ------------*/
-   strcpy(strtend,asctime(&tm));
-   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
+     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
-   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-   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));
+     printf("Computing pij: result on file '%s' \n", filerespij);
-   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-   /*  printf("Total time was %d uSec.\n", total_usecs);*/
- /*   if(fileappend(fichtm,optionfilehtm)){ */
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
-   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     /*if (stepm<=24) stepsize=2;*/
-   fclose(fichtm);
-   fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
+     agelim=AGESUP;
-   fclose(fichtmcov);
+     hstepm=stepsize*YEARM; /* Every year of age */
-   fclose(ficgp);
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-   fclose(ficlog);
-   /*------ End -----------*/
+     /* 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 ");
-    printf("Before Current directory %s!\n",pathcd);
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-    if(chdir(pathcd) != 0)
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     printf("Can't move to directory %s!\n",path);
+         k=k+1;
-   if(getcwd(pathcd,MAXLINE) > 0)
+         fprintf(ficrespij,"\n#****** ");
-     printf("Current directory %s!\n",pathcd);
+         for(j=1;j<=cptcoveff;j++)
-   /*strcat(plotcmd,CHARSEPARATOR);*/
+           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-   sprintf(plotcmd,"gnuplot");
+         fprintf(ficrespij,"******\n");
- #ifndef UNIX
-   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- #endif
+           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-   if(!stat(plotcmd,&info)){
+           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
-     if(!stat(getenv("GNUPLOTBIN"),&info)){
+           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
-     }else
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-       strcpy(pplotcmd,plotcmd);
+           oldm=oldms;savm=savms;
- #ifdef UNIX
+           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-     strcpy(plotcmd,GNUPLOTPROGRAM);
+           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-     if(!stat(plotcmd,&info)){
+           for(i=1; i<=nlstate;i++)
-       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+             for(j=1; j<=nlstate+ndeath;j++)
-     }else
+               fprintf(ficrespij," %1d-%1d",i,j);
-       strcpy(pplotcmd,plotcmd);
+           fprintf(ficrespij,"\n");
- #endif
+           for (h=0; h<=nhstepm; h++){
-   }else
+             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-     strcpy(pplotcmd,plotcmd);
+             for(i=1; i<=nlstate;i++)
+               for(j=1; j<=nlstate+ndeath;j++)
-   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+             fprintf(ficrespij,"\n");
+           }
-   if((outcmd=system(plotcmd)) != 0){
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     printf("\n Problem with gnuplot\n");
+           fprintf(ficrespij,"\n");
-   }
+         }
-   printf(" Wait...");
+       }
-   while (z[0] != 'q') {
+     }
-     /* chdir(path); */
-     printf("\nType e to edit output files, g to graph again and q for exiting: ");
+     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     scanf("%s",z);
- /*     if (z[0] == 'c') system("./imach"); */
+     fclose(ficrespij);
-     if (z[0] == 'e') {
-       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
+     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       system(optionfilehtm);
+     for(i=1;i<=AGESUP;i++)
-     }
+       for(j=1;j<=NCOVMAX;j++)
-     else if (z[0] == 'g') system(plotcmd);
+         for(k=1;k<=NCOVMAX;k++)
-     else if (z[0] == 'q') exit(0);
+           probs[i][j][k]=0.;
-   }
-   end:
+     /*---------- Forecasting ------------------*/
-   while (z[0] != 'q') {
+     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
-     printf("\nType  q for exiting: ");
+     if(prevfcast==1){
-     scanf("%s",z);
+       /*    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);
+   }
+ }

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