Diff for /imach/src/imach.c between versions 1.128 and 1.186

version 1.128, 2006/06/30 13:02:05 version 1.186, 2015/04/23 12:01:52
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
     Revision 1.183  2015/03/10 20:34:32  brouard
     Summary: 0.98q0, trying with directest, mnbrak fixed
   
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
     Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
     Author: Nicolas Brouard
   
     Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
     Author:
   
     Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
     Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   
     Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
     Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
   
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
     Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
   
     Testing on Linux 64
   
     Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
   
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     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    Revision 1.128  2006/06/30 13:02:05  brouard
   (Module): Clarifications on computing e.j    (Module): Clarifications on computing e.j
   
Line 157 Line 397
   
   The same imach parameter file can be used but the option for mle should be -3.    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    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.    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 output is very simple: only an estimate of the intercept and of
Line 290 Line 530
   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 period (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 317 Line 557
       begin-prev-date,...        begin-prev-date,...
   open gnuplot file    open gnuplot file
   open html file    open html file
   period (stable) prevalence    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
    for age prevalim()     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   h Pij x                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   variance of p varprob      freexexit2 possible for memory heap.
   
     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 333 Line 585
  end   end
 */  */
   
   #define POWELL /* Instead of NLOPT */
   /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
   /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
   
    
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   
   #ifdef _WIN32
   #include <io.h>
   #include <windows.h>
   #include <tchar.h>
   #else
 #include <unistd.h>  #include <unistd.h>
   #endif
   
 #include <limits.h>  #include <limits.h>
 #include <sys/types.h>  #include <sys/types.h>
   
   #if defined(__GNUC__)
   #include <sys/utsname.h> /* Doesn't work on Windows */
   #endif
   
 #include <sys/stat.h>  #include <sys/stat.h>
 #include <errno.h>  #include <errno.h>
 extern int errno;  /* extern int errno; */
   
   /* #ifdef LINUX */
   /* #include <time.h> */
   /* #include "timeval.h" */
   /* #else */
 /* #include <sys/time.h> */  /* #include <sys/time.h> */
   /* #endif */
   
 #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"*/
Line 364  extern int errno; Line 647  extern int errno;
 #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
 #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef UNIX  #ifdef _WIN32
 #define DIRSEPARATOR '/'  
 #define CHARSEPARATOR "/"  
 #define ODIRSEPARATOR '\\'  
 #else  
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #define CHARSEPARATOR "\\"  #define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'  #define ODIRSEPARATOR '/'
   #else
   #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";  char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;  int nvar=0, nforce=0; /* Number of variables, number of forces */
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  /* 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 ijmin, ijmax; /* Individuals having jmin and jmax */   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 int gipmx, gsw; /* Global variables on the number of contributions   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, *ficresp, *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 filerespow[FILENAMELENGTH];
 char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
Line 454  char popfile[FILENAMELENGTH]; Line 748  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;  char *endptr;
Line 489  static double maxarg1,maxarg2; Line 788  static double maxarg1,maxarg2;
       
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)  #define rint(a) floor(a+0.5)
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   #define mytinydouble 1.0e-16
   /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
 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;} 
Line 512  double dateintmean=0; Line 816  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 *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 )
Line 526  static int split( char *path, char *dirc Line 837  static int split( char *path, char *dirc
      the name of the file (name), its extension only (ext) and its first part of the name (finame)       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=0, l2=0;                             /* 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 );
Line 537  static int split( char *path, char *dirc Line 848  static int split( char *path, char *dirc
       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 */
     /*    extern  char* getcwd ( char *buf , int len);*/      /*    extern  char* getcwd ( char *buf , int len);*/
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   #else
           if (getcwd(dirc, FILENAME_MAX) == NULL) {
   #endif
       return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
     }      }
     /* got dirc from getcwd*/      /* got dirc from getcwd*/
Line 548  static int split( char *path, char *dirc Line 863  static int split( char *path, char *dirc
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     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);      printf(" DIRC2 = %s \n",dirc);
   }    }
   /* We add a separator at the end of dirc if not exists */    /* We add a separator at the end of dirc if not exists */
Line 586  void replace_back_to_slash(char *s, char Line 901  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 598  int nbocc(char *s, char occ) Line 984  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 ends before first occurence of char 'occ'   /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
      and v starts after first occurence of char 'occ' : 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++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   /* } */
   
    for(j=0; j<= lg; j++) {  #ifdef _WIN32
     if (j>=(p+1))(v[j-p-1] = t[j]);  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 727  double **matrix(long nrl, long nrh, long Line 1131  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 817  char *subdirf3(char fileres[], char *pre Line 1223  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 840  double brent(double ax, double bx, doubl Line 1259  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 855  double brent(double ax, double bx, doubl Line 1274  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 890  double brent(double ax, double bx, doubl Line 1309  double brent(double ax, double bx, doubl
     if (fu <= fx) {       if (fu <= fx) { 
       if (u >= x) a=x; else b=x;         if (u >= x) a=x; else b=x; 
       SHFT(v,w,x,u)         SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu)         SHFT(fv,fw,fx,fu) 
         } else {       } else { 
           if (u < x) a=u; else b=u;         if (u < x) a=u; else b=u; 
           if (fu <= fw || w == x) {         if (fu <= fw || w == x) { 
             v=w;           v=w; 
             w=u;           w=u; 
             fv=fw;           fv=fw; 
             fw=fu;           fw=fu; 
           } else if (fu <= fv || v == x || v == w) {         } else if (fu <= fv || v == x || v == w) { 
             v=u;           v=u; 
             fv=fu;           fv=fu; 
           }         } 
         }       } 
   }     } 
   nrerror("Too many iterations in brent");     nrerror("Too many iterations in brent"); 
   *xmin=x;     *xmin=x; 
Line 913  double brent(double ax, double bx, doubl Line 1332  double brent(double ax, double bx, doubl
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             double (*func)(double))               double (*func)(double)) 
 {   { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   the downhill direction (defined by the function as evaluated at the initial points) and returns
   new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
   values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
      */
   double ulim,u,r,q, dum;    double ulim,u,r,q, dum;
   double fu;     double fu; 
     
Line 921  void mnbrak(double *ax, double *bx, doub Line 1344  void mnbrak(double *ax, double *bx, doub
   *fb=(*func)(*bx);     *fb=(*func)(*bx); 
   if (*fb > *fa) {     if (*fb > *fa) { 
     SHFT(dum,*ax,*bx,dum)       SHFT(dum,*ax,*bx,dum) 
       SHFT(dum,*fb,*fa,dum)       SHFT(dum,*fb,*fa,dum) 
       }     } 
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
   while (*fb > *fc) {   #ifdef DEBUG
     printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
     fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
   #endif
     while (*fb > *fc) { /* Declining a,b,c with 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 abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx);       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
     if ((*bx-u)*(u-*cx) > 0.0) {       if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is 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);
         /* And thus,it can be that fu > *fc even if fparabu < *fc */
         /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
         /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
   #endif 
   #ifdef MNBRAKORIGINAL
   #else
         if (fu > *fc) {
   #ifdef DEBUG
         printf("mnbrak4  fu > fc \n");
         fprintf(ficlog, "mnbrak4 fu > fc\n");
   #endif
           /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
           /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
           dum=u; /* Shifting c and u */
           u = *cx;
           *cx = dum;
           dum = fu;
           fu = *fc;
           *fc =dum;
         } else { /* end */
   #ifdef DEBUG
         printf("mnbrak3  fu < fc \n");
         fprintf(ficlog, "mnbrak3 fu < fc\n");
   #endif
           dum=u; /* Shifting c and u */
           u = *cx;
           *cx = dum;
           dum = fu;
           fu = *fc;
           *fc =dum;
         }
   #endif
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
   #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim AND fu < fc\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   #endif
         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) */
   #ifdef DEBUG
         printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
         fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else {       } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
         printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   #endif
       u=(*cx)+GOLD*(*cx-*bx);         u=(*cx)+GOLD*(*cx-*bx); 
       fu=(*func)(u);         fu=(*func)(u); 
     }       } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
       SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
       }   #ifdef DEBUG
         printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
         fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
   #endif
     } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
   
 /*************** 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 978  void linmin(double p[], double xi[], int Line 1469  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 992  void linmin(double p[], double xi[], int Line 1483  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 1013  void powell(double p[], double **xi, int Line 1500  void powell(double p[], double **xi, int
               double (*func)(double []));                 double (*func)(double [])); 
   int i,ibig,j;     int i,ibig,j; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
     double directest;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
Line 1023  void powell(double p[], double **xi, int Line 1511  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); fflush(ficlog);      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);
       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++) {     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]);
Line 1041  void powell(double p[], double **xi, int Line 1532  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(&tm));        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')  /* Windows outputs with a new line */        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 i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          printf("   - 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 i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(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);
       linmin(p,xit,n,fret,func);         linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
       if (fabs(fptt-(*fret)) > del) {         if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
                                          because that direction will be replaced unless the gain del is small
                                         in comparison with the 'probable' gain, mu^2, with the last average direction.
                                         Unless the n directions are conjugate some gain in the determinant may be obtained
                                         with the new direction.
                                         */
         del=fabs(fptt-(*fret));           del=fabs(fptt-(*fret)); 
         ibig=i;           ibig=i; 
       }         } 
Line 1085  void powell(double p[], double **xi, int Line 1579  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))) { /* Did we reach enough precision? */
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
       k[0]=1;        k[0]=1;
Line 1124  void powell(double p[], double **xi, int Line 1618  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 the extrapolated point P_0 + 2 (P_n-P_0) */
       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); /* f_3 */
     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 */
         /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   #ifdef NRCORIGINAL
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
         t= t- del*SQR(fp-fptt);
   #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   #ifdef DEBUG
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
         fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
         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
   #ifdef POWELLORIGINAL
         if (t < 0.0) { /* Then we use it for new direction */
   #else
         if (directest*t < 0.0) { /* Contradiction between both tests */
         printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       } 
         if (directest < 0.0) { /* Then we use it for new direction */
   #endif
           linmin(p,xit,n,fret,func); /* computes minimum 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 direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];             xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
         }          }
           printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\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 1148  void powell(double p[], double **xi, int Line 1678  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)  */
   }     } 
 }   } 
   
Line 1159  double **prevalim(double **prlim, int nl Line 1689  double **prevalim(double **prlim, int nl
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached */
     
   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 */
     
   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++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     
    cov[1]=1.;    cov[1]=1.;
      
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   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];      /*wrong? 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<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for (k=1; k<=cptcovprod;k++) /* Useless */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       /*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 cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* 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 1203  double **prevalim(double **prlim, int nl Line 1736  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]);
       }        }
       maxmin=max-min;        maxmin=max-min;
       maxmax=FMAX(maxmax,maxmin);        maxmax=FMAX(maxmax,maxmin);
     }      } /* j loop */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       return prlim;        return prlim;
     }      }
   }    } /* age loop */
     return prlim; /* should not reach here */
 }  }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
 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++){      for(i=1; i<= nlstate; i++){
       s1=0;        s1=0;
       for(j=1; j<i; j++)        for(j=1; j<i; j++){
         s1+=exp(ps[i][j]);          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for(j=i+1; j<=nlstate+ndeath; j++)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         s1+=exp(ps[i][j]);        }
         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.);        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
       for(j=1; j<i; j++)        for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)        for(j=i+1; j<=nlstate+ndeath; j++)
Line 1264  double **pmij(double **ps, double *cov, Line 1818  double **pmij(double **ps, double *cov,
       }        }
     }      }
           
       
 /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
 /*         printf("ddd %lf ",ps[ii][jj]); */      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 /*       } */      /*   } */
 /*       printf("\n "); */      /*   printf("\n "); */
 /*        } */      /* } */
 /*        printf("\n ");printf("%lf ",cov[2]); */      /* printf("\n ");printf("%lf ",cov[2]);*/
        /*      /*
       for(i=1; i<= npar; i++) printf("%f ",x[i]);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       goto end;*/        goto end;*/
     return ps;      return ps;
Line 1280  double **pmij(double **ps, double *cov, Line 1834  double **pmij(double **ps, double *cov,
   
 /**************** 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 1314  double ***hpxij(double ***po, int nhstep Line 1869  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 1330  double ***hpxij(double ***po, int nhstep Line 1885  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++) 
       for (k=1; k<=cptcovage;k++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
       for (k=1; k<=cptcovprod;k++)          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
         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 1355  double ***hpxij(double ***po, int nhstep Line 1912  double ***hpxij(double ***po, int nhstep
   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 1373  double func( double *x) Line 1949  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 1390  double func( double *x) Line 1979  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 1442  double func( double *x) Line 2031  double func( double *x)
         which slows down the processing. The difference can be up to 10%          which slows down the processing. The difference can be up to 10%
         lower mortality.          lower mortality.
           */            */
           lli=log(out[s1][s2] - savm[s1][s2]);          /* If, at the beginning of the maximization mostly, the
              cumulative probability or probability to be dead is
              constant (ie = 1) over time d, the difference is equal to
              0.  out[s1][3] = savm[s1][3]: probability, being at state
              s1 at precedent wave, to be dead a month before current
              wave is equal to probability, being at state s1 at
              precedent wave, to be dead at mont of the current
              wave. Then the observed probability (that this person died)
              is null according to current estimated parameter. In fact,
              it should be very low but not zero otherwise the log go to
              infinity.
           */
   /* #ifdef INFINITYORIGINAL */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
   /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   /*          lli=log(mytinydouble); */
   /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #endif */
               lli=log(out[s1][s2] - savm[s1][s2]);
   
         } else if  (s2==-2) {          } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
Line 1474  double func( double *x) Line 2082  double func( double *x)
         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;
           /* if (lli < log(mytinydouble)){ */
           /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
           /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
           /* } */
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   }  else if(mle==2){    }  else if(mle==2){
Line 1614  double funcone( double *x) Line 2226  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 1644  double funcone( double *x) Line 2256  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 1670  double funcone( double *x) Line 2285  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 %2d %2d %1d %1d %3d %11.6f %8.4f\          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  %11.6f %11.6f %11.6f ", \   %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]);
Line 1740  void likelione(FILE *ficres,double p[], Line 2356  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter;    int i,j, iter=0;
   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 1761  void mlikeli(FILE *ficres,double p[], in Line 2389  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);    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("#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,"#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,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
Line 1777  void hesscov(double **matcov, double p[] Line 2432  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 (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
Line 1881  double hessii(double x[], double delta, Line 2536  double hessii(double x[], double delta,
   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=0.0001, 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;
Line 1890  double hessii(double x[], double delta, Line 2545  double hessii(double x[], double delta,
   
   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 1911  double hessii(double x[], double delta, Line 2566  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 1926  double hessii(double x[], double delta, Line 2581  double hessii(double x[], double delta,
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  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 2041  void pstamp(FILE *fichier) Line 2696  void pstamp(FILE *fichier)
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  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;
Line 2065  void  freqsummary(char fileres[], int ia Line 2720  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=-5; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-5; 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 2107  void  freqsummary(char fileres[], int ia Line 2770  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);        pstamp(ficresp);
Line 2115  void  freqsummary(char fileres[], int ia Line 2778  void  freqsummary(char fileres[], int ia
         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 2139  void  freqsummary(char fileres[], int ia Line 2805  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 2191  void  freqsummary(char fileres[], int ia Line 2857  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; 
     
Line 2210  void prevalence(double ***probs, double Line 2876  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 2224  void prevalence(double ***probs, double Line 2891  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 2259  void prevalence(double ***probs, double Line 2927  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              } else{
               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);                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 2299  void  concatwav(int wav[], int **dh, int Line 2970  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++){
Line 2394  void  concatwav(int wav[], int **dh, int Line 3065  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 2420  void  concatwav(int wav[], int **dh, int Line 3091  void  concatwav(int wav[], int **dh, int
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);    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++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
                                modality*/       for (i=1; i<=imx; i++) { /* Loop 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, 5, 6, 7. 
          If Ndum[1]=0, Ndum[2]=0, 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 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
          defining two dummy variables: 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 k 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 statement 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(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
Line 2807  void varevsij(char optionfilefiname[], d Line 3529  void varevsij(char optionfilefiname[], d
   /* 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);*/
   /* double **newm;*/    /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
   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 3077  void varevsij(char optionfilefiname[], d Line 3802  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 3110  void varprevlim(char fileres[], double * Line 3835  void varprevlim(char fileres[], double *
 {  {
   /* 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;
Line 3192  void varprevlim(char fileres[], double * Line 3916  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, char strstart[])  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 3256  void varprob(char optionfilefiname[], do Line 3979  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 3281  standard deviations wide on each axis. < Line 4004  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 3309  To be simple, these graphs help to under Line 4033  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<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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 3359  To be simple, these graphs help to under Line 4089  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 3396  To be simple, these graphs help to under Line 4122  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 3419  To be simple, these graphs help to under Line 4150  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 3440  To be simple, these graphs help to under Line 4171  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 3459  To be simple, these graphs help to under Line 4200  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 3490  To be simple, these graphs help to under Line 4231  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);
Line 3536  void printinghtml(char fileres[], char t Line 4277  void printinghtml(char fileres[], char t
   
 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 3550  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4291  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: <a href=\"%s%d1.png\">%s%d1.png</a><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,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: <a href=\"%s%d2.png\">%s%d2.png</a><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,subdirf2(optionfilefiname,"pe"),jj1);   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Period (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>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \           fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
 <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);  <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, 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>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \          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,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 3610  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4351  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 3625  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4366  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). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
Line 3644  true period expectancies (those weighted Line 4385  true period expectancies (those weighted
 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 3659  void printinggnuplot(char fileres[], cha Line 4400  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\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" 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;
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%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== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       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)");
       }           }   
       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 3724  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4465  plot [%.f:%.f] \"%s\" every :::%d::%d u
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        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 3745  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4485  plot [%.f:%.f] \"%s\" every :::%d::%d u
   }    }
       
   /* 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 3780  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4521  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 3798  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4539  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]]);
Line 3830  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 Line 4571  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 3877  int movingaverage(double ***probs, doubl Line 4619  int movingaverage(double ***probs, doubl
   
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      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 4001  prevforecast(char fileres[], double anpr Line 4742  prevforecast(char fileres[], double anpr
 }  }
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
Line 4178  void prwizard(int ncovmodel, int nlstate Line 4919  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 4331  double gompertz(double x[]) Line 5072  double gompertz(double x[])
   return -2*L*num/sump;    return -2*L*num/sump;
 }  }
   
   #ifdef GSL
   /******************* 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]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
Line 4359  fprintf(fichtm,"<ul><li><h4>Life table</ Line 5141  fprintf(fichtm,"<ul><li><h4>Life table</
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(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 ng;    int ng;
   
   
Line 4372  void printinggnuplotmort(char fileres[], Line 5154  void printinggnuplotmort(char fileres[],
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   fprintf(ficgp,"set out \"graphmort.png\"\n ");     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
   fprintf(ficgp, "set ter png small\n set log y\n");     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, "set size 0.65,0.65\n"); */
   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
 }   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   
   
   
 /***********************************************/  
 /**************** Main Program *****************/  
 /***********************************************/  
   
 int main(int argc, char *argv[])  
 {  {
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);  
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;  
   int linei, month, year,iout;  
   int jj, ll, li, lj, lk, imk;  
   int numlinepar=0; /* Current linenumber of parameter file */  
   int itimes;  
   int NDIM=2;  
   int vpopbased=0;  
   
   char ca[32], cb[32], cc[32];    /*-------- data file ----------*/
     FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   /*  FILE *fichtm; *//* Html File */    int i=0, j=0, n=0;
   /* FILE *ficgp;*/ /*Gnuplot File */    int linei, month, year,iout;
   struct stat info;    char line[MAXLINE], linetmp[MAXLINE];
   double agedeb, agefin,hf;    char stra[MAXLINE], strb[MAXLINE];
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   
   double fret;  
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */  
   double ***p3mat;  
   double ***mobaverage;  
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];  
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];  
   char pathr[MAXLINE], pathimach[MAXLINE];   
   char **bp, *tok, *val; /* pathtot */  
   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;  
   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, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  
   double **prlim;  
   double *severity;  
   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 kk1, kk2;  
   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];  
   int *dcwave;  
   
   char z[1]="c", occ;  
   
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   char  *strt, strtend[80];  
   char *stratrunc;    char *stratrunc;
   int lstra;    int lstra;
   
   long total_usecs;  
    
 /*   setlocale (LC_ALL, ""); */  
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */  
 /*   textdomain (PACKAGE); */  
 /*   setlocale (LC_CTYPE, ""); */  
 /*   setlocale (LC_MESSAGES, ""); */  
   
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   (void) gettimeofday(&start_time,&tzp);  
   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); */    if((fic=fopen(datafile,"r"))==NULL)    {
 /*  tp.tv_sec = tp.tv_sec +86400; */      printf("Problem while opening datafile: %s\n", datafile);return 1;
 /*  tm = *localtime(&start_time.tv_sec); */      fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
 /*   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 */    i=1;
   nbwarn=0;    linei=0;
   getcwd(pathcd, size);    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
   printf("\n%s\n%s",version,fullversion);      for (j=maxwav;j>=1;j--){
   if(argc <=1){        cutv(stra, strb, line, ' '); 
     printf("\nEnter the parameter file name: ");        if(strb[0]=='.') { /* Missing status */
     fgets(pathr,FILENAMELENGTH,stdin);          lval=-1;
     i=strlen(pathr);        }else{
     if(pathr[i-1]=='\n')          errno=0;
       pathr[i-1]='\0';          lval=strtol(strb,&endptr,10); 
    for (tok = pathr; tok != NULL; ){        /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
       printf("Pathr |%s|\n",pathr);          if( strb[0]=='\0' || (*endptr != '\0')){
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\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);
       printf("val= |%s| pathr=%s\n",val,pathr);            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);
       strcpy (pathtot, val);            return 1;
       if(pathr[0] == '\0') break; /* Dirty */          }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         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){
   else{        month=99;
     strcpy(pathtot,argv[1]);        year=9999;
   }      }else{
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/        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);
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          return 1;
   /* cutv(path,optionfile,pathtot,'\\');*/      }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       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 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);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
   /* Split argv[0], imach program to get pathimach */      }
   printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);      annais[i]=(double)(year);
   split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);      moisnais[i]=(double)(month); 
   printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);      strcpy(line,stra);
  /*   strcpy(pathimach,argv[0]); */      
   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */      cutv(stra, strb,line,' '); 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      errno=0;
   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("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,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             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);
             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);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         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 */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - 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 */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       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); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         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;
       }
       
       /*   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 []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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 */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*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) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             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 */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           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);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             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");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** 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 fret;
     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;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     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);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
   chdir(path); /* Can be a relative path */    chdir(path); /* Can be a relative path */
   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */    if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
     printf("Current directory %s!\n",pathcd);  #endif
     printf("Current directory %s!\n",pathcd);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);      printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
     /* fclose(ficlog); */      /* fclose(ficlog); */
 /*     exit(1); */  /*     exit(1); */
Line 4538  int main(int argc, char *argv[]) Line 6124  int main(int argc, char *argv[])
   
   /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Main Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
   strcat(filelog,".log");    /* */    strcat(filelog,".log");    /* */
   if((ficlog=fopen(filelog,"w"))==NULL)    {    if((ficlog=fopen(filelog,"w"))==NULL)    {
Line 4552  int main(int argc, char *argv[]) Line 6138  int main(int argc, char *argv[])
  path=%s \n\   path=%s \n\
  optionfile=%s\n\   optionfile=%s\n\
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
   fflush(ficlog);    fflush(ficlog);
 /*   (void) gettimeofday(&curr_time,&tzp); */  /*   (void) gettimeofday(&curr_time,&tzp); */
 /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */  /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /* Main ---------arguments file --------*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fflush(ficlog);      fflush(ficlog);
     goto end;      /* goto end; */
       exit(70); 
   }    }
   
   
Line 4591  int main(int argc, char *argv[]) Line 6180  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     numlinepar++;      numlinepar++;
     puts(line);      fputs(line,stdout);
     fputs(line,ficparo);      fputs(line,ficparo);
     fputs(line,ficlog);      fputs(line,ficlog);
   }    }
Line 4599  int main(int argc, char *argv[]) Line 6188  int main(int argc, char *argv[])
   
   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);    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++;    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);    /* 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); */
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
     /*
   
   
   
      */
     printf("\nftol=%e \n", ftol);
     printf("stepm=%d \n", stepm);
     printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);
     printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);
     printf("model=%s\n",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(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);    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);    fflush(ficlog);
Line 4607  int main(int argc, char *argv[]) Line 6207  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     numlinepar++;      numlinepar++;
     puts(line);      fputs(line, stdout);
       //puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
     fputs(line,ficlog);      fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
         
   covar=matrix(0,NCOVMAX,1,n);     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    */
     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 */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/    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);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   delti=delti3[1][1];    delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
Line 4635  int main(int argc, char *argv[]) Line 6247  int main(int argc, char *argv[])
     goto end;      goto end;
     exit(0);      exit(0);
   }    }
   else if(mle==-3) {    else if(mle==-3) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      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);      fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 4643  int main(int argc, char *argv[]) Line 6255  int main(int argc, char *argv[])
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   }    }
   else{    else{
     /* Read guess parameters */      /* Read guessed parameters */
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       numlinepar++;        numlinepar++;
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
Line 4692  run imach with mle=-1 to get a correct t Line 6304  run imach with mle=-1 to get a correct t
     }        }  
     fflush(ficlog);      fflush(ficlog);
   
       /* Reads scales values */
     p=param[1][1];      p=param[1][1];
           
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
Line 4699  run imach with mle=-1 to get a correct t Line 6312  run imach with mle=-1 to get a correct t
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       numlinepar++;        numlinepar++;
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
Line 4708  run imach with mle=-1 to get a correct t Line 6321  run imach with mle=-1 to get a correct t
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){          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);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
Line 4730  run imach with mle=-1 to get a correct t Line 6343  run imach with mle=-1 to get a correct t
     }      }
     fflush(ficlog);      fflush(ficlog);
   
       /* Reads covariance matrix */
     delti=delti3[1][1];      delti=delti3[1][1];
   
   
Line 4740  run imach with mle=-1 to get a correct t Line 6354  run imach with mle=-1 to get a correct t
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       numlinepar++;        numlinepar++;
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
       
     matcov=matrix(1,npar,1,npar);      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++){      for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);        fscanf(ficpar,"%s",str);
       if(mle==1)        if(mle==1)
         printf("%s",str);          printf("%s",str);
       fprintf(ficlog,"%s",str);        fprintf(ficlog,"%s",str);
Line 4787  run imach with mle=-1 to get a correct t Line 6404  run imach with mle=-1 to get a correct t
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"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);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
   
   /*-------- data file ----------*/  
   if((fic=fopen(datafile,"r"))==NULL)    {  
     printf("Problem while opening datafile: %s\n", datafile);goto end;  
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;  
   }  
   
   n= lastobs;  
   severity = vector(1,maxwav);  
   outcome=imatrix(1,maxwav+1,1,n);  
   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);  
   tab=ivector(1,NCOVMAX);  
   ncodemax=ivector(1,8);  
   
   i=1;  
   linei=0;  
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {  
     linei=linei+1;  
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */  
       if(line[j] == '\t')  
         line[j] = ' ';  
     }  
     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){  
       ;  
     };  
     line[j+1]=0;  /* Trims blanks at end of line */  
     if(line[0]=='#'){  
       fprintf(ficlog,"Comment line\n%s\n",line);  
       printf("Comment line\n%s\n",line);  
       continue;  
     }  
   
     for (j=maxwav;j>=1;j--){  
       cutv(stra, strb,line,' ');   
       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 '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);  
         exit(1);  
       }  
       s[j][i]=lval;  
         
       strcpy(line,stra);  
       cutv(stra, strb,line,' ');  
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){  
       }  
       else  if(iout=sscanf(strb,"%s.") != 0){  
         month=99;  
         year=9999;  
       }else{  
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);  
         exit(1);  
       }  
       anint[j][i]= (double) year;   
       mint[j][i]= (double)month;   
       strcpy(line,stra);  
     } /* ENd Waves */  
       
     cutv(stra, strb,line,' ');   
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){  
     }  
     else  if(iout=sscanf(strb,"%s.",dummy) != 0){  
       month=99;  
       year=9999;  
     }else{  
       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);  
       exit(1);  
     }  
     andc[i]=(double) year;   
     moisdc[i]=(double) month;   
     strcpy(line,stra);  
       
     cutv(stra, strb,line,' ');   
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){  
     }  
     else  if(iout=sscanf(strb,"%s.") != 0){  
       month=99;  
       year=9999;  
     }else{  
       printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);  
       exit(1);  
     }  
     annais[i]=(double)(year);  
     moisnais[i]=(double)(month);   
     strcpy(line,stra);  
       
     cutv(stra, strb,line,' ');   
     errno=0;  
     dval=strtod(strb,&endptr);   
     if( strb[0]=='\0' || (*endptr != '\0')){  
       printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);  
       exit(1);  
     }  
     weight[i]=dval;   
     strcpy(line,stra);  
       
     for (j=ncovcol;j>=1;j--){  
       cutv(stra, strb,line,' ');   
       errno=0;  
       lval=strtol(strb,&endptr,10);   
       if( strb[0]=='\0' || (*endptr != '\0')){  
         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);  
         exit(1);  
       }  
       if(lval <-1 || lval >1){  
         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \  
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \  
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \  
  For example, for multinomial values like 1, 2 and 3,\n \  
  build V1=0 V2=0 for the reference value (1),\n \  
         V1=1 V2=0 for (2) \n \  
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \  
  output of IMaCh is often meaningless.\n \  
  Exiting.\n",lval,linei, i,line,j);  
         exit(1);  
       }  
       covar[j][i]=(double)(lval);  
       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 */  
   fclose(fic);  
   /* 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;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/  
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;   
      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
     
   /* 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 parameters from char model */  
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */  
   Tprod=ivector(1,15);   
   Tvaraff=ivector(1,15);   
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);        
      
   if (strlen(model) >1){ /* If there is at least 1 covariate */  
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+'); /* j=Number of '+' */  
     j1=nbocc(model,'*'); /* j1=Number of '*' */  
     cptcovn=j+1;   
     cptcovprod=j1; /*Number of products */  
       
     strcpy(modelsav,model);   
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  
       fprintf(ficlog,"Error. Non available option model=%s ",model);  
       goto end;  
     }  
       
     /* This loop fills the array Tvar from the string 'model'.*/  
   
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  /* Model includes a product */  
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/  
         if (strcmp(strc,"age")==0) { /* Vn*age */  
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/  
           cptcovage++;  
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  
         }  
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);  
           cptcovage++;  
           Tage[cptcovage]=i;  
         }  
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */  
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc); /* m*/  
           Tvard[k1][2]=atoi(stre); /* n */  
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   
           for (k=1; k<=lastobs;k++)   
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;  
           k2=k2+2;  
         }  
       }  
       else { /* no more sum */  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);  
       }  
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  
     } /* end of loop + */  
   } /* end model */  
     
   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.  
     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/  
   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /*  Main data
   printf("cptcovprod=%d ", cptcovprod);     */
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    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 */
   
   scanf("%d ",i);*/    /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /*  if(mle==1){*/    /* Calculation of the number of parameters from char model */
   if (weightopt != 1) { /* Maximisation without weights*/      /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
     for(i=1;i<=n;i++) weight[i]=1.0;          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
   }          k=3 V4 Tvar[k=3]= 4 (from V4)
     /*-calculation of age at interview from date of interview and age at death -*/          k=2 V1 Tvar[k=2]= 1 (from V1)
   agev=matrix(1,maxwav,1,imx);          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
                         */  
   
   for (i=1; i<=imx; i++) {  /* Main decodemodel */
     for(m=2; (m<= maxwav); m++) {  
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){  
         anint[m][i]=9999;  
         s[m][i]=-1;  
       }  
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){  
         nberr++;  
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);  
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);  
         s[m][i]=-1;  
       }  
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){  
         nberr++;  
         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);   
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);   
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */  
       }  
     }  
   }  
   
   for (i=1; i<=imx; i++)  {    if(decodemodel(model, lastobs) == 1)
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      goto end;
     for(m=firstpass; (m<= lastpass); m++){  
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){    if((double)(lastobs-imx)/(double)imx > 1.10){
         if (s[m][i] >= nlstate+1) {      nbwarn++;
           if(agedc[i]>0)      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); 
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)      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); 
               agev[m][i]=agedc[i];  
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
             else {  
               if ((int)andc[i]!=9999){  
                 nbwarn++;  
                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);  
                 fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);  
                 agev[m][i]=-1;  
               }  
             }  
         }  
         else if(s[m][i] !=9){ /* Standard case, age in fractional  
                                  years but with the precision of a month */  
           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
           if((int)mint[m][i]==99 || (int)anint[m][i]==9999)  
             agev[m][i]=1;  
           else if(agev[m][i] <agemin){   
             agemin=agev[m][i];  
             /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
           }  
           else if(agev[m][i] >agemax){  
             agemax=agev[m][i];  
             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
           }  
           /*agev[m][i]=anint[m][i]-annais[i];*/  
           /*     agev[m][i] = age[i]+2*m;*/  
         }  
         else { /* =9 */  
           agev[m][i]=1;  
           s[m][i]=-1;  
         }  
       }  
       else /*= 0 Unknown */  
         agev[m][i]=1;  
     }  
       
   }    }
   for (i=1; i<=imx; i++)  {      /*  if(mle==1){*/
     for(m=firstpass; (m<=lastpass); m++){    if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       if (s[m][i] > (nlstate+ndeath)) {      for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
         nberr++;  
         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);       
         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);       
         goto end;  
       }  
     }  
   }    }
   
   /*for (i=1; i<=imx; i++){      /*-calculation of age at interview from date of interview and age at death -*/
   for (m=firstpass; (m<lastpass); m++){    agev=matrix(1,maxwav,1,imx);
      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);  
 }  
   
 }*/  
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   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);   
   
   agegomp=(int)agemin;    agegomp=(int)agemin;
   free_vector(severity,1,maxwav);  
   free_imatrix(outcome,1,maxwav+1,1,n);  
   free_vector(moisnais,1,n);    free_vector(moisnais,1,n);
   free_vector(annais,1,n);    free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   free_vector(moisdc,1,n);    free_vector(moisdc,1,n);
   free_vector(andc,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 5145  run imach with mle=-1 to get a correct t Line 6497  run imach with mle=-1 to get a correct t
         
   /* 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*/    /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
     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]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   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
              * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   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[12][3]=1; */
             /*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 5173  run imach with mle=-1 to get a correct t Line 6562  run imach with mle=-1 to get a correct t
      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 -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-mort");
Line 5191  run imach with mle=-1 to get a correct t Line 6584  run imach with mle=-1 to get a correct t
   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 --------*/  
   
     /* Initialisation of --------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
     strcat(optionfilehtm,"-mort");      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 5235  Title=%s <br>Datafile=%s Firstpass=%d La Line 6632  Title=%s <br>Datafile=%s Firstpass=%d La
   
   strcpy(pathr,path);    strcpy(pathr,path);
   strcat(pathr,optionfilefiname);    strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
   chdir(optionfilefiname); /* Move to directory named optionfile */    chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
       
   /* 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'. */
Line 5258  Interval (in months) between two waves: Line 6660  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*/
     /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);      ximort=matrix(1,NDIM,1,NDIM); 
       /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
Line 5298  Interval (in months) between two waves: Line 6701  Interval (in months) between two waves:
         ximort[i][j]=(i == j ? 1.0 : 0.0);          ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     p[1]=0.0268; p[NDIM]=0.083;      /*p[1]=0.0268; p[NDIM]=0.083;*/
     /*printf("%lf %lf", p[1], p[2]);*/      /*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");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"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");      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
     /*  for (i=1;i<=nlstate;i++)      /*  for (i=1;i<=nlstate;i++)
         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 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 */
           
     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);      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);      fclose(ficrespow);
           
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
Line 5377  Interval (in months) between two waves: Line 6865  Interval (in months) between two waves:
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,AGESUP);
   } /* Endof if mle==-3 */  #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 mortality only */
     /* Standard maximisation */
   else{ /* For mle >=1 */    else{ /* For mle >=1 */
         globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     globpr=1; /* to print the contributions */      globpr=1; /* again, to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      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);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */      if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
           
Line 5537  Interval (in months) between two waves: Line 7032  Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 5553  Interval (in months) between two waves: Line 7048  Interval (in months) between two waves:
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 5571  Interval (in months) between two waves: Line 7067  Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 5587  Interval (in months) between two waves: Line 7083  Interval (in months) between two waves:
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       puts(line);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 5601  Interval (in months) between two waves: Line 7097  Interval (in months) between two waves:
           
           
           
     /*  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); */
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
Line 5626  Interval (in months) between two waves: Line 7122  Interval (in months) between two waves:
     fclose(ficres);      fclose(ficres);
   
   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /* Other results (useful)*/
     
     strcpy(filerespl,"pl");  
     strcat(filerespl,fileres);  
     if((ficrespl=fopen(filerespl,"w"))==NULL) {  
       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;  
       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;  
     }  
     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);  
     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);  
     pstamp(ficrespl);  
     fprintf(ficrespl,"# Period (stable) prevalence \n");  
     fprintf(ficrespl,"#Age ");  
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
     fprintf(ficrespl,"\n");  
     
     prlim=matrix(1,nlstate,1,nlstate);  
   
     agebase=ageminpar;  
     agelim=agemaxpar;  
     ftolpl=1.e-10;  
     i1=cptcoveff;  
     if (cptcovn < 1){i1=1;}  
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
         k=k+1;      prlim=matrix(1,nlstate,1,nlstate);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      prevalence_limit(p, prlim,  ageminpar, agemaxpar);
         fprintf(ficrespl,"\n#******");  
         printf("\n#******");  
         fprintf(ficlog,"\n#******");  
         for(j=1;j<=cptcoveff;j++) {  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         }  
         fprintf(ficrespl,"******\n");  
         printf("******\n");  
         fprintf(ficlog,"******\n");  
           
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f ",age );  
           for(j=1;j<=cptcoveff;j++)  
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           for(i=1; i<=nlstate;i++)  
             fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");  
         }  
       }  
     }  
     fclose(ficrespl);      fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/  #ifdef FREEEXIT2
     #include "freeexit2.h"
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);  #endif
     if((ficrespij=fopen(filerespij,"w"))==NULL) {  
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;  
     }  
     printf("Computing pij: result on file '%s' \n", filerespij);  
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);  
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;  
     /*if (stepm<=24) stepsize=2;*/  
   
     agelim=AGESUP;  
     hstepm=stepsize*YEARM; /* Every year of age */  
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   
   
     /* hstepm=1;   aff par mois*/  
     pstamp(ficrespij);  
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");  
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;  
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)   
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");  
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
   
           /*      nhstepm=nhstepm*YEARM; aff par mois*/  
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /*------------- h Pij x at various ages ------------*/
           oldm=oldms;savm=savms;      /*#include "hpijx.h"*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        hPijx(p, bage, fage);
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");      fclose(ficrespij);
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");  
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  
         }  
       }  
     }  
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
     fclose(ficrespij);  
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
Line 5757  Interval (in months) between two waves: Line 7164  Interval (in months) between two waves:
       /*        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); */        /*        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); */
       /*      } */        /*      } */
     }      }
      
       /* ------ Other prevalence ratios------------ */
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
Line 5785  Interval (in months) between two waves: Line 7193  Interval (in months) between two waves:
     }      }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"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(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
         k=k+1;             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
Line 5799  Interval (in months) between two waves: Line 7208  Interval (in months) between two waves:
         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);            evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
               
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       }        /*}*/
     }      }
     fclose(ficreseij);      fclose(ficreseij);
   
Line 5844  Interval (in months) between two waves: Line 7253  Interval (in months) between two waves:
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
         k=k+1;             
         fprintf(ficrest,"\n#****** ");      for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
Line 5869  Interval (in months) between two waves: Line 7279  Interval (in months) between two waves:
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);            cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
     
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         pstamp(ficrest);          pstamp(ficrest);
   
   
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms;            oldm=oldms;savm=savms; /* Segmentation fault */
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");            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 */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           if(vpopbased==1)            if(vpopbased==1)
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);              fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
           else            else
Line 5918  Interval (in months) between two waves: Line 7335  Interval (in months) between two waves:
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);          free_vector(epj,1,nlstate+1);
       }        /*}*/
     }      }
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n);       free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,1,n);
Line 5943  Interval (in months) between two waves: Line 7360  Interval (in months) between two waves:
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);      printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
         k=k+1;            
         fprintf(ficresvpl,"\n#****** ");      for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");          fprintf(ficresvpl,"******\n");
Line 5955  Interval (in months) between two waves: Line 7373  Interval (in months) between two waves:
         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,strstart);          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);
Line 5963  Interval (in months) between two waves: Line 7381  Interval (in months) between two waves:
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
   free_matrix(prlim,1,nlstate,1,nlstate);   /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
Line 5977  Interval (in months) between two waves: Line 7395  Interval (in months) between two waves:
     free_matrix(agev,1,maxwav,1,imx);      free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
     free_ivector(ncodemax,1,8);      free_ivector(ncodemax,1,NCOVMAX);
     free_ivector(Tvar,1,15);      free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,15);      free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,15);      free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(Tage,1,15);      free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tcode,1,100);  
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);      free_imatrix(codtab,1,100,1,10);
Line 5999  Interval (in months) between two waves: Line 7416  Interval (in months) between two waves:
   }    }
   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); */
     strcpy(strtend,asctime(&end_time));
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     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>\n</body></html>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
Line 6022  Interval (in months) between two waves: Line 7440  Interval (in months) between two waves:
   
   
    printf("Before Current directory %s!\n",pathcd);     printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
    if(chdir(pathcd) != 0)     if(chdir(pathcd) != 0)
     printf("Can't move to directory %s!\n",path);             printf("Can't move to directory %s!\n", path);
   if(getcwd(pathcd,MAXLINE) > 0)     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");
 #ifndef UNIX  #ifdef _WIN32
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);    sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 #endif  #endif
   if(!stat(plotcmd,&info)){    if(!stat(plotcmd,&info)){
     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);      printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     if(!stat(getenv("GNUPLOTBIN"),&info)){      if(!stat(getenv("GNUPLOTBIN"),&info)){
       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);        printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #ifdef UNIX  #ifdef __unix
     strcpy(plotcmd,GNUPLOTPROGRAM);      strcpy(plotcmd,GNUPLOTPROGRAM);
     if(!stat(plotcmd,&info)){      if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);        printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #endif  #endif
Line 6048  Interval (in months) between two waves: Line 7472  Interval (in months) between two waves:
     strcpy(pplotcmd,plotcmd);      strcpy(pplotcmd,plotcmd);
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("\n 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') {      if (z[0] == 'e') {
       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);  #ifdef __APPLE__
       system(optionfilehtm);        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 6072  Interval (in months) between two waves: Line 7507  Interval (in months) between two waves:
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }
   
   
   

Removed from v.1.128  
changed lines
  Added in v.1.186


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