Diff for /imach/src/imach.c between versions 1.97 and 1.164

version 1.97, 2004/02/20 13:25:42 version 1.164, 2014/12/16 10:52:11
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
   
     Revision 1.1  2014/09/16 11:06:58  brouard
     Summary: With some code (wrong) for nlopt
   
     Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
   
     Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
   
     Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
     Author: Brouard
   
     Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   
     Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
     Author: Brouard
   
     In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
   
     Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
   
     Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
     Author: Brouard
   
     Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
   
     Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
   
     Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
     Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
   
     Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
   
     Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
   
     Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
     Author: Brouard
   
     Just a new packaging for OS/X version 0.98nS
   
     Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
   
     Revision 1.146  2014/06/16 10:20:28  brouard
     Summary: Merge
     Author: Brouard
   
     Merge, before building revised version.
   
     Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
     Author: Nicolas Brouard
   
     Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
     No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
     the source code.
   
     Revision 1.143  2014/01/26 09:45:38  brouard
     Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
     Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
     Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
     Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
   
     Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
     Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
   
     Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
   
     Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
     Some cleaning of code and comments added.
   
     Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
   
     Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
   
     Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
     Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
     Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
     Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
   
     Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
     computation.
     In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
     Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     Version 0.98h
   
     Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
   
     Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
   
     Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   
     * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
     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
     1.
     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.
   
     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    Revision 1.97  2004/02/20 13:25:42  lievre
   Version 0.96d. Population forecasting command line is (temporarily)    Version 0.96d. Population forecasting command line is (temporarily)
   suppressed.    suppressed.
Line 121 Line 440
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the stable prevalence.     of the life expectancies. It also computes the period (stable) prevalence. 
       
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
Line 150 Line 469
       begin-prev-date,...        begin-prev-date,...
   open gnuplot file    open gnuplot file
   open html file    open html file
   stable prevalence    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
    for age prevalim()     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   h Pij x                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   variance of p varprob      freexexit2 possible for memory heap.
   
     h Pij x                         | pij_nom  ficrestpij
      # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
          1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
          1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   
          1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
          1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
      Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
      Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   
   forecasting if prevfcast==1 prevforecast call prevalence()    forecasting if prevfcast==1 prevforecast call prevalence()
   health expectancies    health expectancies
   Variance-covariance of DFLE    Variance-covariance of DFLE
Line 162 Line 493
   varevsij()     varevsij() 
   if popbased==1 varevsij(,popbased)    if popbased==1 varevsij(,popbased)
   total life expectancies    total life expectancies
   Variance of stable prevalence    Variance of period (stable) prevalence
  end   end
 */  */
   
Line 172 Line 503
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
   #include <string.h>
   
   #ifdef _WIN32
   #include <io.h>
   #else
 #include <unistd.h>  #include <unistd.h>
   #endif
   
   #include <limits.h>
   #include <sys/types.h>
   #include <sys/stat.h>
   #include <errno.h>
   /* extern int errno; */
   
   /* #ifdef LINUX */
   /* #include <time.h> */
   /* #include "timeval.h" */
   /* #else */
   /* #include <sys/time.h> */
   /* #endif */
   
 #include <sys/time.h>  
 #include <time.h>  #include <time.h>
 #include "timeval.h"  
   #ifdef GSL
   #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
   #endif
   
   #ifdef NLOPT
   #include <nlopt.h>
   typedef struct {
     double (* function)(double [] );
   } myfunc_data ;
   #endif
   
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 256  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 132  #define FILENAMELENGTH 132
 /*#define DEBUG*/  
 /*#define windows*/  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
 #ifdef unix  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #define DIRSEPARATOR '/'  #ifdef _WIN32
 #define ODIRSEPARATOR '\\'  
 #else  
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'  #define ODIRSEPARATOR '/'
   #else
   #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  char strstart[80];
 int nvar;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar=0, nforce=0; /* Number of variables, number of forces */
   /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
   int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int cptcov=0; /* Working variable */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav=0; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 int gipmx, gsw; /* Global variables on the number of contributions   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                    to the likelihood and the sum of weights (done by funcone)*/                     to the likelihood and the sum of weights (done by funcone)*/
 int mle, weightopt;  int mle=1, weightopt=0;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double jmean; /* Mean space between 2 waves */  int countcallfunc=0;  /* Count the number of calls to func */
   double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  /*FILE *fic ; */ /* Used in readdata only */
   FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
 int globpr; /* Global variable for printing or not */  int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
 long ipmx; /* Number of contributions */  long ipmx=0; /* Number of contributions */
 double sw; /* Sum of weights */  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 FILE *ficresilk;  FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
Line 249  FILE *ficresprobmorprev; Line 627  FILE *ficresprobmorprev;
 FILE *fichtm, *fichtmcov; /* Html File */  FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;  FILE *ficreseij;
 char filerese[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 char command[FILENAMELENGTH];  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
Line 269  char popfile[FILENAMELENGTH]; Line 651  char popfile[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 struct timeval start_time, end_time, curr_time, last_time, forecast_time;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
 struct timezone tzp;  /* struct timezone tzp; */
 extern int gettimeofday();  /* extern int gettimeofday(); */
 struct tm tmg, tm, tmf, *gmtime(), *localtime();  struct tm tml, *gmtime(), *localtime();
 long time_value;  
 extern long time();  extern time_t time();
   
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
   
 char strcurr[80], strfor[80];  char strcurr[80], strfor[80];
   
   char *endptr;
   long lval;
   double dval;
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
Line 304  static double maxarg1,maxarg2; Line 695  static double maxarg1,maxarg2;
 static double sqrarg;  static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   
 int imx;   int imx; 
 int stepm;  int stepm=1;
 /* Stepm, step in month: minimum step interpolation*/  /* Stepm, step in month: minimum step interpolation*/
   
 int estepm;  int estepm;
Line 314  int estepm; Line 706  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc, **covar, idx;  double *agedc;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double  idx; 
   int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 double ftolhess; /* Tolerance for computing hessian */  double ftolhess; /**< Tolerance for computing hessian */
   
 /**************** split *************************/  /**************** split *************************/
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   char  *ss;                            /* pointer */    char  *ss;                            /* pointer */
   int   l1, l2;                         /* length counters */    int   l1, l2;                         /* length counters */
   
   l1 = strlen(path );                   /* length of path */    l1 = strlen(path );                   /* length of path */
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   ss= strrchr( path, DIRSEPARATOR );            /* find last / */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if ( ss == NULL ) {                   /* no directory, so use current */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
     /*if(strrchr(path, ODIRSEPARATOR )==NULL)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* get current working directory */      /* get current working directory */
Line 344  static int split( char *path, char *dirc Line 749  static int split( char *path, char *dirc
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
     }      }
     strcpy( name, path );               /* we've got it */      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
   } else {                              /* strip direcotry from path */    } else {                              /* strip direcotry from path */
     ss++;                               /* after this, the filename */      ss++;                               /* after this, the filename */
     l2 = strlen( ss );                  /* length of filename */      l2 = strlen( ss );                  /* length of filename */
Line 352  static int split( char *path, char *dirc Line 758  static int split( char *path, char *dirc
     strcpy( name, ss );         /* save file name */      strcpy( name, ss );         /* save file name */
     strncpy( dirc, path, l1 - l2 );     /* now the directory */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     dirc[l1-l2] = 0;                    /* add zero */      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
   }    }
     /* We add a separator at the end of dirc if not exists */
   l1 = strlen( dirc );                  /* length of directory */    l1 = strlen( dirc );                  /* length of directory */
   /*#ifdef windows    if( dirc[l1-1] != DIRSEPARATOR ){
   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }      dirc[l1] =  DIRSEPARATOR;
 #else      dirc[l1+1] = 0; 
   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }      printf(" DIRC3 = %s \n",dirc);
 #endif    }
   */  
   ss = strrchr( name, '.' );            /* find last / */    ss = strrchr( name, '.' );            /* find last / */
   ss++;    if (ss >0){
   strcpy(ext,ss);                       /* save extension */      ss++;
   l1= strlen( name);      strcpy(ext,ss);                     /* save extension */
   l2= strlen(ss)+1;      l1= strlen( name);
   strncpy( finame, name, l1-l2);      l2= strlen(ss)+1;
   finame[l1-l2]= 0;      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
     }
   
   return( 0 );                          /* we're done */    return( 0 );                          /* we're done */
 }  }
   
Line 385  void replace_back_to_slash(char *s, char Line 795  void replace_back_to_slash(char *s, char
   }    }
 }  }
   
   char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
     s=out;
     while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
       }
       *out++ = *in++;
     }
     *out='\0';
     return s;
   }
   
   char *cutl(char *blocc, char *alocc, char *in, char occ)
   {
     /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
        and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
     char *s, *t;
     t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
       *alocc++ = *in++;
     }
     if( *in == occ){
       *(alocc)='\0';
       s=++in;
     }
    
     if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
       in=s;
     }
     while ( *in != '\0'){
       *blocc++ = *in++;
     }
   
     *blocc='\0';
     return t;
   }
   char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
     /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
     char *s, *t;
     t=in;s=in;
     while (*in != '\0'){
       while( *in == occ){
         *blocc++ = *in++;
         s=in;
       }
       *blocc++ = *in++;
     }
     if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
     else
       *(blocc-(in-s)-1)='\0';
     in=s;
     while ( *in != '\0'){
       *alocc++ = *in++;
     }
   
     *alocc='\0';
     return s;
   }
   
 int nbocc(char *s, char occ)  int nbocc(char *s, char occ)
 {  {
   int i,j=0;    int i,j=0;
Line 397  int nbocc(char *s, char occ) Line 878  int nbocc(char *s, char occ)
   return j;    return j;
 }  }
   
 void cutv(char *u,char *v, char*t, char occ)  /* void cutv(char *u,char *v, char*t, char occ) */
 {  /* { */
   /* cuts string t into u and v where u is ended by char occ excluding it  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
      gives u="abcedf" and v="ghi2j" */  /*      gives u="abcdef2ghi" and v="j" *\/ */
   int i,lg,j,p=0;  /*   int i,lg,j,p=0; */
   i=0;  /*   i=0; */
   for(j=0; j<=strlen(t)-1; j++) {  /*   lg=strlen(t); */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  /*   for(j=0; j<=lg-1; j++) { */
   }  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
   
   lg=strlen(t);  /*   for(j=0; j<p; j++) { */
   for(j=0; j<p; j++) {  /*     (u[j] = t[j]); */
     (u[j] = t[j]);  /*   } */
   }  /*      u[p]='\0'; */
      u[p]='\0';  
   
    for(j=0; j<= lg; j++) {  /*    for(j=0; j<= lg; j++) { */
     if (j>=(p+1))(v[j-p-1] = t[j]);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   }  /*   } */
   /* } */
   
   #ifdef _WIN32
   char * strsep(char **pp, const char *delim)
   {
     char *p, *q;
            
     if ((p = *pp) == NULL)
       return 0;
     if ((q = strpbrk (p, delim)) != NULL)
     {
       *pp = q + 1;
       *q = '\0';
     }
     else
       *pp = 0;
     return p;
 }  }
   #endif
   
 /********************** nrerror ********************/  /********************** nrerror ********************/
   
Line 526  double **matrix(long nrl, long nrh, long Line 1025  double **matrix(long nrl, long nrh, long
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;    return m;
   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
    */     */
 }  }
   
Line 616  char *subdirf3(char fileres[], char *pre Line 1117  char *subdirf3(char fileres[], char *pre
   return tmpout;    return tmpout;
 }  }
   
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
   
 /***************** f1dim *************************/  /***************** f1dim *************************/
 extern int ncom;   extern int ncom; 
 extern double *pcom,*xicom;  extern double *pcom,*xicom;
Line 639  double brent(double ax, double bx, doubl Line 1153  double brent(double ax, double bx, doubl
 {   { 
   int iter;     int iter; 
   double a,b,d,etemp;    double a,b,d,etemp;
   double fu,fv,fw,fx;    double fu=0,fv,fw,fx;
   double ftemp;    double ftemp=0.;
   double p,q,r,tol1,tol2,u,v,w,x,xm;     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double e=0.0;     double e=0.0; 
     
Line 654  double brent(double ax, double bx, doubl Line 1168  double brent(double ax, double bx, doubl
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     printf(".");fflush(stdout);      printf(".");fflush(stdout);
     fprintf(ficlog,".");fflush(ficlog);      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUGBRENT
     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);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      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)))) { */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
Line 724  void mnbrak(double *ax, double *bx, doub Line 1238  void mnbrak(double *ax, double *bx, doub
       }         } 
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
   while (*fb > *fc) {     while (*fb > *fc) { /* Declining fa, fb, fc */
     r=(*bx-*ax)*(*fb-*fc);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx);       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
     if ((*bx-u)*(u-*cx) > 0.0) {       if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
       fu=(*func)(u);         fu=(*func)(u); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {   #ifdef DEBUG
         /* f(x)=A(x-u)**2+f(u) */
         double A, fparabu; 
         A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
         printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   #endif 
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
           SHFT(*fb,*fc,fu,(*func)(u))             SHFT(*fb,*fc,fu,(*func)(u)) 
           }             } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else {       } else { 
Line 751  void mnbrak(double *ax, double *bx, doub Line 1273  void mnbrak(double *ax, double *bx, doub
 }   } 
   
 /*************** linmin ************************/  /*************** linmin ************************/
   /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   the value of func at the returned location p . This is actually all accomplished by calling the
   routines mnbrak and brent .*/
 int ncom;   int ncom; 
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
Line 777  void linmin(double p[], double xi[], int Line 1303  void linmin(double p[], double xi[], int
   }     } 
   ax=0.0;     ax=0.0; 
   xx=1.0;     xx=1.0; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
 #ifdef DEBUG  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
Line 791  void linmin(double p[], double xi[], int Line 1317  void linmin(double p[], double xi[], int
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
   
 char *asc_diff_time(long time_sec, char ascdiff[])  
 {  
   long sec_left, days, hours, minutes;  
   days = (time_sec) / (60*60*24);  
   sec_left = (time_sec) % (60*60*24);  
   hours = (sec_left) / (60*60) ;  
   sec_left = (sec_left) %(60*60);  
   minutes = (sec_left) /60;  
   sec_left = (sec_left) % (60);  
   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);    
   return ascdiff;  
 }  
   
 /*************** powell ************************/  /*************** powell ************************/
   /*
   Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
Line 822  void powell(double p[], double **xi, int Line 1344  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
       rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret);       fp=(*fret); 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     last_time=curr_time;      rlast_time=rcurr_time;
     (void) gettimeofday(&curr_time,&tzp);      /* (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);      rcurr_time = time(NULL);  
     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);      curr_time = *localtime(&rcurr_time);
     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     for (i=1;i<=n;i++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 840  void powell(double p[], double **xi, int Line 1365  void powell(double p[], double **xi, int
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){      if(*iter <=3){
       tm = *localtime(&curr_time.tv_sec);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tmf));        strcpy(strcurr,asctime(&tml));
 /*       asctime_r(&tm,strcurr); */        rforecast_time=rcurr_time; 
       forecast_time=curr_time;  
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       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,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         tmf = *localtime(&forecast_time.tv_sec);          forecast_time = *localtime(&rforecast_time);
 /*      asctime_r(&tmf,strfor); */          strcpy(strfor,asctime(&forecast_time));
         strcpy(strfor,asctime(&tmf));  
         itmp = strlen(strfor);          itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';          strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf \n",*fret);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficlog,"fret=%lf \n",*fret);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
       printf("%d",i);fflush(stdout);        printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
Line 884  void powell(double p[], double **xi, int Line 1407  void powell(double p[], double **xi, int
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p=%.12e",p[j]);          printf(" p(%d)=%.12e",j,p[j]);
         fprintf(ficlog," p=%.12e",p[j]);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     }       } /* end i */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
Line 923  void powell(double p[], double **xi, int Line 1446  void powell(double p[], double **xi, int
       return;         return; 
     }       } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) {       for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt);       fptt=(*func)(ptt); 
     if (fptt < fp) {       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       if (t < 0.0) {         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         linmin(p,xit,n,fret,func);         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
         /* Thus we compare delta(2h) with observed f1-f3 */
         /* or best gain on one ancient line 'del' with total  */
         /* gain f1-f2 = f1 - f2 - 'del' with del  */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         t= t- del*SQR(fp-fptt);
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
   #ifdef DEBUG
         printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   #endif
         if (t < 0.0) { /* Then we use it for last direction */
           linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n];             xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
           xi[j][n]=xit[j];             xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
         }          }
           printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 947  void powell(double p[], double **xi, int Line 1495  void powell(double p[], double **xi, int
         printf("\n");          printf("\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       }        } /* end of t negative */
     }       } /* end if (fptt < fp)  */
   }     } 
 }   } 
   
 /**** Prevalence limit (stable prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 {  {
Line 961  double **prevalim(double **prlim, int nl Line 1509  double **prevalim(double **prlim, int nl
   
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   double **matprod2();    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=50 ; /* Max number of years to converge */
   
Line 977  double **prevalim(double **prlim, int nl Line 1525  double **prevalim(double **prlim, int nl
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
      cov[2]=agefin;      cov[2]=agefin;
         
       for (k=1; k<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }      }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for (k=1; k<=cptcovprod;k++)      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*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=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
     maxmax=0.;      maxmax=0.;
Line 1002  double **prevalim(double **prlim, int nl Line 1552  double **prevalim(double **prlim, int nl
         sumnew=0;          sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         prlim[i][j]= newm[i][j]/(1-sumnew);          prlim[i][j]= newm[i][j]/(1-sumnew);
           /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
         max=FMAX(max,prlim[i][j]);          max=FMAX(max,prlim[i][j]);
         min=FMIN(min,prlim[i][j]);          min=FMIN(min,prlim[i][j]);
       }        }
Line 1018  double **prevalim(double **prlim, int nl Line 1569  double **prevalim(double **prlim, int nl
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   double s1, s2;    /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
        lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
     double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
   int i,j,j1, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
     for(j=1; j<i;j++){        for(j=1; j<i;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         /*s2 += param[i][j][nc]*cov[nc];*/            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }          }
       ps[i][j]=s2;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     }        }
     for(j=i+1; j<=nlstate+ndeath;j++){        for(j=i+1; j<=nlstate+ndeath;j++){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            /*lnpijopii += 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);*/            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       ps[i][j]=s2;          }
     }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   }        }
     /*ps[3][2]=1;*/  
   
   for(i=1; i<= nlstate; i++){  
      s1=0;  
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  
       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];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  
       ps[ii][ii]=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]); /* In fact sums pij/pii */
      printf("%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]); /* In fact sums pij/pii */
           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
         /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
         for(j=1; j<i; j++)
           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];
         /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
       
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
           ps[ii][ii]=1;
         }
     }      }
     printf("\n ");printf("%lf ",cov[2]);*/      
 /*      
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   goto end;*/      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       /*   } */
       /*   printf("\n "); */
       /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
     return ps;      return ps;
 }  }
   
 /**************** Product of 2 matrices ******************/  /**************** Product of 2 matrices ******************/
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
 {  {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   /* in, b, out are matrice of pointers which should have been initialized     /* in, b, out are matrice of pointers which should have been initialized 
      before: only the contents of out is modified. The function returns       before: only the contents of out is modified. The function returns
      a pointer to pointers identical to out */       a pointer to pointers identical to out */
   long i, j, k;    int i, j, k;
   for(i=nrl; i<= nrh; i++)    for(i=nrl; i<= nrh; i++)
     for(k=ncolol; k<=ncoloh; k++)      for(k=ncolol; k<=ncoloh; k++){
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        out[i][k]=0.;
         out[i][k] +=in[i][j]*b[j][k];        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
       }
   return out;    return out;
 }  }
   
Line 1113  double ***hpxij(double ***po, int nhstep Line 1684  double ***hpxij(double ***po, int nhstep
      */       */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
Line 1129  double ***hpxij(double ***po, int nhstep Line 1700  double ***hpxij(double ***po, int nhstep
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   
Line 1146  double ***hpxij(double ***po, int nhstep Line 1718  double ***hpxij(double ***po, int nhstep
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
         po[i][j][h]=newm[i][j];          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]);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
          */  
       }        }
       /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
   /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
   #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
     double *xt;
     int j;
     myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
    free_vector(xt,1,n);
     return fret;
   }
   #endif
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
Line 1171  double func( double *x) Line 1763  double func( double *x)
   /*for(i=1;i<imx;i++)     /*for(i=1;i<imx;i++) 
     printf(" %d\n",s[4][i]);      printf(" %d\n",s[4][i]);
   */    */
   
     ++countcallfunc;
   
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   if(mle==1){    if(mle==1){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
          */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
         }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            has been calculated etc */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1188  double func( double *x) Line 1793  double func( double *x)
           newm=savm;            newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1197  double func( double *x) Line 1802  double func( double *x)
         } /* end mult */          } /* end mult */
               
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */          /*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 and large stepm.          /* But now since version 0.9 we anticipate for bias at large stepm.
          * If stepm is larger than one month (smallest stepm) and if the exact delay            * 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            * (in months) between two waves is not a multiple of stepm, we rounded to 
          * the nearest (and in case of equal distance, to the lowest) interval but now           * 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           * we keep into memory the bias bh[mi][i] and also the previous matrix product
          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
          * probability in order to take into account the bias as a fraction of the way           * probability in order to take into account the bias as a fraction of the way
          * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
          * -stepm/2 to stepm/2 .           * -stepm/2 to stepm/2 .
          * For stepm=1 the results are the same as for previous versions of Imach.           * For stepm=1 the results are the same as for previous versions of Imach.
          * For stepm > 1 the results are less biased than in previous versions.            * For stepm > 1 the results are less biased than in previous versions. 
Line 1212  double func( double *x) Line 1817  double func( double *x)
         s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration          /* bias bh is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.           * is higher than the multiple of stepm and negative otherwise.
          */           */
         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/          /* lli= (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){           if( s2 > nlstate){ 
           /* i.e. if s2 is a death state and if the date of death is known then the contribution            /* i.e. if s2 is a death state and if the date of death is known 
              to the likelihood is the probability to die between last step unit time and current                then the contribution to the likelihood is the probability to 
              step unit time, which is also the differences between probability to die before dh                die between last step unit time and current  step unit time, 
              and probability to die before dh-stepm .                which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
              In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
         as if date of death was unknown. Death was treated as any other          as if date of death was unknown. Death was treated as any other
         health state: the date of the interview describes the actual state          health state: the date of the interview describes the actual state
Line 1240  double func( double *x) Line 1846  double func( double *x)
         lower mortality.          lower mortality.
           */            */
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
         }else{  
   
           } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
             lli= log(survp);
           }
           
           else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
   
           else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
           
           else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  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 */
         }           } 
Line 1390  double funcone( double *x) Line 2017  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
Line 1420  double funcone( double *x) Line 2047  double funcone( double *x)
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         savm=oldm;          savm=oldm;
         oldm=newm;          oldm=newm;
       } /* end mult */        } /* end mult */
Line 1434  double funcone( double *x) Line 2064  double funcone( double *x)
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);          lli=log(out[s1][s2] - savm[s1][s2]);
       } else if (mle==1){        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
         }else if (mle==1){
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       } else if(mle==2){        } else if(mle==2){
         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */          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 */
Line 1442  double funcone( double *x) Line 2076  double funcone( double *x)
         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 */          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       } else if (mle==4){  /* mle=4 no inter-extrapolation */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         lli=log(out[s1][s2]); /* Original formula */          lli=log(out[s1][s2]); /* Original formula */
       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */        } else{  /* mle=0 back to 1 */
         lli=log(out[s1][s2]); /* Original formula */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
       } /* End of if */        } /* End of if */
       ipmx +=1;        ipmx +=1;
       sw += weight[i];        sw += weight[i];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        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]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  %10.6f %10.6f %10.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
Line 1516  void mlikeli(FILE *ficres,double p[], in Line 2151  void mlikeli(FILE *ficres,double p[], in
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
   char filerespow[FILENAMELENGTH];    /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
Line 1533  void mlikeli(FILE *ficres,double p[], in Line 2180  void mlikeli(FILE *ficres,double p[], in
     for(j=1;j<=nlstate+ndeath;j++)      for(j=1;j<=nlstate+ndeath;j++)
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");    fprintf(ficrespow,"\n");
   #ifdef POWELL
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
     free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
Line 1548  void hesscov(double **matcov, double p[] Line 2223  void hesscov(double **matcov, double p[]
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    double **hess;
   int i, j,jk;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[]);    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 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 lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    hess=matrix(1,npar,1,npar);
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
Line 1563  void hesscov(double **matcov, double p[] Line 2238  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);     
     /*printf(" %f ",p[i]);*/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     /*printf(" %lf ",hess[i][i]);*/      
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
       
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
Line 1573  void hesscov(double **matcov, double p[] Line 2250  void hesscov(double **matcov, double p[]
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
       }        }
Line 1644  void hesscov(double **matcov, double p[] Line 2322  void hesscov(double **matcov, double p[]
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii( double x[], double delta, int theta, double delti[])  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2;
   double p2[NPARMAX+1];    double p2[MAXPARM+1]; /* identical to x */
   double res;    double res;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;    double fx;
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
   
   fx=func(x);    fx=func(x);
   for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=1;i<=npar;i++) p2[i]=x[i];
   for(l=0 ; l <=lmax; l++){    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     l1=pow(10,l);      l1=pow(10,l);
     delts=delt;      delts=delt;
     for(k=1 ; k <kmax; k=k+1){      for(k=1 ; k <kmax; k=k+1){
       delt = delta*(l1*k);        delt = delta*(l1*k);
       p2[theta]=x[theta] +delt;        p2[theta]=x[theta] +delt;
       k1=func(p2)-fx;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       p2[theta]=x[theta]-delt;        p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;        k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               
 #ifdef DEBUG  #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);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        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  #endif
Line 1679  double hessii( double x[], double delta, Line 2357  double hessii( double x[], double delta,
         k=kmax;          k=kmax;
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         k=kmax; l=lmax*10.;          k=kmax; l=lmax*10;
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
Line 1691  double hessii( double x[], double delta, Line 2369  double hessii( double x[], double delta,
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[NPARMAX+1];    double p2[MAXPARM+1];
   int k;    int k;
   
   fx=func(x);    fx=func(x);
Line 1800  void lubksb(double **a, int n, int *indx Line 2478  void lubksb(double **a, int n, int *indx
   }     } 
 }   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   
 /************ Frequencies ********************/  /************ 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)  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, j1, bool, z1,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
   double pos,posprop, k2, dateintsum=0,k2cpt=0;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
Line 1821  void  freqsummary(char fileres[], int ia Line 2503  void  freqsummary(char fileres[], int ia
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;    j1=0;
       
   j=cptcoveff;    j=cptcoveff;
Line 1829  void  freqsummary(char fileres[], int ia Line 2511  void  freqsummary(char fileres[], int ia
   
   first=1;    first=1;
   
   for(k1=1; k1<=j;k1++){    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     for(i1=1; i1<=ncodemax[k1];i1++){    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       j1++;    /*    j1++;
   */
     for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-1; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-5; jk<=nlstate+ndeath; jk++)  
           for(m=iagemin; m <= iagemax+3; m++)            for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;              freq[i][jk][m]=0;
         
     for (i=1; i<=nlstate; i++)          for (i=1; i<=nlstate; i++)  
       for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
         prop[i][m]=0;            prop[i][m]=0;
               
       dateintsum=0;        dateintsum=0;
       k2cpt=0;        k2cpt=0;
       for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) {
         bool=1;          bool=1;
         if  (cptcovn>0) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<=cptcoveff; z1++)             for (z1=1; z1<=cptcoveff; z1++)       
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
               bool=0;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
               } 
         }          }
    
         if (bool==1){          if (bool==1){
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
             k2=anint[m][i]+(mint[m][i]/12.);              k2=anint[m][i]+(mint[m][i]/12.);
Line 1871  void  freqsummary(char fileres[], int ia Line 2562  void  freqsummary(char fileres[], int ia
               /*}*/                /*}*/
           }            }
         }          }
       }        } /* end i */
                 
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],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]]);
         fprintf(ficresp, "**********\n#");          fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog, "**********\n#");
       }        }
       for(i=1; i<=nlstate;i++)         for(i=1; i<=nlstate;i++) 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
Line 1903  void  freqsummary(char fileres[], int ia Line 2597  void  freqsummary(char fileres[], int ia
             pos += freq[jk][m][i];              pos += freq[jk][m][i];
           if(pp[jk]>=1.e-10){            if(pp[jk]>=1.e-10){
             if(first==1){              if(first==1){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }              }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }else{            }else{
Line 1955  void  freqsummary(char fileres[], int ia Line 2649  void  freqsummary(char fileres[], int ia
           printf("Others in log...\n");            printf("Others in log...\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       }        }
     }        /*}*/
   }    }
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* End of Freq */    /* End of Freq */
Line 1974  void prevalence(double ***probs, double Line 2668  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, m, jk, j1, bool, z1,j;
   double ***freq; /* Frequencies */  
   double *pp, **prop;    double **prop;
   double pos,posprop;     double posprop; 
   double  y2; /* in fractional years */    double  y2; /* in fractional years */
   int iagemin, iagemax;    int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
   
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
Line 1988  void prevalence(double ***probs, double Line 2683  void prevalence(double ***probs, double
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
   j=cptcoveff;    /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   for(k1=1; k1<=j;k1++){    first=1;
     for(i1=1; i1<=ncodemax[k1];i1++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       j1++;      /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
               
       for (i=1; i<=nlstate; i++)          for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
Line 2023  void prevalence(double ***probs, double Line 2719  void prevalence(double ***probs, double
         }          }
       }        }
       for(i=iagemin; i <= iagemax+3; i++){          for(i=iagemin; i <= iagemax+3; i++){  
           
         for(jk=1,posprop=0; jk <=nlstate ; jk++) {           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           posprop += prop[jk][i];             posprop += prop[jk][i]; 
         }           } 
           
         for(jk=1; jk <=nlstate ; jk++){               for(jk=1; jk <=nlstate ; jk++){     
           if( i <=  iagemax){             if( i <=  iagemax){ 
             if(posprop>=1.e-5){               if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;                probs[i][jk][j1]= prop[jk][i]/posprop;
             }               } else{
                 if(first==1){
                   first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                 }
               }
           }             } 
         }/* end jk */           }/* end jk */ 
       }/* end i */         }/* end i */ 
     } /* end i1 */      /*} *//* end i1 */
   } /* end k1 */    } /* end j1 */
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
Line 2062  void  concatwav(int wav[], int **dh, int Line 2762  void  concatwav(int wav[], int **dh, int
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
   jmin=1e+5;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){      while(s[m][i] <= nlstate){
       if(s[m][i]>=1)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         mw[++mi][i]=m;          mw[++mi][i]=m;
       if(m >=lastpass)        if(m >=lastpass)
         break;          break;
Line 2087  void  concatwav(int wav[], int **dh, int Line 2787  void  concatwav(int wav[], int **dh, int
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
         printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;          first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
Line 2109  void  concatwav(int wav[], int **dh, int Line 2809  void  concatwav(int wav[], int **dh, int
               nberr++;                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]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               j=1; /* Temporary Dangerous patch */                j=1; /* Temporary Dangerous patch */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);                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,"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.\n  You MUST fix the contradiction between dates.\n",stepm);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }              }
             k=k+1;              k=k+1;
             if (j >= jmax) jmax=j;              if (j >= jmax){
             if (j <= jmin) jmin=j;                jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
             sum=sum+j;              sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/              /*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);*/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
Line 2123  void  concatwav(int wav[], int **dh, int Line 2829  void  concatwav(int wav[], int **dh, int
         }          }
         else{          else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) {
           else if (j <= jmin)jmin=j;              jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               jmin=j;
               ijmin=i;
             }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        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]);*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           if(j<0){            if(j<0){
Line 2144  void  concatwav(int wav[], int **dh, int Line 2857  void  concatwav(int wav[], int **dh, int
             dh[mi][i]=jk;              dh[mi][i]=jk;
             bh[mi][i]=0;              bh[mi][i]=0;
           }else{ /* We want a negative bias in order to only have interpolation ie            }else{ /* We want a negative bias in order to only have interpolation ie
                   * at the price of an extra matrix product in likelihood */                    * to avoid the price of an extra matrix product in likelihood */
             dh[mi][i]=jk+1;              dh[mi][i]=jk+1;
             bh[mi][i]=ju;              bh[mi][i]=ju;
           }            }
Line 2169  void  concatwav(int wav[], int **dh, int Line 2882  void  concatwav(int wav[], int **dh, int
     } /* end wave */      } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    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 Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }   }
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
 {  {
       /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   int Ndum[20],ij=1, k, j, i, maxncov=19;    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   int cptcode=0;    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     /* nbcode[Tvar[j]][1]= 
     */
   
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   
   
   cptcoveff=0;     cptcoveff=0; 
     
   for (k=0; k<maxncov; k++) Ndum[k]=0;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /* Loop on covariates without age and products */
     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum     for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
                                modality*/       for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/                                 modality of this covariate Vj*/ 
       Ndum[ij]++; /*store the modality */        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
           modmaxcovj=ij; 
         else if (ij < modmincovj) 
           modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable         /* getting the maximum value of the modality of the covariate
                                        Tvar[j]. If V=sex and male is 0 and            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                                        female is 1, then  cptcode=1.*/           female is 1, then modmaxcovj=1.*/
     }      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     for (i=0; i<=cptcode; i++) {      cptcode=modmaxcovj;
       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 */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     }     /*for (i=0; i<=cptcode; i++) {*/
       for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     ij=1;         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
     for (i=1; i<=ncodemax[j]; i++) {        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       for (k=0; k<= maxncov; k++) {          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         if (Ndum[k] != 0) {        }
           nbcode[Tvar[j]][ij]=k;         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           /* 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; */           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                 } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
       /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
          variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
       */
       ij=1; /* ij is similar to i but can jumps over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           ij++;            ij++;
         }          }
         if (ij > ncodemax[j]) break;           if (ij > ncodemax[j]) break; 
       }          }  /* end of loop on */
     }       } /* end of loop on modality */ 
   }      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     
  for (k=0; k< maxncov; k++) Ndum[k]=0;   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
  for (i=1; i<=ncovmodel-2; i++) {     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/     /* 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];     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
    Ndum[ij]++;     Ndum[ij]++; 
  }   } 
   
  ij=1;   ij=1;
  for (i=1; i<= maxncov; i++) {   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){     if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i; /*For printing */       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
      ij++;       ij++;
    }     }else
          Tvaraff[ij]=0;
  }   }
     ij--;
  cptcoveff=ij-1; /*Number of simple covariates*/   cptcoveff=ij; /*Number of total covariates*/
   
 }  }
   
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     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
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like 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
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* 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 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       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++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   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[] )
   
 {  {
   /* Health expectancies */    /* Covariances of health expectancies eij and of total life expectancies according
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;     to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat,***varhe;    double ***p3matp, ***p3matm, ***varhe;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double *xp;    double *xp, *xm;
   double **gp, **gm;    double **gp, **gm;
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   int theta;    int theta;
   
     double eip, vip;
   
   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   xp=vector(1,npar);    xp=vector(1,npar);
     xm=vector(1,npar);
   dnewm=matrix(1,nlstate*nlstate,1,npar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       
   fprintf(ficreseij,"# Health expectancies\n");    pstamp(ficresstdeij);
   fprintf(ficreseij,"# Age");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   for(i=1; i<=nlstate;i++)    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   fprintf(ficreseij,"\n");      fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
   if(estepm < stepm){    if(estepm < stepm){
     printf ("Problem %d lower than %d\n",estepm, stepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
Line 2288  void evsij(char fileres[], double ***eij Line 3184  void evsij(char fileres[], double ***eij
   */    */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
   agelim=AGESUP;    agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* nhstepm age range expressed in number of stepm */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);  
     gp=matrix(0,nhstepm,1,nlstate*nlstate);  
     gm=matrix(0,nhstepm,1,nlstate*nlstate);  
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
    
   
       /* If stepm=6 months */
       /* 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. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     /* Computing  Variances of health expectancies */      /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
      for(theta=1; theta <=npar; theta++){         decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       
       cptj=0;  
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
           cptj=cptj+1;            for(h=0; h<=nhstepm-1; h++){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           }            }
         }          }
       }        }
             
              for(ij=1; ij<= nlstate*nlstate; ij++)
       for(i=1; i<=npar; i++)   
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
         
       cptj=0;  
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;  
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
   
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  
         }  
       }  
       for(j=1; j<= nlstate*nlstate; j++)  
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         }          }
      }       }/* End theta */
          
 /* End theta */      
       for(h=0; h<=nhstepm-1; h++)
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);  
   
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
            
   
      for(i=1;i<=nlstate*nlstate;i++)       for(ij=1;ij<=nlstate*nlstate;ij++)
       for(j=1;j<=nlstate*nlstate;j++)        for(ji=1;ji<=nlstate*nlstate;ji++)
         varhe[i][j][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
   
      printf("%d|",(int)age);fflush(stdout);       printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
Line 2366  void evsij(char fileres[], double ***eij Line 3254  void evsij(char fileres[], double ***eij
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         for(i=1;i<=nlstate*nlstate;i++)          for(ij=1;ij<=nlstate*nlstate;ij++)
           for(j=1;j<=nlstate*nlstate;j++)            for(ji=1;ji<=nlstate*nlstate;ji++)
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
   
     /* Computing expectancies */      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                       
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
         }          }
   
     fprintf(ficreseij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     cptj=0;      for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           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));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         cptj++;          cptj= (j-1)*nlstate+i;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
       }        }
     fprintf(ficreseij,"\n");      fprintf(ficrescveij,"\n");
         
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);  
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
Line 2406  void evsij(char fileres[], double ***eij Line 3316  void evsij(char fileres[], double ***eij
 }  }
   
 /************ Variance ******************/  /************ Variance ******************/
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {  {
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
Line 2414  void varevsij(char optionfilefiname[], d Line 3324  void varevsij(char optionfilefiname[], d
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double **dnewmp,**doldmp;    double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k;
   double *xp;    double *xp;
   double **gp, **gm;  /* for var eij */    double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */    double ***gradg, ***trgradg; /*for var eij */
Line 2457  void varevsij(char optionfilefiname[], d Line 3367  void varevsij(char optionfilefiname[], d
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2467  void varevsij(char optionfilefiname[], d Line 3379  void varevsij(char optionfilefiname[], d
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */  /*   } */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fprintf(ficresvij,"# Age");    fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   fprintf(ficresvij,"\n");    fprintf(ficresvij,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
Line 2498  void varevsij(char optionfilefiname[], d Line 3415  void varevsij(char optionfilefiname[], d
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim        nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin.        nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size       Look at function hpijx to understand why (it is linked to memory size questions) */
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* 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       survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed every two years of age and if       means that if the survival funtion is printed every two years of age and if
Line 2565  void varevsij(char optionfilefiname[], d Line 3481  void varevsij(char optionfilefiname[], d
         }          }
       }        }
   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 2675  void varevsij(char optionfilefiname[], d Line 3591  void varevsij(char optionfilefiname[], d
   free_vector(gmp,nlstate+1,nlstate+ndeath);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);    /*  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);
Line 2704  void varevsij(char optionfilefiname[], d Line 3620  void varevsij(char optionfilefiname[], d
 }  /* end varevsij */  }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ 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)  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 */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;  
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   int k, cptcode;  
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
        
   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");    pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
Line 2787  void varprevlim(char fileres[], double * Line 3703  void varprevlim(char fileres[], double *
 }  }
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  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[])
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;    int k2, l2, j1,  z1;
   int k=0,l, cptcode;    int k=0, l;
   int first=1, first1;    int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double **mu;    double **mu;
   double age,agelim, cov[NCOVMAX];    double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];    char fileresprobcov[FILENAMELENGTH];
   char fileresprobcor[FILENAMELENGTH];    char fileresprobcor[FILENAMELENGTH];
   
   double ***varpij;    double ***varpij;
   
   strcpy(fileresprob,"prob");     strcpy(fileresprob,"prob"); 
Line 2832  void varprob(char optionfilefiname[], do Line 3747  void varprob(char optionfilefiname[], do
   fprintf(ficlog,"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);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcor,"# Age");
   
   
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
Line 2851  void varprob(char optionfilefiname[], do Line 3768  void varprob(char optionfilefiname[], do
   fprintf(ficresprobcov,"\n");    fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");    fprintf(ficresprobcor,"\n");
  */   */
  xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
Line 2876  standard deviations wide on each axis. < Line 3793  standard deviations wide on each axis. <
 To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   cov[1]=1;    cov[1]=1;
   tj=cptcoveff;    /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;    j1=0;
   for(t=1; t<=tj;t++){    for(j1=1; j1<=tj;j1++){
     for(i1=1; i1<=ncodemax[t];i1++){       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       j1++;      /*j1++;*/
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");           fprintf(ficresprob, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 2904  To be simple, these graphs help to under Line 3822  To be simple, these graphs help to under
         fprintf(ficresprobcor, "**********\n#");              fprintf(ficresprobcor, "**********\n#");    
       }        }
               
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
       for (age=bage; age<=fage; age ++){         for (age=bage; age<=fage; age ++){ 
         cov[2]=age;          cov[2]=age;
         for (k=1; k<=cptcovn;k++) {          for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)          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]]];            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));  
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
           for(i=1; i<=npar; i++)            for(i=1; i<=npar; i++)
Line 2954  To be simple, these graphs help to under Line 3877  To be simple, these graphs help to under
                   
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);           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);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);          pmij(pmmij,cov,ncovmodel,x,nlstate);
                   
Line 2991  To be simple, these graphs help to under Line 3910  To be simple, these graphs help to under
         i=0;          i=0;
         for (k=1; k<=(nlstate);k++){          for (k=1; k<=(nlstate);k++){
           for (l=1; l<=(nlstate+ndeath);l++){             for (l=1; l<=(nlstate+ndeath);l++){ 
             i=i++;              i++;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             for (j=1; j<=i;j++){              for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);                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(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             }              }
           }            }
         }/* end of loop for state */          }/* end of loop for state */
       } /* end of loop for age */        } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
       /* Confidence intervalle of pij  */        /* Confidence intervalle of pij  */
       /*        /*
         fprintf(ficgp,"\nset noparametric;unset label");          fprintf(ficgp,"\nunset parametric;unset label");
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
Line 3014  To be simple, these graphs help to under Line 3938  To be simple, these graphs help to under
       */        */
   
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       first1=1;        first1=1;first2=2;
       for (k2=1; k2<=(nlstate);k2++){        for (k2=1; k2<=(nlstate);k2++){
         for (l2=1; l2<=(nlstate+ndeath);l2++){           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           if(l2==k2) continue;            if(l2==k2) continue;
Line 3035  To be simple, these graphs help to under Line 3959  To be simple, these graphs help to under
                   /* Computing eigen value of matrix of covariance */                    /* Computing eigen value of matrix of covariance */
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                   /* Eigen vectors */                    /* Eigen vectors */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /*v21=sqrt(1.-v11*v11); *//* error */                    /*v21=sqrt(1.-v11*v11); *//* error */
Line 3054  To be simple, these graphs help to under Line 3988  To be simple, these graphs help to under
                     first=0;                      first=0;
                     fprintf(ficgp,"\nset parametric;unset label");                      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,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");                      fprintf(ficgp,"\nset ter png small size 320, 240");
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
Line 3085  To be simple, these graphs help to under Line 4019  To be simple, these graphs help to under
           } /* k12 */            } /* k12 */
         } /*l1 */          } /*l1 */
       }/* k1 */        }/* k1 */
     } /* loop covariates */        /* } /* loop covariates */
   }    }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     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);    free_vector(xp,1,npar);
   fclose(ficresprob);    fclose(ficresprob);
   fclose(ficresprobcov);    fclose(ficresprobcov);
Line 3107  void printinghtml(char fileres[], char t Line 4043  void printinghtml(char fileres[], char t
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Life expectancies by age and initial health status (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n",
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
  m=cptcoveff;   m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;   jj1=0;
Line 3137  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4079  fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
 <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
 <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Stable prevalence in each health state */         /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \           fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <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);  <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
Line 3158  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4100  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
   
  fprintf(fichtm,"\   fprintf(fichtm,"\
 \n<br><li><h4> Result files (second order: variances)</h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 3171  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4113  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",   - 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",
          subdirf2(fileres,"t"),subdirf2(fileres,"t"));           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
Line 3189  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4139  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  fflush(fichtm);   fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=cptcoveff;   m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;   jj1=0;
Line 3204  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4154  fprintf(fichtm," \n<ul><li><b>Graphs</b>
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\  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);    <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2): %s%d.png<br>\  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
Line 3220  health expectancies in states (1) and (2 Line 4173  health expectancies in states (1) and (2
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng;    int ng=0;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 3235  void printinggnuplot(char fileres[], cha Line 4188  void printinggnuplot(char fileres[], cha
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
    for (k1=1; k1<= m ; k1 ++) {      for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);       fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
      fprintf(ficgp,"set xlabel \"Age\" \n\       fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n\  set ylabel \"Probability\" \n\
 set ter png small\n\  set ter png small size 320, 240\n\
 set size 0.65,0.65\n\  
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else        fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }     }
   }    }
   /*2 eme*/    /*2 eme*/
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
           
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
Line 3282  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4235  plot [%.f:%.f] \"%s\" every :::%d::%d u
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficgp,"\" t\"\" w l lt 0,");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        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 ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
       else fprintf(ficgp,"\" t\"\" w l 0,");        else fprintf(ficgp,"\" t\"\" w l lt 0,");
     }      }
   }    }
       
Line 3297  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4250  plot [%.f:%.f] \"%s\" every :::%d::%d u
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);        /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
       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,"exp"),cpt,k1);
       fprintf(ficgp,"set ter png small\n\        fprintf(ficgp,"set ter png small size 320, 240\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:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+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*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
Line 3311  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4264  plot [%.f:%.f] \"%s\" every :::%d::%d u
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*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+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," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
   /* CV preval stable (period) */    /* CV preval stable (period) */
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) {      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;        k=3;
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter png small\nset size 0.65,0.65\n\  set ter png small size 320, 240\n\
 unset log y\n\  unset log y\n\
 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
               for (i=1; i<= nlstate ; i ++){
       for (i=1; i< nlstate ; i ++)          if(i==1)
         fprintf(ficgp,"+$%d",k+i+1);            fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          else
                   fprintf(ficgp,", '' ");
       l=3+(nlstate+ndeath)*cpt;          l=(nlstate+ndeath)*(i-1)+1;
       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
       for (i=1; i< nlstate ; i ++) {          for (j=1; j<= (nlstate-1) ; j ++)
         l=3+(nlstate+ndeath)*cpt;            fprintf(ficgp,"+$%d",k+l+j);
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       }        } /* nlstate */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);           fprintf(ficgp,"\n");
     }       } /* end cpt state*/ 
   }      } /* end covariate */  
       
   /* proba elementaires */    /* proba elementaires */
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
Line 3353  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4309  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
       }        }
     }      }
    }     }
     /*goto avoid;*/
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)         if (ng==2)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else         else
          fprintf(ficgp,"\nset title \"Probability\"\n");           fprintf(ficgp,"\nset title \"Probability\"\n");
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);         fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;         i=1;
        for(k2=1; k2<=nlstate; k2++) {         for(k2=1; k2<=nlstate; k2++) {
          k3=i;           k3=i;
Line 3371  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4327  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
              else               else
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
              ij=1;               ij=1;/* To be checked else nbcode[0][0] wrong */
              for(j=3; j <=ncovmodel; j++) {               for(j=3; j <=ncovmodel; j++) {
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                 /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                 /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  ij++;                 /*        ij++; */
                }                 /* } */
                else                 /* else */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
              }               }
              fprintf(ficgp,")/(1");               fprintf(ficgp,")/(1");
Line 3386  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4342  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                ij=1;                 ij=1;
                for(j=3; j <=ncovmodel; j++){                 for(j=3; j <=ncovmodel; j++){
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                   /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                   /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    ij++;                   /*   ij++; */
                  }                   /* } */
                  else                   /* else */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
Line 3403  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4359  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
        } /* end k2 */         } /* end k2 */
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
    /* avoid: */
    fflush(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
Line 3456  prevforecast(char fileres[], double anpr Line 4413  prevforecast(char fileres[], double anpr
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
   int *popage;  
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
Line 3751  void prwizard(int ncovmodel, int nlstate Line 4707  void prwizard(int ncovmodel, int nlstate
   
   /* Wizard to print covariance matrix template */    /* Wizard to print covariance matrix template */
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;    int i,j, k, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;    int numlinepar;
   
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 3867  void prwizard(int ncovmodel, int nlstate Line 4823  void prwizard(int ncovmodel, int nlstate
   } /* end itimes */    } /* end itimes */
   
 } /* end of prwizard */  } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* 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]);*/
   
 /***********************************************/    for (i=1;i<=imx ; i++)
 /**************** Main Program *****************/      {
 /***********************************************/        if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
 int main(int argc, char *argv[])        
 {        if (cens[i] == 0 && wav[i]>1)
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;               +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
   int jj, ll, li, lj, lk, imk;        
   int numlinepar=0; /* Current linenumber of parameter file */        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
   int itimes;        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]);*/
         }
       }
   
   char ca[32], cb[32], cc[32];   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
   /*  FILE *fichtm; *//* Html File */   
   /* FILE *ficgp;*/ /*Gnuplot File */    return -2*L*num/sump;
   double agedeb, agefin,hf;  }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   
   double fret;  #ifdef GSL
   double **xi,tmp,delta;  /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* 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]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
   double dum; /* Dummy variable */   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
   double ***p3mat;    printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
   double ***mobaverage;   
   int *indx;    return -2*LL*num/sump;
   char line[MAXLINE], linepar[MAXLINE];  }
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];  #endif
   char pathr[MAXLINE];   
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;   
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */  
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  
   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;  
   
   double bage, fage, age, agelim, agebase;  /******************* Printing html file ***********/
   double ftolpl=FTOL;  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
   double **prlim;                    int lastpass, int stepm, int weightopt, char model[],\
   double *severity;                    int imx,  double p[],double **matcov,double agemortsup){
   double ***param; /* Matrix of parameters */    int i,k;
   double  *p;  
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  
   double *delti; /* Scale */  
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;  
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       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\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
   char z[1]="c", occ;   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 stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];   for (k=agegomp;k<(agemortsup-2);k++) 
   char strstart[80], *strt, strtend[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 *stratrunc;  
   int lstra;  
   
   long total_usecs;  
     
 /*   setlocale (LC_ALL, ""); */    fflush(fichtm);
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */  }
 /*   textdomain (PACKAGE); */  
 /*   setlocale (LC_CTYPE, ""); */  
 /*   setlocale (LC_MESSAGES, ""); */  
   
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  /******************* Gnuplot file **************/
   (void) gettimeofday(&start_time,&tzp);  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   curr_time=start_time;  
   tm = *localtime(&start_time.tv_sec);  
   tmg = *gmtime(&start_time.tv_sec);  
   strcpy(strstart,asctime(&tm));  
   
 /*  printf("Localtime (at start)=%s",strstart); */    char dirfileres[132],optfileres[132];
 /*  tp.tv_sec = tp.tv_sec +86400; */  
 /*  tm = *localtime(&start_time.tv_sec); */  
 /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */  
 /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */  
 /*   tmg.tm_hour=tmg.tm_hour + 1; */  
 /*   tp.tv_sec = mktime(&tmg); */  
 /*   strt=asctime(&tmg); */  
 /*   printf("Time(after) =%s",strstart);  */  
 /*  (void) time (&time_value);  
 *  printf("time=%d,t-=%d\n",time_value,time_value-86400);  
 *  tm = *localtime(&time_value);  
 *  strstart=asctime(&tm);  
 *  printf("tim_value=%d,asctime=%s\n",time_value,strstart);   
 */  
   
   nberr=0; /* Number of errors and warnings */    int ng;
   nbwarn=0;  
   getcwd(pathcd, size);  
   
   printf("\n%s\n%s",version,fullversion);  
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);  
   }  
   else{  
     strcpy(pathtot,argv[1]);  
   }  
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);  
   strcpy(command,"mkdir ");  
   strcat(command,optionfilefiname);  
   if((outcmd=system(command)) != 0){  
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);  
     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */  
     /* fclose(ficlog); */  
 /*     exit(1); */  
   }  
 /*   if((imk=mkdir(optionfilefiname))<0){ */  
 /*     perror("mkdir"); */  
 /*   } */  
   
   /*-------- arguments in the command line --------*/  
   
   /* Log file */  
   strcat(filelog, optionfilefiname);  
   strcat(filelog,".log");    /* */  
   if((ficlog=fopen(filelog,"w"))==NULL)    {  
     printf("Problem with logfile %s\n",filelog);  
     goto end;  
   }  
   fprintf(ficlog,"Log filename:%s\n",filelog);  
   fprintf(ficlog,"\n%s\n%s",version,fullversion);  
   fprintf(ficlog,"\nEnter the parameter file name: ");  
   fprintf(ficlog,"pathtot=%s\n\  
  path=%s \n\  
  optionfile=%s\n\  
  optionfilext=%s\n\  
  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   
   printf("Local time (at start):%s",strstart);  
   fprintf(ficlog,"Local time (at start): %s",strstart);  
   fflush(ficlog);  
 /*   (void) gettimeofday(&curr_time,&tzp); */  
 /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */  
   
   /* */  
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */  
   
   /*---------arguments file --------*/  
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /*#ifdef windows */
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      /*#endif */
     fflush(ficlog);  
     goto end;  
   }  
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* 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);
   
   strcpy(filereso,"o");  } 
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */  
     printf("Problem with Output resultfile: %s\n", filereso);  
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);  
     fflush(ficlog);  
     goto end;  
   }  
   
   /* Reads comments: lines beginning with '#' */  int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   numlinepar=0;  {
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     numlinepar++;  
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }  
   ungetc(c,ficpar);  
   
   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);    /*-------- data file ----------*/
   numlinepar++;    FILE *fic;
   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);    char dummy[]="                         ";
   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);    int i=0, j=0, n=0;
   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);    int linei, month, year,iout;
   fflush(ficlog);    char line[MAXLINE], linetmp[MAXLINE];
   while((c=getc(ficpar))=='#' && c!= EOF){    char stra[MAXLINE], strb[MAXLINE];
     ungetc(c,ficpar);    char *stratrunc;
     fgets(line, MAXLINE, ficpar);    int lstra;
     numlinepar++;  
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }  
   ungetc(c,ficpar);  
   
      
   covar=matrix(0,NCOVMAX,1,n);   
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    if((fic=fopen(datafile,"r"))==NULL)    {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf("Problem while opening datafile: %s\n", datafile);return 1;
        fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);  
     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);  
     fclose (ficparo);  
     fclose (ficlog);  
     exit(0);  
   }  
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     numlinepar++;  
     puts(line);  
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }    }
   ungetc(c,ficpar);  
   
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    i=1;
   for(i=1; i <=nlstate; i++){    linei=0;
     j=0;    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
     for(jj=1; jj <=nlstate+ndeath; jj++){      linei=linei+1;
       if(jj==i) continue;      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
       j++;        if(line[j] == '\t')
       fscanf(ficpar,"%1d%1d",&i1,&j1);          line[j] = ' ';
       if ((i1 != i) && (j1 != j)){      }
         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);      for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         exit(1);        ;
       }      };
       fprintf(ficparo,"%1d%1d",i1,j1);      line[j+1]=0;  /* Trims blanks at end of line */
       if(mle==1)      if(line[0]=='#'){
         printf("%1d%1d",i,j);        fprintf(ficlog,"Comment line\n%s\n",line);
       fprintf(ficlog,"%1d%1d",i,j);        printf("Comment line\n%s\n",line);
       for(k=1; k<=ncovmodel;k++){        continue;
         fscanf(ficpar," %lf",&param[i][j][k]);      }
         if(mle==1){      trimbb(linetmp,line); /* Trims multiple blanks in line */
           printf(" %lf",param[i][j][k]);      strcpy(line, linetmp);
           fprintf(ficlog," %lf",param[i][j][k]);    
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
         }          }
         else  
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  
       }        }
       fscanf(ficpar,"\n");        s[j][i]=lval;
       numlinepar++;        
       if(mle==1)        strcpy(line,stra);
         printf("\n");        cutv(stra, strb,line,' ');
       fprintf(ficlog,"\n");        if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       fprintf(ficparo,"\n");        }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
     }      }
   }        else  if(iout=sscanf(strb,"%s.",dummy) != 0){
   fflush(ficlog);        month=99;
         year=9999;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/      }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
   p=param[1][1];          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
             return 1;
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){      andc[i]=(double) year; 
     ungetc(c,ficpar);      moisdc[i]=(double) month; 
     fgets(line, MAXLINE, ficpar);      strcpy(line,stra);
     numlinepar++;      
     puts(line);      cutv(stra, strb,line,' '); 
     fputs(line,ficparo);      if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
     fputs(line,ficlog);  
   }  
   ungetc(c,ficpar);  
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       if ((i1-i)*(j1-j)!=0){  
         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);  
         exit(1);  
       }  
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  
       fprintf(ficlog,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);  
         fprintf(ficlog," %le",delti3[i][j][k]);  
       }  
       fscanf(ficpar,"\n");  
       numlinepar++;  
       printf("\n");  
       fprintf(ficparo,"\n");  
       fprintf(ficlog,"\n");  
     }      }
   }      else  if(iout=sscanf(strb,"%s.", dummy) != 0){
   fflush(ficlog);        month=99;
         year=9999;
   delti=delti3[1][1];      }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */          return 1;
         }
   /* Reads comments: lines beginning with '#' */      if (year==9999) {
   while((c=getc(ficpar))=='#' && c!= EOF){        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
     ungetc(c,ficpar);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
     fgets(line, MAXLINE, ficpar);          return 1;
     numlinepar++;  
     puts(line);      }
     fputs(line,ficparo);      annais[i]=(double)(year);
     fputs(line,ficlog);      moisnais[i]=(double)(month); 
   }      strcpy(line,stra);
   ungetc(c,ficpar);      
         cutv(stra, strb,line,' '); 
   matcov=matrix(1,npar,1,npar);      errno=0;
   for(i=1; i <=npar; i++){      dval=strtod(strb,&endptr); 
     fscanf(ficpar,"%s",&str);      if( strb[0]=='\0' || (*endptr != '\0')){
     if(mle==1)        printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
       printf("%s",str);        fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
     fprintf(ficlog,"%s",str);        fflush(ficlog);
     fprintf(ficparo,"%s",str);        return 1;
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);  
       if(mle==1){  
         printf(" %.5le",matcov[i][j]);  
       }  
       fprintf(ficlog," %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }      }
     fscanf(ficpar,"\n");      weight[i]=dval; 
     numlinepar++;      strcpy(line,stra);
     if(mle==1)  
       printf("\n");  
     fprintf(ficlog,"\n");  
     fprintf(ficparo,"\n");  
   }  
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];  
      
   if(mle==1)  
     printf("\n");  
   fprintf(ficlog,"\n");  
   
   fflush(ficlog);  
   
   /*-------- Rewriting paramater file ----------*/  
   strcpy(rfileres,"r");    /* "Rparameterfile */  
   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
   strcat(rfileres,".");    /* */  
   strcat(rfileres,optionfilext);    /* Other files have txt extension */  
   if((ficres =fopen(rfileres,"w"))==NULL) {  
     printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  
   }  
   fprintf(ficres,"#%s\n",version);  
           
   /*-------- data file ----------*/      for (j=ncovcol;j>=1;j--){
   if((fic=fopen(datafile,"r"))==NULL)    {        cutv(stra, strb,line,' '); 
     printf("Problem with datafile: %s\n", datafile);goto end;        if(strb[0]=='.') { /* Missing status */
     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;          lval=-1;
   }        }else{
           errno=0;
   n= lastobs;          lval=strtol(strb,&endptr,10); 
   severity = vector(1,maxwav);          if( strb[0]=='\0' || (*endptr != '\0')){
   outcome=imatrix(1,maxwav+1,1,n);            printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
   num=lvector(1,n);            fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
   moisnais=vector(1,n);            return 1;
   annais=vector(1,n);          }
   moisdc=vector(1,n);        }
   andc=vector(1,n);        if(lval <-1 || lval >1){
   agedc=vector(1,n);          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   cod=ivector(1,n);   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   weight=vector(1,n);   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   For example, for multinomial values like 1, 2 and 3,\n \
   mint=matrix(1,maxwav,1,n);   build V1=0 V2=0 for the reference value (1),\n \
   anint=matrix(1,maxwav,1,n);          V1=1 V2=0 for (2) \n \
   s=imatrix(1,maxwav+1,1,n);   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
   tab=ivector(1,NCOVMAX);   output of IMaCh is often meaningless.\n \
   ncodemax=ivector(1,8);   Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   i=1;   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   while (fgets(line, MAXLINE, fic) != NULL)    {   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
     if ((i >= firstobs) && (i <=lastobs)) {   For example, for multinomial values like 1, 2 and 3,\n \
            build V1=0 V2=0 for the reference value (1),\n \
       for (j=maxwav;j>=1;j--){          V1=1 V2=0 for (2) \n \
         cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
         strcpy(line,stra);   output of IMaCh is often meaningless.\n \
         cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
         cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          return 1;
       }        }
                 covar[j][i]=(double)(lval);
       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    *imax=i-1; /* Number of individuals */
       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
       for (j=ncovcol;j>=1;j--){  
         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
       }   
       lstra=strlen(stra);  
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */  
         stratrunc = &(stra[lstra-9]);  
         num[i]=atol(stratrunc);  
       }  
       else  
         num[i]=atol(stra);  
           
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
   
       i=i+1;  
     }  
   }  
   /* printf("ii=%d", ij);  
      scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */  
   
   /* for (i=1; i<=imx; i++){  }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  void removespace(char *str) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    char *p1 = str, *p2 = str;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    do
     }*/      while (*p2 == ' ')
    /*  for (i=1; i<=imx; i++){        p2++;
      if (s[4][i]==9)  s[4][i]=-1;     while (*p1++ = *p2++);
      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]));}*/  }
     
  for (i=1; i<=imx; i++)  
    
    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;  
      else weight[i]=1;*/  
   
   /* Calculation of the number of parameter from char model*/  int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */     * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
   Tprod=ivector(1,15);      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
   Tvaraff=ivector(1,15);      * - cptcovn or number of covariates k of the models excluding age*products =6
   Tvard=imatrix(1,15,1,2);     * - cptcovage number of covariates with age*products =2
   Tage=ivector(1,15);           * - cptcovs number of simple covariates
         * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=1, k2=1;      j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
     j=nbocc(model,'+'); /* j=Number of '+' */      j=nbocc(model,'+'); /**< j=Number of '+' */
     j1=nbocc(model,'*'); /* j1=Number of '*' */      j1=nbocc(model,'*'); /**< j1=Number of '*' */
     cptcovn=j+1;       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
     cptcovprod=j1; /*Number of products */      cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                         /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if (strstr(model,"AGE") !=0){
       printf("Error. Non available option model=%s ",model);        printf("Error. AGE must be in lower case 'age' model=%s ",model);
       fprintf(ficlog,"Error. Non available option model=%s ",model);        fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
       goto end;        return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
     }      }
           
     /* This loop fills the array Tvar from the string 'model'.*/      /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
     for(i=(j+1); i>=1;i--){      /* This loop fills the array Tvar from the string 'model'.*/
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/        /*scanf("%d",i);*/
       if (strchr(strb,'*')) {  /* Model includes a product */        if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/          cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
         if (strcmp(strc,"age")==0) { /* Vn*age */          if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
           cptcovprod--;            cptcovprod--;
           cutv(strb,stre,strd,'V');            cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/            Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
           cptcovage++;            cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=i;            Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/            /*printf("stre=%s ", stre);*/
         }          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  
           cptcovprod--;            cptcovprod--;
           cutv(strb,stre,strc,'V');            cutl(stre,strb,strc,'V');
           Tvar[i]=atoi(stre);            Tvar[k]=atoi(stre);
           cptcovage++;            cptcovage++;
           Tage[cptcovage]=i;            Tage[cptcovage]=k;
         }          } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
         else {  /* Age is not in the model */            /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/            cptcovn++;
           Tvar[i]=ncovcol+k1;            cptcovprodnoage++;k1++;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */            cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
           Tprod[k1]=i;            Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
           Tvard[k1][1]=atoi(strc); /* m*/                                    because this model-covariate is a construction we invent a new column
           Tvard[k1][2]=atoi(stre); /* n */                                    ncovcol + k1
           Tvar[cptcovn+k2]=Tvard[k1][1];                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
           for (k=1; k<=lastobs;k++)             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
           k1++;            Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
           k2=k2+2;            k2=k2+2;
         }            Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
       }            Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
       else { /* no more sum */        else { /* no more sum */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
        /*  scanf("%d",i);*/         /*  scanf("%d",i);*/
       cutv(strd,strc,strb,'V');          cutl(strd,strc,strb,'V');
       Tvar[i]=atoi(strc);          ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
       }        }
       strcpy(modelsav,stra);          strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
         scanf("%d",i);*/          scanf("%d",i);*/
     } /* end of loop + */      } /* end of loop + */
Line 4394  int main(int argc, char *argv[]) Line 5300  int main(int argc, char *argv[])
   printf("cptcovprod=%d ", cptcovprod);    printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
   scanf("%d ",i);    scanf("%d ",i);*/
   fclose(fic);*/  
   
     /*  if(mle==1){*/  
   if (weightopt != 1) { /* Maximisation without weights*/    return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     for(i=1;i<=n;i++) weight[i]=1.0;    /*endread:*/
   }      printf("Exiting decodemodel: ");
     /*-calculation of age at interview from date of interview and age at death -*/      return (1);
   agev=matrix(1,maxwav,1,imx);  }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
   for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
     for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
Line 4411  int main(int argc, char *argv[]) Line 5320  int main(int argc, char *argv[])
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         nberr++;          *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);          printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         nberr++;          *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]);           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
Line 4428  int main(int argc, char *argv[]) Line 5337  int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0){        if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0)            if(agedc[i]>0)
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
Line 4444  int main(int argc, char *argv[]) Line 5353  int main(int argc, char *argv[])
             }              }
         }          }
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a                                   years but with the precision of a month */
                                  month */  
           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            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)            if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
             agev[m][i]=1;              agev[m][i]=1;
           else if(agev[m][i] <agemin){             else if(agev[m][i] < *agemin){ 
             agemin=agev[m][i];              *agemin=agev[m][i];
             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
           }            }
           else if(agev[m][i] >agemax){            else if(agev[m][i] >*agemax){
             agemax=agev[m][i];              *agemax=agev[m][i];
             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
Line 4473  int main(int argc, char *argv[]) Line 5381  int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
         nberr++;          *nberr++;
         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               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);               fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         goto end;          return 1;
       }        }
     }      }
   }    }
Line 4489  int main(int argc, char *argv[]) Line 5397  int main(int argc, char *argv[])
 }*/  }*/
   
   
   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
   free_vector(severity,1,maxwav);    return (0);
   free_imatrix(outcome,1,maxwav+1,1,n);   /* endread:*/
   free_vector(moisnais,1,n);      printf("Exiting calandcheckages: ");
   free_vector(annais,1,n);      return (1);
   /* free_matrix(mint,1,maxwav,1,n);  }
      free_matrix(anint,1,maxwav,1,n);*/  
   free_vector(moisdc,1,n);  
   free_vector(andc,1,n);  /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* 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 */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
         
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     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
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     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);
       fflush(stdout);
       fclose (ficlog);
       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 */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       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);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           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);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
   wav=ivector(1,imx);    wav=ivector(1,imx);
   dh=imatrix(1,lastpass-firstpass+1,1,imx);    dh=imatrix(1,lastpass-firstpass+1,1,imx);
   bh=imatrix(1,lastpass-firstpass+1,1,imx);    bh=imatrix(1,lastpass-firstpass+1,1,imx);
Line 4509  int main(int argc, char *argv[]) Line 5924  int main(int argc, char *argv[])
         
   /* Concatenates waves */    /* Concatenates waves */
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
   Tcode=ivector(1,100);  
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   if (cptcovn > 0) tricode(Tvar,nbcode,imx);    Ndum =ivector(-1,NCOVMAX);  
           if (ncovmodel > 2)
   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
                                  the estimations*/  
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
   h=0;    h=0;
   
   
     /*if (cptcovn > 0) */
         
    
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){    for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
     for(i=1; i <=(m/pow(2,k));i++){      for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
       for(j=1; j <= ncodemax[k]; j++){        for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
           h++;            h++;
           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            if (h>m) 
           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             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]]);
         }           } 
       }        }
     }      }
Line 4537  int main(int argc, char *argv[]) Line 5982  int main(int argc, char *argv[])
      codtab[1][2]=1;codtab[2][2]=2; */       codtab[1][2]=1;codtab[2][2]=2; */
   /* for(i=1; i <=m ;i++){     /* for(i=1; i <=m ;i++){ 
      for(k=1; k <=cptcovn; k++){       for(k=1; k <=cptcovn; k++){
      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);         printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
      }       }
      printf("\n");       printf("\n");
      }       }
      scanf("%d",i);*/       scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
           
   /*------------ gnuplot -------------*/    /*------------ gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
   else{    else{
     fprintf(ficgp,"\n# %s\n", version);       fprintf(ficgp,"\n# %s\n", version); 
     fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
     fprintf(ficgp,"set missing 'NaNq'\n");      //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
   }    }
   /*  fclose(ficgp);*/    /*  fclose(ficgp);*/
   /*--------- index.htm --------*/    /*--------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);      printf("Problem with %s \n",optionfilehtm);
       exit(0);
   }    }
   
   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */    strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
Line 4569  int main(int argc, char *argv[]) Line 6025  int main(int argc, char *argv[])
     printf("Problem with %s \n",optionfilehtmcov), exit(0);      printf("Problem with %s \n",optionfilehtmcov), exit(0);
   }    }
   else{    else{
   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \    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\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \    fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\   - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <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",\   - Date and time at start: %s</ul>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\            optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
           fileres,fileres,\            fileres,fileres,\
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
   fflush(fichtm);    fflush(fichtm);
Line 4596  Title=%s <br>Datafile=%s Firstpass=%d La Line 6054  Title=%s <br>Datafile=%s Firstpass=%d La
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 4615  Interval (in months) between two waves: Line 6073  Interval (in months) between two waves:
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */  
   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);    if (mle==-3){
   for (k=1; k<=npar;k++)      ximort=matrix(1,NDIM,1,NDIM); 
     printf(" %d %8.5f",k,p[k]);  /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
   printf("\n");      cens=ivector(1,n);
   globpr=1; /* to print the contributions */      ageexmed=vector(1,n);
   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      agecens=vector(1,n);
   printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      dcwave=ivector(1,n);
   for (k=1; k<=npar;k++)   
     printf(" %d %8.5f",k,p[k]);      for (i=1; i<=imx; i++){
   printf("\n");        dcwave[i]=-1;
   if(mle>=1){ /* Could be 1 or 2 */        for (m=firstpass; m<=lastpass; m++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          if (s[m][i]>nlstate) {
   }            dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
           
   /*--------- results files --------------*/      hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   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(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(i=1; i <=NDIM; i++)
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for(j=i+1;j<=NDIM;j++)
   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          matcov[i][j]=matcov[j][i];
   for(i=1,jk=1; i <=nlstate; i++){      
     for(k=1; k <=(nlstate+ndeath); k++){      printf("\nCovariance matrix\n ");
       if (k != i) {      for(i=1; i <=NDIM; i++) {
         printf("%d%d ",i,k);        for(j=1;j<=NDIM;j++){ 
         fprintf(ficlog,"%d%d ",i,k);          printf("%f ",matcov[i][j]);
         fprintf(ficres,"%1d%1d ",i,k);  
         for(j=1; j <=ncovmodel; j++){  
           printf("%f ",p[jk]);  
           fprintf(ficlog,"%f ",p[jk]);  
           fprintf(ficres,"%f ",p[jk]);  
           jk++;   
         }  
         printf("\n");  
         fprintf(ficlog,"\n");  
         fprintf(ficres,"\n");  
       }        }
         printf("\n ");
     }      }
   }      
   if(mle!=0){      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
     /* Computing hessian and covariance matrix */      for (i=1;i<=NDIM;i++) 
     ftolhess=ftol; /* Usually correct */        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     hesscov(matcov, p, npar, delti, ftolhess, func);  
   }      lsurv=vector(1,AGESUP);
   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      lpop=vector(1,AGESUP);
   printf("# Scales (for hessian or gradient estimation)\n");      tpop=vector(1,AGESUP);
   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      lsurv[agegomp]=100000;
   for(i=1,jk=1; i <=nlstate; i++){      
     for(j=1; j <=nlstate+ndeath; j++){      for (k=agegomp;k<=AGESUP;k++) {
       if (j!=i) {        agemortsup=k;
         fprintf(ficres,"%1d%1d",i,j);        if (p[1]*exp(p[2]*(k-agegomp))>1) break;
         printf("%1d%1d",i,j);      }
         fprintf(ficlog,"%1d%1d",i,j);      
         for(k=1; k<=ncovmodel;k++){      for (k=agegomp;k<agemortsup;k++)
           printf(" %.5e",delti[jk]);        lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
           fprintf(ficlog," %.5e",delti[jk]);      
           fprintf(ficres," %.5e",delti[jk]);      for (k=agegomp;k<agemortsup;k++){
           jk++;        lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
         }          }
         printf("\n");  
         fprintf(ficlog,"\n");  
         fprintf(ficres,"\n");  
       }        }
     }      }
   }      if(mle!=0){
            /* Computing hessian and covariance matrix */
   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");        ftolhess=ftol; /* Usually correct */
   if(mle>=1)        hesscov(matcov, p, npar, delti, ftolhess, func);
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      }
   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
 /* # 121 Var(a12)\n\ */      printf("# Scales (for hessian or gradient estimation)\n");
 /* # 122 Cov(b12,a12) Var(b12)\n\ */      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
 /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */      for(i=1,jk=1; i <=nlstate; i++){
 /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */  
 /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */  
 /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */  
 /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */  
 /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */  
   
   
 /* Just to have a covariance matrix which will be more understandable  
    even is we still don't want to manage dictionary of variables  
 */  
   for(itimes=1;itimes<=2;itimes++){  
     jj=0;  
     for(i=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;          if (j!=i) {
         for(k=1; k<=ncovmodel;k++){            fprintf(ficres,"%1d%1d",i,j);
           jj++;            printf("%1d%1d",i,j);
           ca[0]= k+'a'-1;ca[1]='\0';            fprintf(ficlog,"%1d%1d",i,j);
           if(itimes==1){            for(k=1; k<=ncovmodel;k++){
             if(mle>=1)              printf(" %.5e",delti[jk]);
               printf("#%1d%1d%d",i,j,k);              fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficlog,"#%1d%1d%d",i,j,k);              fprintf(ficres," %.5e",delti[jk]);
             fprintf(ficres,"#%1d%1d%d",i,j,k);              jk++;
           }else{  
             if(mle>=1)  
               printf("%1d%1d%d",i,j,k);  
             fprintf(ficlog,"%1d%1d%d",i,j,k);  
             fprintf(ficres,"%1d%1d%d",i,j,k);  
           }            }
           ll=0;            printf("\n");
           for(li=1;li <=nlstate; li++){            fprintf(ficlog,"\n");
             for(lj=1;lj <=nlstate+ndeath; lj++){            fprintf(ficres,"\n");
               if(lj==li) continue;          }
               for(lk=1;lk<=ncovmodel;lk++){        }
                 ll++;      }
                 if(ll<=jj){      
                   cb[0]= lk +'a'-1;cb[1]='\0';      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(ll<jj){      if(mle>=1)
                     if(itimes==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");
                       if(mle>=1)      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(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 121 Var(a12)\n\ */
                       fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 122 Cov(b12,a12) Var(b12)\n\ */
                       fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);      /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                     }else{      /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                       if(mle>=1)      /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                         printf(" %.5e",matcov[jj][ll]);       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                       fprintf(ficlog," %.5e",matcov[jj][ll]);       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                       fprintf(ficres," %.5e",matcov[jj][ll]);       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                     }      
                   }else{      
                     if(itimes==1){      /* Just to have a covariance matrix which will be more understandable
                       if(mle>=1)         even is we still don't want to manage dictionary of variables
                         printf(" Var(%s%1d%1d)",ca,i,j);      */
                       fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);      for(itimes=1;itimes<=2;itimes++){
                       fprintf(ficres," Var(%s%1d%1d)",ca,i,j);        jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                     }else{                      }else{
                       if(mle>=1)                        if(itimes==1){
                         printf(" %.5e",matcov[jj][ll]);                           if(mle>=1)
                       fprintf(ficlog," %.5e",matcov[jj][ll]);                             printf(" Var(%s%1d%1d)",ca,i,j);
                       fprintf(ficres," %.5e",matcov[jj][ll]);                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                     }                      }
                   }                    }
                 }                  } /* end lk */
               } /* end lk */                } /* end lj */
             } /* end lj */              } /* end li */
           } /* end li */              if(mle>=1)
           if(mle>=1)                printf("\n");
             printf("\n");              fprintf(ficlog,"\n");
           fprintf(ficlog,"\n");              fprintf(ficres,"\n");
           fprintf(ficres,"\n");              numlinepar++;
           numlinepar++;            } /* end k*/
         } /* end k*/          } /*end j */
       } /*end j */        } /* end i */
     } /* end i */      } /* end itimes */
   } /* end itimes */      
       fflush(ficlog);
   fflush(ficlog);      fflush(ficres);
   fflush(ficres);      
       while((c=getc(ficpar))=='#' && c!= EOF){
   while((c=getc(ficpar))=='#' && c!= EOF){        ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      estepm=0;
     fputs(line,ficparo);      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;
   ungetc(c,ficpar);      if (fage <= 2) {
         bage = ageminpar;
   estepm=0;        fage = agemaxpar;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      }
   if (estepm==0 || estepm < stepm) estepm=stepm;      
   if (fage <= 2) {      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     bage = ageminpar;      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fage = agemaxpar;      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   }      
          while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        ungetc(c,ficpar);
   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        fgets(line, MAXLINE, ficpar);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        fputs(line,stdout);
            fputs(line,ficparo);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      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);
     fputs(line,ficparo);      fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   }      fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   ungetc(c,ficpar);      printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);      
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      while((c=getc(ficpar))=='#' && c!= EOF){
   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);        ungetc(c,ficpar);
   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        fgets(line, MAXLINE, ficpar);
   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);        fputs(line,stdout);
            fputs(line,ficparo);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      
     fputs(line,ficparo);      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
   }      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   ungetc(c,ficpar);      
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
     
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;  #ifdef FREEEXIT2
   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;  #include "freeexit2.h"
   #endif
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);      /*------------- h Pij x at various ages ------------*/
   fprintf(ficparo,"pop_based=%d\n",popbased);     #include "hpijx.h"
   fprintf(ficres,"pop_based=%d\n",popbased);         fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
       
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  
   
   fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);  
   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
   printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
   fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
   fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
   /* day and month of proj2 are not used but only year anproj2.*/  
   
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  
   
   /*  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      /*  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(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);*/          ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/  
   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/  
   
   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */  
   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);  
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\  
                model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\  
                jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
    
   /*------------ free_vector  -------------*/  
   /*  chdir(path); */  
    
   free_ivector(wav,1,imx);  
   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);  
   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     
   free_lvector(num,1,n);  
   free_vector(agedc,1,n);  
   /*free_matrix(covar,0,NCOVMAX,1,n);*/  
   /*free_matrix(covar,1,NCOVMAX,1,n);*/  
   fclose(ficparo);  
   fclose(ficres);  
   
   
   /*--------------- Prevalence limit  (stable prevalence) --------------*/  
     
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;  
     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;  
   }  
   printf("Computing stable prevalence: result on file '%s' \n", filerespl);  
   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Stable prevalence \n");  
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  
     
   prlim=matrix(1,nlstate,1,nlstate);  
   
   agebase=ageminpar;  
   agelim=agemaxpar;  
   ftolpl=1.e-10;  
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}  
   
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){      if (mobilav!=0) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=k+1;        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficrespl,"\n#******");          printf(" Error in movingaverage mobilav=%d\n",mobilav);
       printf("\n#******");  
       fprintf(ficlog,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }  
       fprintf(ficrespl,"******\n");  
       printf("******\n");  
       fprintf(ficlog,"******\n");  
           
       for (age=agebase; age<=agelim; age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         fprintf(ficrespl,"%.0f ",age );  
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  
         fprintf(ficrespl,"\n");  
       }        }
     }      }
   }  
   fclose(ficrespl);  
   
   /*------------- h Pij x at various ages ------------*/  
     
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);  
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);  
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/  
   
   agelim=AGESUP;      /*---------- Health expectancies, no variances ------------*/
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   
   
   /* hstepm=1;   aff par mois*/  
   
   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");  
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  
       fprintf(ficrespij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)   
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrespij,"******\n");  
           
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
   
         /*        nhstepm=nhstepm*YEARM; aff par mois*/      strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");        
         for(i=1; i<=nlstate;i++)          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           for(j=1; j<=nlstate+ndeath;j++)        /*}*/
             fprintf(ficrespij," %1d-%1d",i,j);  
         fprintf(ficrespij,"\n");  
         for (h=0; h<=nhstepm; h++){  
           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
           fprintf(ficrespij,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespij,"\n");  
       }  
     }      }
   }      fclose(ficreseij);
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);  
   
   fclose(ficrespij);      /*---------- Health expectancies and variances ------------*/
   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   for(i=1;i<=AGESUP;i++)  
     for(j=1;j<=NCOVMAX;j++)  
       for(k=1;k<=NCOVMAX;k++)  
         probs[i][j][k]=0.;  
   
   /*---------- Forecasting ------------------*/      strcpy(filerest,"t");
   /*if((stepm == 1) && (strcmp(model,".")==0)){*/      strcat(filerest,fileres);
   if(prevfcast==1){      if((ficrest=fopen(filerest,"w"))==NULL) {
     /*    if(stepm ==1){*/        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/      }
 /*      }  */      printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
 /*      else{ */      fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
 /*        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); */  
 /*      } */  
   }  
     
   
   /*---------- Health expectancies and variances ------------*/  
   
   strcpy(filerest,"t");      strcpy(fileresstde,"stde");
   strcat(filerest,fileres);      strcat(fileresstde,fileres);
   if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
   }      }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);       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(filerese,"e");      strcpy(fileresv,"v");
   strcat(filerese,fileres);      strcat(fileresv,fileres);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
   }      }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
   strcpy(fileresv,"v");      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
   strcat(fileresv,fileres);        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for (k=1; k <= (int) pow(2,cptcoveff); k++){
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);          fprintf(ficrest,"\n#****** ");
   }          for(j=1;j<=cptcoveff;j++) 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          fprintf(ficrest,"******\n");
   
   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */          fprintf(ficresstdeij,"\n#****** ");
   prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);          fprintf(ficrescveij,"\n#****** ");
   /*  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",\          for(j=1;j<=cptcoveff;j++) {
 ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);            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");
   
   if (mobilav!=0) {          fprintf(ficresvij,"\n#****** ");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(j=1;j<=cptcoveff;j++) 
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){            fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);          fprintf(ficresvij,"******\n");
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          oldm=oldms;savm=savms;
       k=k+1;           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
       fprintf(ficrest,"\n#****** ");          /*
       for(j=1;j<=cptcoveff;j++)            */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          /* goto endfree; */
       fprintf(ficrest,"******\n");  
   
       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");  
   
       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;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
     
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;          pstamp(ficrest);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);  
       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);  
       }  
   
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            oldm=oldms;savm=savms; /* Segmentation fault */
       fprintf(ficrest,"\n");            cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
       epj=vector(1,nlstate+1);            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 ");
       for(age=bage; age <=fage ;age++){            if(vpopbased==1)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              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);
         if (popbased==1) {            else
           if(mobilav ==0){              fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             for(i=1; i<=nlstate;i++)            fprintf(ficrest,"# Age e.. (std) ");
               prlim[i][i]=probs[(int)age][i][k];            for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           }else{ /* mobilav */             fprintf(ficrest,"\n");
             for(i=1; i<=nlstate;i++)  
               prlim[i][i]=mobaverage[(int)age][i][k];            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);              fprintf(ficrest," %4.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                for(i=1, epj[j]=0.;i <=nlstate;i++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                  epj[j] += prlim[i][i]*eij[i][j][(int)age];
             /*  printf("%lf %lf ", 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");
           }            }
           epj[nlstate+1] +=epj[j];  
         }          }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         for(i=1, vepp=0.;i <=nlstate;i++)          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           for(j=1;j <=nlstate;j++)          free_vector(epj,1,nlstate+1);
             vepp += vareij[i][j][(int)age];        /*}*/
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      }
         for(j=1;j <=nlstate;j++){      free_vector(weight,1,n);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      free_imatrix(Tvard,1,NCOVMAX,1,2);
         }      free_imatrix(s,1,maxwav+1,1,n);
         fprintf(ficrest,"\n");      free_matrix(anint,1,maxwav,1,n); 
       }      free_matrix(mint,1,maxwav,1,n);
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      free_ivector(cod,1,n);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      free_ivector(tab,1,NCOVMAX);
       free_vector(epj,1,nlstate+1);      fclose(ficresstdeij);
     }      fclose(ficrescveij);
   }      fclose(ficresvij);
   free_vector(weight,1,n);      fclose(ficrest);
   free_imatrix(Tvard,1,15,1,2);      fclose(ficpar);
   free_imatrix(s,1,maxwav+1,1,n);    
   free_matrix(anint,1,maxwav,1,n);       /*------- Variance of period (stable) prevalence------*/   
   free_matrix(mint,1,maxwav,1,n);  
   free_ivector(cod,1,n);      strcpy(fileresvpl,"vpl");
   free_ivector(tab,1,NCOVMAX);      strcat(fileresvpl,fileres);
   fclose(ficreseij);      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
   fclose(ficresvij);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
   fclose(ficrest);        exit(0);
   fclose(ficpar);      }
         printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   /*------- Variance of stable prevalence------*/     
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
   strcpy(fileresvpl,"vpl");        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
   strcat(fileresvpl,fileres);            
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      for (k=1; k <= (int) pow(2,cptcoveff); k++){
     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);          fprintf(ficresvpl,"\n#****** ");
     exit(0);          for(j=1;j<=cptcoveff;j++) 
   }            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);          fprintf(ficresvpl,"******\n");
   
   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);          varpl=matrix(1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          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);          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     }        /*}*/
   }      }
   
   fclose(ficresvpl);      fclose(ficresvpl);
   
   /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    }  /* mle==-3 arrives here for freeing */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   /* endfree:*/
         free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
   free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(matcov,1,npar,1,npar);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   /*free_vector(delti,1,npar);*/      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(agev,1,maxwav,1,imx);      free_matrix(covar,0,NCOVMAX,1,n);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_matrix(matcov,1,npar,1,npar);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*free_vector(delti,1,npar);*/
   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
   free_ivector(ncodemax,1,8);      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   free_ivector(Tvar,1,15);  
   free_ivector(Tprod,1,15);      free_ivector(ncodemax,1,NCOVMAX);
   free_ivector(Tvaraff,1,15);      free_ivector(Tvar,1,NCOVMAX);
   free_ivector(Tage,1,15);      free_ivector(Tprod,1,NCOVMAX);
   free_ivector(Tcode,1,100);      free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
Line 5190  ageminpar, agemax, s[lastpass][imx], age Line 6820  ageminpar, agemax, s[lastpass][imx], age
   }    }
   printf("See log file on %s\n",filelog);    printf("See log file on %s\n",filelog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
   (void) gettimeofday(&end_time,&tzp);    /*(void) gettimeofday(&end_time,&tzp);*/
   tm = *localtime(&end_time.tv_sec);    rend_time = time(NULL);  
   tmg = *gmtime(&end_time.tv_sec);    end_time = *localtime(&rend_time);
   strcpy(strtend,asctime(&tm));    /* tml = *localtime(&end_time.tm_sec); */
   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend);     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     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 used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   /*  printf("Total time was %d uSec.\n", total_usecs);*/    /*  printf("Total time was %d uSec.\n", total_usecs);*/
 /*   if(fileappend(fichtm,optionfilehtm)){ */  /*   if(fileappend(fichtm,optionfilehtm)){ */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
   fclose(fichtm);    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(fichtmcov);
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
   
   chdir(path);  
   strcpy(plotcmd,GNUPLOTPROGRAM);     printf("Before Current directory %s!\n",pathcd);
   strcat(plotcmd," ");     if(chdir(pathcd) != 0)
   strcat(plotcmd,optionfilegnuplot);      printf("Can't move to directory %s!\n",path);
   printf("Starting graphs with: %s",plotcmd);fflush(stdout);    if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf(" Problem with gnuplot\n");      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
   }    }
   printf(" Wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {
     /* chdir(path); */      /* chdir(path); */
     printf("\nType e to edit output files, g to graph again and q for exiting: ");      printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
     scanf("%s",z);      scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */  /*     if (z[0] == 'c') system("./imach"); */
     if (z[0] == 'e') system(optionfilehtm);      if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
Line 5234  ageminpar, agemax, s[lastpass][imx], age Line 6905  ageminpar, agemax, s[lastpass][imx], age
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }
   
   
   

Removed from v.1.97  
changed lines
  Added in v.1.164


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