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Diff for /imach/src/imach.c between versions 1.129 and 1.175

-version 1.129, 2007/08/31 13:49:27
+version 1.175, 2015/01/03 16:33:42
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
- Line 160
+ Line 352
    The same imach parameter file can be used but the option for mle should be -3.
-   Agn�s, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
- Line 293
+ Line 485
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'�tudes d�mographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 320
+ Line 512
        begin-prev-date,...
    open gnuplot 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
+ 85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
+ 85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
+ 65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
+ 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()
    health expectancies
    Variance-covariance of DFLE
- Line 336
+ Line 540
   end
  */
+ #define POWELL /* Instead of NLOPT */
  #include <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
+ #ifdef _WIN32
+ #include <io.h>
+ #include <windows.h>
+ #include <tchar.h>
+ #else
  #include <unistd.h>
+ #endif
  #include <limits.h>
  #include <sys/types.h>
+ #if defined(__GNUC__)
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
  #include <sys/stat.h>
  #include <errno.h>
- extern int errno;
+ /* extern int errno; */
+ /* #ifdef LINUX */
+ /* #include <time.h> */
+ /* #include "timeval.h" */
+ /* #else */
  /* #include <sys/time.h> */
+ /* #endif */
  #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> */
  /* #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 "..\\gp37mgw\\wgnuplot"*/
- Line 367  extern int errno;
+ Line 600  extern int errno;
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #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 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 YEARM 12. /* Number of months per year */
+ #define YEARM 12. /**< Number of months per year */
  #define AGESUP 130
  #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 CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
+ #else
+ #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
+ #define ODIRSEPARATOR '\\'
  #endif
  /* $Id$ */
  /* $State$ */
- char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
+ char version[]="Imach version 0.98p, December 2014,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 strstart[80];
  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 nlstate=2; /* Number of live 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 *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)*/
- int mle, weightopt;
+ int mle=1, weightopt=0;
  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  int **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. */
- 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 **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;
- int globpr; /* Global variable for printing or not */
+ int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- long ipmx; /* Number of contributions */
+ long ipmx=0; /* Number of contributions */
  double sw; /* Sum of weights */
  char filerespow[FILENAMELENGTH];
  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
- Line 457  char popfile[FILENAMELENGTH];
+ Line 701  char popfile[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 *endptr;
- Line 492  static double maxarg1,maxarg2;
+ Line 741  static double maxarg1,maxarg2;
  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  #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;
  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
- Line 515  double dateintmean=0;
+ Line 769  double dateintmean=0;
  double *weight;
  int **s; /* Status */
- double *agedc, **covar, idx;
+ double *agedc;
- int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ double  **covar; /**< covar[j,i], value of jth covariate for individual i,
+                   * covar=matrix(0,NCOVMAX,1,n);
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
+ double  idx;
+ int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ int *Ndum; /** Freq of modality (tricode */
+ int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double *lsurv, *lpop, *tpop;
- double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+ double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- double ftolhess; /* Tolerance for computing hessian */
+ double ftolhess; /**< Tolerance for computing hessian */
  /**************** split *************************/
  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
- Line 589  void replace_back_to_slash(char *s, char
+ Line 850  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 i,j=0;
- Line 601  int nbocc(char *s, char occ)
+ Line 933  int nbocc(char *s, char occ)
    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 ********************/
- Line 730  double **matrix(long nrl, long nrh, long
+ Line 1080  double **matrix(long nrl, long nrh, long
    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    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 820  char *subdirf3(char fileres[], char *pre
+ Line 1172  char *subdirf3(char fileres[], char *pre
    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 *************************/
  extern int ncom;
  extern double *pcom,*xicom;
- Line 843  double brent(double ax, double bx, doubl
+ Line 1208  double brent(double ax, double bx, doubl
  {
    int iter;
    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 e=0.0;
- Line 858  double brent(double ax, double bx, doubl
+ Line 1223  double brent(double ax, double bx, doubl
      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      printf(".");fflush(stdout);
      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);
      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)))) { */
- Line 928  void mnbrak(double *ax, double *bx, doub
+ Line 1293  void mnbrak(double *ax, double *bx, doub
        }
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
-   while (*fb > *fc) {
+   while (*fb > *fc) { /* Declining fa, fb, fc */
      r=(*bx-*ax)*(*fb-*fc);
      q=(*bx-*cx)*(*fb-*fa);
      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
-       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
-     if ((*bx-u)*(u-*cx) > 0.0) {
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
        fu=(*func)(u);
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ #ifdef DEBUG
+       /* f(x)=A(x-u)**2+f(u) */
+       double A, fparabu;
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+ #endif
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
        fu=(*func)(u);
        if (fu < *fc) {
          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
            SHFT(*fb,*fc,fu,(*func)(u))
            }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
        u=ulim;
        fu=(*func)(u);
      } else {
- Line 955  void mnbrak(double *ax, double *bx, doub
+ Line 1328  void mnbrak(double *ax, double *bx, doub
  }
  /*************** 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;
  double *pcom,*xicom;
  double (*nrfunc)(double []);
- Line 981  void linmin(double p[], double xi[], int
+ Line 1358  void linmin(double p[], double xi[], int
    }
    ax=0.0;
    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
    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- Line 995  void linmin(double p[], double xi[], int
+ Line 1372  void linmin(double p[], double xi[], int
    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 ************************/
+ /*
+ 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,
              double (*func)(double []))
  {
- Line 1026  void powell(double p[], double **xi, int
+ Line 1399  void powell(double p[], double **xi, int
    xits=vector(1,n);
    *fret=(*func)(p);
    for (j=1;j<=n;j++) pt[j]=p[j];
+     rcurr_time = time(NULL);
    for (*iter=1;;++(*iter)) {
      fp=(*fret);
      ibig=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++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
- Line 1044  void powell(double p[], double **xi, int
+ Line 1420  void powell(double p[], double **xi, int
      fprintf(ficlog,"\n");
      fprintf(ficrespow,"\n");fflush(ficrespow);
      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);
        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
          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){
-         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);
          if(strfor[itmp-1]=='\n')
          strfor[itmp-1]='\0';
-         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
+         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 (j=1;j<=n;j++) xit[j]=xi[j][i];
        fptt=(*fret);
  #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
        printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
- Line 1088  void powell(double p[], double **xi, int
+ Line 1462  void powell(double p[], double **xi, int
          fprintf(ficlog," x(%d)=%.12e",j,xit[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");
        fprintf(ficlog,"\n");
  #endif
-     }
+     } /* end i */
      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
  #ifdef DEBUG
        int k[2],l;
- Line 1127  void powell(double p[], double **xi, int
+ Line 1501  void powell(double p[], double **xi, int
        return;
      }
      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-     for (j=1;j<=n;j++) {
+     for (j=1;j<=n;j++) { /* Computes an extrapolated point */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
        pt[j]=p[j];
      }
      fptt=(*func)(ptt);
-     if (fptt < fp) {
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
-       if (t < 0.0) {
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
-         linmin(p,xit,n,fret,func);
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+       /* Thus we compare delta(2h) with observed f1-f3 */
+       /* or best gain on one ancient line 'del' with total  */
+       /* gain f1-f2 = f1 - f2 - 'del' with del  */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
+       t= t- del*SQR(fp-fptt);
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+ #ifdef DEBUG
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+ #endif
+       if (t < 0.0) { /* Then we use it for last direction */
+         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
          for (j=1;j<=n;j++) {
-           xi[j][ibig]=xi[j][n];
+           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
-           xi[j][n]=xit[j];
+           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
          }
+         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          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);
- Line 1151  void powell(double p[], double **xi, int
+ Line 1550  void powell(double p[], double **xi, int
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
-       }
+       } /* end of t negative */
-     }
+     } /* end if (fptt < fp)  */
    }
  }
- Line 1162  double **prevalim(double **prlim, int nl
+ Line 1561  double **prevalim(double **prlim, int nl
  {
    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       matrix by transitions matrix until convergence is reached */
    int i, ii,j,k;
    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 agefin, delaymax=50 ; /* Max number of years to converge */
    for (ii=1;ii<=nlstate+ndeath;ii++)
      for (j=1;j<=nlstate+ndeath;j++){
        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){
      newm=savm;
      /* Covariates have to be included here again */
-      cov[2]=agefin;
+     cov[2]=agefin;
-       for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=cptcovn;k++) {
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
-       }
+     }
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for (k=1; k<=cptcovprod;k++)
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
-       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
      maxmax=0.;
- Line 1206  double **prevalim(double **prlim, int nl
+ Line 1607  double **prevalim(double **prlim, int nl
          sumnew=0;
          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
          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]);
          min=FMIN(min,prlim[i][j]);
        }
        maxmin=max-min;
        maxmax=FMAX(maxmax,maxmin);
-     }
+     } /* j loop */
      if(maxmax < ftolpl){
        return prlim;
      }
-   }
+   } /* age loop */
+   return prlim; /* should not reach here */
  }
  /*************** transition probabilities ***************/
  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;*/
-   int i,j,j1, nc, ii, jj;
+   int i,j, nc, ii, jj;
      for(i=1; i<= nlstate; i++){
        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 (nc=1, s2=0.;nc <=ncovmodel; nc++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
- /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
          }
-         ps[i][j]=s2;
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        }
      }
-     /*ps[3][2]=1;*/
      for(i=1; i<= nlstate; i++){
        s1=0;
-       for(j=1; j<i; j++)
+       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.);
+       /* Computing other pijs */
        for(j=1; j<i; j++)
          ps[i][j]= exp(ps[i][j])*ps[i][i];
        for(j=i+1; j<=nlstate+ndeath; j++)
- Line 1267  double **pmij(double **ps, double *cov,
+ Line 1689  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]);
        goto end;*/
      return ps;
- Line 1283  double **pmij(double **ps, double *cov,
+ Line 1705  double **pmij(double **ps, double *cov,
  /**************** 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
       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
       a pointer to pointers identical to out */
-   long i, j, k;
+   int i, j, k;
    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;
  }
- Line 1317  double ***hpxij(double ***po, int nhstep
+ Line 1740  double ***hpxij(double ***po, int nhstep
       */
    int i, j, d, h, k;
-   double **out, cov[NCOVMAX];
+   double **out, cov[NCOVMAX+1];
    double **newm;
    /* Hstepm could be zero and should return the unit matrix */
- Line 1333  double ***hpxij(double ***po, int nhstep
+ Line 1756  double ***hpxij(double ***po, int nhstep
        /* Covariates have to be included here again */
        cov[1]=1.;
        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       for (k=1; k<=cptcovn;k++)
+         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (k=1; k<=cptcovage;k++)
          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-       for (k=1; k<=cptcovprod;k++)
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- Line 1358  double ***hpxij(double ***po, int nhstep
+ Line 1782  double ***hpxij(double ***po, int nhstep
    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 *************/
  double func( double *x)
  {
    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 sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
- Line 1376  double func( double *x)
+ Line 1819  double func( double *x)
    /*for(i=1;i<imx;i++)
      printf(" %d\n",s[4][i]);
    */
+   ++countcallfunc;
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    if(mle==1){
      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 (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1393  double func( double *x)
+ Line 1849  double func( double *x)
            newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             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,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1617  double funcone( double *x)
+ Line 2073  double funcone( double *x)
  {
    /* Same as likeli but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
-   double l, ll[NLSTATEMAX], cov[NCOVMAX];
+   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
- Line 1647  double funcone( double *x)
+ Line 2103  double funcone( double *x)
          for (kk=1; kk<=cptcovage;kk++) {
            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,
 ,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;
          oldm=newm;
        } /* end mult */
- Line 1673  double funcone( double *x)
+ Line 2132  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 */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
          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 */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
+       /*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){
-         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 ", \
                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
- Line 1743  void likelione(FILE *ficres,double p[],
+ Line 2203  void likelione(FILE *ficres,double p[],
  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 fret;
    double fretone; /* Only one call to likelihood */
    /*  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);
    for (i=1;i<=npar;i++)
      for (j=1;j<=npar;j++)
- Line 1764  void mlikeli(FILE *ficres,double p[], in
+ Line 2236  void mlikeli(FILE *ficres,double p[], in
      for(j=1;j<=nlstate+ndeath;j++)
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
+ #ifdef POWELL
    powell(p,xi,npar,ftol,&iter,&fret,func);
+ #endif
+ #ifdef NLOPT
+ #ifdef NEWUOA
+   opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
+ #else
+   opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
+ #endif
+   lb=vector(0,npar-1);
+   for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
+   nlopt_set_lower_bounds(opt, lb);
+   nlopt_set_initial_step1(opt, 0.1);
+   p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
+   d->function = func;
+   printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
+   nlopt_set_min_objective(opt, myfunc, d);
+   nlopt_set_xtol_rel(opt, ftol);
+   if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
+     printf("nlopt failed! %d\n",creturn);
+   }
+   else {
+     printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
+     printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
+     iter=1; /* not equal */
+   }
+   nlopt_destroy(opt);
+ #endif
    free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
-   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  }
- Line 1780  void hesscov(double **matcov, double p[]
+ Line 2279  void hesscov(double **matcov, double p[]
  {
    double  **a,**y,*x,pd;
    double **hess;
-   int i, j,jk;
+   int i, j;
    int *indx;
    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
- Line 1884  double hessii(double x[], double delta,
+ Line 2383  double hessii(double x[], double delta,
    int i;
    int l=1, lmax=20;
    double k1,k2;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1]; /* identical to x */
    double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    double fx;
- Line 1893  double hessii(double x[], double delta,
+ Line 2392  double hessii(double x[], double delta,
    fx=func(x);
    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);
      delts=delt;
      for(k=1 ; k <kmax; k=k+1){
        delt = delta*(l1*k);
        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;
        k2=func(p2)-fx;
        /*res= (k1-2.0*fx+k2)/delt/delt; */
        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
- #ifdef DEBUG
+ #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);
        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
- Line 1914  double hessii(double x[], double delta,
+ Line 2413  double hessii(double x[], double delta,
          k=kmax;
        }
        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)){
          delts=delt;
- Line 1929  double hessii(double x[], double delta,
+ Line 2428  double hessii(double x[], double delta,
  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  {
    int i;
-   int l=1, l1, lmax=20;
+   int l=1, lmax=20;
    double k1,k2,k3,k4,res,fx;
-   double p2[NPARMAX+1];
+   double p2[MAXPARM+1];
    int k;
    fx=func(x);
- Line 2044  void pstamp(FILE *fichier)
+ Line 2543  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[])
  {  /* Some frequencies */
-   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+   int i, m, jk, j1, bool, z1,j;
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
- Line 2068  void  freqsummary(char fileres[], int ia
+ Line 2567  void  freqsummary(char fileres[], int ia
    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]);
          scanf("%d", i);*/
        for (i=-5; i<=nlstate+ndeath; i++)
          for (jk=-5; jk<=nlstate+ndeath; jk++)
            for(m=iagemin; m <= iagemax+3; m++)
              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;
        k2cpt=0;
        for (i=1; i<=imx; i++) {
          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++)
-             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){
            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);
- Line 2110  void  freqsummary(char fileres[], int ia
+ Line 2617  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);*/
        pstamp(ficresp);
- Line 2118  void  freqsummary(char fileres[], int ia
+ Line 2625  void  freqsummary(char fileres[], int ia
          fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          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++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- Line 2142  void  freqsummary(char fileres[], int ia
+ Line 2652  void  freqsummary(char fileres[], int ia
              pos += freq[jk][m][i];
            if(pp[jk]>=1.e-10){
              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]);
            }else{
- Line 2194  void  freqsummary(char fileres[], int ia
+ Line 2704  void  freqsummary(char fileres[], int ia
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
        }
-     }
+       /*}*/
    }
    dateintmean=dateintsum/k2cpt;
- Line 2213  void prevalence(double ***probs, double
+ Line 2723  void prevalence(double ***probs, double
       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 */
    int iagemin, iagemax;
+   int first; /** to stop verbosity which is redirected to log file */
    iagemin= (int) agemin;
    iagemax= (int) agemax;
- Line 2227  void prevalence(double ***probs, double
+ Line 2738  void prevalence(double ***probs, double
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
-   j=cptcoveff;
+   /*j=cptcoveff;*/
    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(m=iagemin; m <= iagemax+3; m++)
- Line 2262  void prevalence(double ***probs, double
+ Line 2774  void prevalence(double ***probs, double
          }
        }
        for(i=iagemin; i <= iagemax+3; i++){
          for(jk=1,posprop=0; jk <=nlstate ; jk++) {
            posprop += prop[jk][i];
          }
          for(jk=1; jk <=nlstate ; jk++){
            if( i <=  iagemax){
              if(posprop>=1.e-5){
                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 i */
-     } /* end i1 */
+     /*} *//* end i1 */
-   } /* end k1 */
+   } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
- Line 2302  void  concatwav(int wav[], int **dh, int
+ Line 2817  void  concatwav(int wav[], int **dh, int
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
-   jmin=1e+5;
+   jmin=100000;
    jmax=-1;
    jmean=0.;
    for(i=1; i<=imx; i++){
- Line 2397  void  concatwav(int wav[], int **dh, int
+ Line 2912  void  concatwav(int wav[], int **dh, int
              dh[mi][i]=jk;
              bh[mi][i]=0;
            }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;
              bh[mi][i]=ju;
            }
- Line 2423  void  concatwav(int wav[], int **dh, int
+ Line 2938  void  concatwav(int wav[], int **dh, int
    }
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
-   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
+   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 ****************************/
- 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;
-   for (k=0; k<maxncov; k++) Ndum[k]=0;
+   for (k=-1; k < maxncov; k++) Ndum[k]=0;
-   for (k=1; k<=7; k++) ncodemax[k]=0;
+   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   /* Loop on covariates without age and products */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
+   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
-                                modality*/
+     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
-       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
+                                modality of this covariate Vj*/
-       Ndum[ij]++; /*store the modality */
+       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+                                     * If product of Vn*Vm, still boolean *:
+                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+                                       modality of the nth covariate of individual i. */
+       if (ij > modmaxcovj)
+         modmaxcovj=ij;
+       else if (ij < modmincovj)
+         modmincovj=ij;
+       if ((ij < -1) && (ij > NCOVMAX)){
+         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+         exit(1);
+       }else
+       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
+       /* getting the maximum value of the modality of the covariate
-                                        Tvar[j]. If V=sex and male is 0 and
+          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                        female is 1, then  cptcode=1.*/
+          female is 1, then modmaxcovj=1.*/
      }
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
-     for (i=0; i<=cptcode; i++) {
+     cptcode=modmaxcovj;
-       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
+     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     }
+    /*for (i=0; i<=cptcode; i++) {*/
+     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
-     ij=1;
+       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
-     for (i=1; i<=ncodemax[j]; i++) {
+       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
-       for (k=0; k<= maxncov; k++) {
+         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
-         if (Ndum[k] != 0) {
+       }
-           nbcode[Tvar[j]][ij]=k;
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
-           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+     } /* Ndum[-1] number of undefined modalities */
+     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+        modmincovj=3; modmaxcovj = 7;
+        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
+        variables V1_1 and V1_2.
+        nbcode[Tvar[j]][ij]=k;
+        nbcode[Tvar[j]][1]=0;
+        nbcode[Tvar[j]][2]=1;
+        nbcode[Tvar[j]][3]=2;
+     */
+     ij=1; /* ij is similar to i but can jumps over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
+       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+         /*recode from 0 */
+         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+                                      k is a modality. If we have model=V1+V1*sex
+                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            ij++;
          }
          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.*/
-    ij=Tvar[i];
+    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     Ndum[ij]++;
   }
   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)){
-      Tvaraff[ij]=i; /*For printing */
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+      Tvaraff[ij]=i; /*For printing (unclear) */
       ij++;
-    }
+    }else
+        Tvaraff[ij]=0;
   }
+  ij--;
-  cptcoveff=ij-1; /*Number of simple covariates*/
+  cptcoveff=ij; /*Number of total covariates*/
  }
  /*********** 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[] )
  {
    /* 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 */
    double age, agelim, hf;
    double ***p3mat;
- Line 2810  void varevsij(char optionfilefiname[], d
+ Line 3376  void varevsij(char optionfilefiname[], d
    /* Variance of health expectancies */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    /* double **newm;*/
+   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+   int movingaverage();
    double **dnewm,**doldm;
    double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;
-   int k, cptcode;
+   int k;
    double *xp;
    double **gp, **gm;  /* for var eij */
    double ***gradg, ***trgradg; /*for var eij */
- Line 3080  void varevsij(char optionfilefiname[], d
+ Line 3649  void varevsij(char optionfilefiname[], d
    free_vector(gmp,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*/
-   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 */
-   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 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 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> 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);
- Line 3113  void varprevlim(char fileres[], double *
+ Line 3682  void varprevlim(char fileres[], double *
  {
    /* Variance of prevalence limit */
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **newm;
    double **dnewm,**doldm;
    int i, j, nhstepm, hstepm;
-   int k, cptcode;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
- Line 3195  void varprevlim(char fileres[], double *
+ Line 3763  void varprevlim(char fileres[], double *
  /************ 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[])
  {
-   int i, j=0,  i1, k1, l1, t, tj;
+   int i, j=0,  k1, l1, tj;
    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 **dnewm,**doldm;
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
    double **mu;
-   double age,agelim, cov[NCOVMAX];
+   double age, cov[NCOVMAX+1];
    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    int theta;
    char fileresprob[FILENAMELENGTH];
    char fileresprobcov[FILENAMELENGTH];
    char fileresprobcor[FILENAMELENGTH];
    double ***varpij;
    strcpy(fileresprob,"prob");
- Line 3259  void varprob(char optionfilefiname[], do
+ Line 3826  void varprob(char optionfilefiname[], do
    fprintf(ficresprobcov,"\n");
    fprintf(ficresprobcor,"\n");
   */
-  xp=vector(1,npar);
+   xp=vector(1,npar);
    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- Line 3284  standard deviations wide on each axis. <
+ Line 3851  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");
    cov[1]=1;
-   tj=cptcoveff;
+   /* tj=cptcoveff; */
+   tj = (int) pow(2,cptcoveff);
    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    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) {
          fprintf(ficresprob, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- Line 3312  To be simple, these graphs help to under
+ Line 3880  To be simple, these graphs help to under
          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 ++){
          cov[2]=age;
          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<=cptcovprod;k++)
            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(i=1; i<=npar; i++)
- Line 3362  To be simple, these graphs help to under
+ Line 3935  To be simple, these graphs help to under
          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-         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);
- Line 3399  To be simple, these graphs help to under
+ Line 3968  To be simple, these graphs help to under
          i=0;
          for (k=1; k<=(nlstate);k++){
            for (l=1; l<=(nlstate+ndeath);l++){
-             i=i++;
+             i++;
              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              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(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 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  */
        /*
-         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 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);
- Line 3422  To be simple, these graphs help to under
+ Line 3996  To be simple, these graphs help to under
        */
        /* 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 (l2=1; l2<=(nlstate+ndeath);l2++){
            if(l2==k2) continue;
- Line 3443  To be simple, these graphs help to under
+ Line 4017  To be simple, these graphs help to under
                    /* Computing eigen value of matrix of covariance */
                    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.;
+                   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 */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
- Line 3462  To be simple, these graphs help to under
+ Line 4046  To be simple, these graphs help to under
                      first=0;
                      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 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>\
   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
- Line 3493  To be simple, these graphs help to under
+ Line 4077  To be simple, these graphs help to under
            } /* k12 */
          } /*l1 */
        }/* k1 */
-     } /* loop covariates */
+       /* } */ /* loop covariates */
    }
    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
- Line 3539  void printinghtml(char fileres[], char t
+ Line 4123  void printinghtml(char fileres[], char t
  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 3553  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 4137  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       /* 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 */
       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 */
-        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++) {
-         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 k1 */
- Line 3613  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 4197  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   fflush(fichtm);
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=cptcoveff;
+  m=pow(2,cptcoveff);
   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   jj1=0;
- Line 3628  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 4212  fprintf(fichtm," \n<ul><li><b>Graphs</b>
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
+ 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 \
  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
- Line 3647  true period expectancies (those weighted
+ Line 4231  true period expectancies (those weighted
  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    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) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3662  void printinggnuplot(char fileres[], cha
+ Line 4246  void printinggnuplot(char fileres[], cha
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
   /* 1eme*/
+   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
    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\
  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 ++) {
-        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 ++) {
-        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*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else fprintf(ficgp," %%*lf (%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%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*/
+   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
    for (k1=1; k1<= m ; 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 ++) {
        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 ++) {
-         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 ,");
        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 ++) {
-         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+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        for (j=1; j<= nlstate+1 ; j ++) {
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         if (j==i) fprintf(ficgp," %%lf (%%lf)");
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+         else fprintf(ficgp," %%*lf (%%*lf)");
        }
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-       else fprintf(ficgp,"\" t\"\" w l 0,");
+       else fprintf(ficgp,"\" t\"\" w l lt 0,");
      }
    }
- Line 3727  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4311  plot [%.f:%.f] \"%s\" every :::%d::%d u
        /*       k=2+nlstate*(2*cpt-2); */
        k=2+(nlstate+1)*(cpt-1);
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+       fprintf(ficgp,"set ter png small size 320, 240\n\
- set size 0.65,0.65\n\
  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- Line 3748  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 4331  plot [%.f:%.f] \"%s\" every :::%d::%d u
    }
    /* 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;
-       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\
- set ter png small\nset size 0.65,0.65\n\
+ set ter png small size 320, 240\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 */
    for(i=1,jk=1; i <=nlstate; i++){
- Line 3783  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4367  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(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)
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
         else
           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;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
- Line 3801  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4385  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
               else
                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              ij=1;
+              ij=1;/* To be checked else nbcode[0][0] wrong */
               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,")/(1");
- Line 3816  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4400  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                 ij=1;
                 for(j=3; j <=ncovmodel; j++){
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
-                    ij++;
+                  /*   ij++; */
-                  }
+                  /* } */
-                  else
+                  /* else */
                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
                 fprintf(ficgp,")");
- Line 3833  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
+ Line 4417  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
         } /* end k2 */
       } /* end jk */
     } /* end ng */
+  /* avoid: */
     fflush(ficgp);
  }  /* end gnuplot */
- Line 3880  int movingaverage(double ***probs, doubl
+ Line 4465  int movingaverage(double ***probs, doubl
  /************** 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
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
       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 agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    double *popeffectif,*popcount;
- Line 4004  prevforecast(char fileres[], double anpr
+ Line 4588  prevforecast(char fileres[], double anpr
  }
  /************** 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 *popage;
- Line 4181  void prwizard(int ncovmodel, int nlstate
+ Line 4765  void prwizard(int ncovmodel, int nlstate
    /* 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;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- Line 4334  double gompertz(double x[])
+ Line 4918  double gompertz(double x[])
    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 ***********/
  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
- Line 4362  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 4987  fprintf(fichtm,"<ul><li><h4>Life table</
  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
    int ng;
- Line 4375  void printinggnuplotmort(char fileres[],
+ Line 5000  void printinggnuplotmort(char fileres[],
    strcpy(optfileres,"vpl");
    fprintf(ficgp,"set out \"graphmort.png\"\n ");
    fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
-   fprintf(ficgp, "set ter png small\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);
  }
+ int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+ {
+   /*-------- data file ----------*/
+   FILE *fic;
+   char dummy[]="                         ";
+   int i=0, j=0, n=0;
+   int linei, month, year,iout;
+   char line[MAXLINE], linetmp[MAXLINE];
+   char stra[MAXLINE], strb[MAXLINE];
+   char *stratrunc;
+   int lstra;
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+   }
+   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;
+     }
+     trimbb(linetmp,line); /* Trims multiple blanks in line */
+     strcpy(line, linetmp);
+     for (j=maxwav;j>=1;j--){
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing status */
+         lval=-1;
+       }else{
+         errno=0;
+         lval=strtol(strb,&endptr,10);
+       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         if( strb[0]=='\0' || (*endptr != '\0')){
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           return 1;
+         }
+       }
+       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){
+       month=99;
+       year=9999;
+     }else{
+       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
+         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+         return 1;
+     }
+     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;
+     }
+     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 %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]]=cov[2+Tage[k]]*cov[2]; */
+     /*
+      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
+     cptcovage=0;
+     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+       /*      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;  /* Tage[1] = 4 */
+           /*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"*/
+ #if defined(__GNUC__)
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+ #include <stdint.h>
+    int cross = CROSS;
+    if (cross){
+      printf("Cross-");
+      fprintf(ficlog,"Cross-");
+    }
+    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
+ /* struct utsname sysInfo;
+    if (uname(&sysInfo) != -1) {
+      printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+      fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+           */
+ #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__);
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+    //   void main()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("The program (probably compile for 32bit) is running under WOW64 (64bit) emulation.\n");
+            fprintf(ficlog, "The program (ie 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("The process is not running under WOW64 (i.e probably on a 64bits windows).\n");
+            frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bits windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+  }
  /***********************************************/
  /**************** Main Program *****************/
- Line 4391  void printinggnuplotmort(char fileres[],
+ Line 5625  void printinggnuplotmort(char fileres[],
  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,m,size=100,cptcode, cptcod;
+   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
-   int linei, month, year,iout;
-   int jj, ll, li, lj, lk, imk;
+   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], cc[32];
+   char ca[32], cb[32];
-   char dummy[]="                         ";
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    struct stat info;
-   double agedeb, agefin,hf;
+   double agedeb;
    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 line[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
-   char **bp, *tok, *val; /* pathtot */
+   char *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
-   int sdeb, sfin; /* Status at beginning and end */
+   int c,  h , cpt;
-   int c,  h , cpt,l;
+   int jl;
-   int ju,jl, mi;
+   int i1, j1, jk, stepsize;
-   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+   int *tab;
-   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;
- Line 4433  int main(int argc, char *argv[])
+ Line 5670  int main(int argc, char *argv[])
    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 bage=0, fage=110, age, agelim, agebase;
    double ftolpl=FTOL;
    double **prlim;
-   double *severity;
    double ***param; /* Matrix of parameters */
    double  *p;
    double **matcov; /* Matrix of covariance */
- Line 4445  int main(int argc, char *argv[])
+ Line 5681  int main(int argc, char *argv[])
    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];
+   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    int *dcwave;
-   char z[1]="c", occ;
+   char z[1]="c";
+   /*char  *strt;*/
+   char strtend[80];
-   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
-   char  *strt, strtend[80];
-   char *stratrunc;
-   int lstra;
-   long total_usecs;
  /*   setlocale (LC_ALL, ""); */
  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
  /*   textdomain (PACKAGE); */
- Line 4467  int main(int argc, char *argv[])
+ Line 5700  int main(int argc, char *argv[])
  /*   setlocale (LC_MESSAGES, ""); */
    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
-   (void) gettimeofday(&start_time,&tzp);
+   rstart_time = time(NULL);
+   /*  (void) gettimeofday(&start_time,&tzp);*/
+   start_time = *localtime(&rstart_time);
    curr_time=start_time;
-   tm = *localtime(&start_time.tv_sec);
+   /*tml = *localtime(&start_time.tm_sec);*/
-   tmg = *gmtime(&start_time.tv_sec);
+   /* strcpy(strstart,asctime(&tml)); */
-   strcpy(strstart,asctime(&tm));
+   strcpy(strstart,asctime(&start_time));
  /*  printf("Localtime (at start)=%s",strstart); */
- /*  tp.tv_sec = tp.tv_sec +86400; */
+ /*  tp.tm_sec = tp.tm_sec +86400; */
- /*  tm = *localtime(&start_time.tv_sec); */
+ /*  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.tv_sec = mktime(&tmg); */
+ /*   tp.tm_sec = mktime(&tmg); */
  /*   strt=asctime(&tmg); */
  /*   printf("Time(after) =%s",strstart);  */
  /*  (void) time (&time_value);
- Line 4500  int main(int argc, char *argv[])
+ Line 5735  int main(int argc, char *argv[])
      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');
- Line 4530  int main(int argc, char *argv[])
+ Line 5768  int main(int argc, char *argv[])
    strcpy(command,"mkdir ");
    strcat(command,optionfilefiname);
    if((outcmd=system(command)) != 0){
-     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
+     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); */
      /* fclose(ficlog); */
  /*     exit(1); */
- Line 4555  int main(int argc, char *argv[])
+ Line 5793  int main(int argc, char *argv[])
   path=%s \n\
   optionfile=%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);
    fprintf(ficlog,"Local time (at start): %s",strstart);
    fflush(ficlog);
  /*   (void) gettimeofday(&curr_time,&tzp); */
- /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
+ /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
    /* */
    strcpy(fileres,"r");
- Line 4571  int main(int argc, char *argv[])
+ Line 5811  int main(int argc, char *argv[])
    /*---------arguments file --------*/
    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);
-     goto end;
+     /* goto end; */
+     exit(70);
    }
- Line 4594  int main(int argc, char *argv[])
+ Line 5835  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
-     puts(line);
+     fputs(line,stdout);
      fputs(line,ficparo);
      fputs(line,ficlog);
    }
- Line 4610  int main(int argc, char *argv[])
+ Line 5851  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
-     puts(line);
+     fputs(line, stdout);
+     //puts(line);
      fputs(line,ficparo);
      fputs(line,ficlog);
    }
    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 */
-   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);
    delti=delti3[1][1];
    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
- Line 4646  int main(int argc, char *argv[])
+ Line 5899  int main(int argc, char *argv[])
      matcov=matrix(1,npar,1,npar);
    }
    else{
-     /* Read guess parameters */
+     /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        numlinepar++;
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
        fputs(line,ficlog);
      }
- Line 4695  run imach with mle=-1 to get a correct t
+ Line 5948  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
+     /* Reads scales values */
      p=param[1][1];
      /* Reads comments: lines beginning with '#' */
- Line 4702  run imach with mle=-1 to get a correct t
+ Line 5956  run imach with mle=-1 to get a correct t
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        numlinepar++;
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
        fputs(line,ficlog);
      }
- Line 4711  run imach with mle=-1 to get a correct t
+ Line 5965  run imach with mle=-1 to get a correct t
      for(i=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath-1; j++){
          fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1-i)*(j1-j)!=0){
+         if ( (i1-i) * (j1-j) != 0){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
            exit(1);
          }
- Line 4733  run imach with mle=-1 to get a correct t
+ Line 5987  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
+     /* Reads covariance matrix */
      delti=delti3[1][1];
- Line 4743  run imach with mle=-1 to get a correct t
+ Line 5998  run imach with mle=-1 to get a correct t
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        numlinepar++;
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
        fputs(line,ficlog);
      }
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     for(i=1; i <=npar; i++)
+       for(j=1; j <=npar; j++) matcov[i][j]=0.;
      for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",&str);
+       fscanf(ficpar,"%s",str);
        if(mle==1)
          printf("%s",str);
        fprintf(ficlog,"%s",str);
        fprintf(ficparo,"%s",str);
        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
            printf(" %.5le",matcov[i][j]);
          }
          fprintf(ficlog," %.5le",matcov[i][j]);
          fprintf(ficparo," %.5le",matcov[i][j]);
-       }
-       fscanf(ficpar,"\n");
-       numlinepar++;
-       if(mle==1)
-         printf("\n");
-       fprintf(ficlog,"\n");
-       fprintf(ficparo,"\n");
-     }
-     for(i=1; i <=npar; i++)
-       for(j=i+1;j<=npar;j++)
-         matcov[i][j]=matcov[j][i];
-     if(mle==1)
-       printf("\n");
-     fprintf(ficlog,"\n");
-     fflush(ficlog);
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", fileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
-     }
-     fprintf(ficres,"#%s\n",version);
-   }    /* End of mle != -3 */
-   /*-------- 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);
-         goto end;
        }
-       covar[j][i]=(double)(lval);
+       fscanf(ficpar,"\n");
-       strcpy(line,stra);
+       numlinepar++;
-     }
+       if(mle==1)
-     lstra=strlen(stra);
+         printf("\n");
+       fprintf(ficlog,"\n");
-     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+       fprintf(ficparo,"\n");
-       stratrunc = &(stra[lstra-9]);
-       num[i]=atol(stratrunc);
      }
-     else
+     for(i=1; i <=npar; i++)
-       num[i]=atol(stra);
+       for(j=i+1;j<=npar;j++)
-     /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+         matcov[i][j]=matcov[j][i];
-       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;
+     if(mle==1)
-   } /* End loop reading  data */
+       printf("\n");
-   fclose(fic);
+     fprintf(ficlog,"\n");
-   /* 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);
+     fflush(ficlog);
-     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'.*/
+     /*-------- Rewriting parameter file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
+     strcat(rfileres,".");    /* */
+     strcat(rfileres,optionfilext);    /* Other files have txt extension */
+     if((ficres =fopen(rfileres,"w"))==NULL) {
+       printf("Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+     }
+     fprintf(ficres,"#%s\n",version);
+   }    /* End of mle != -3 */
-     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]);
+   n= lastobs;
-   printf("cptcovprod=%d ", cptcovprod);
+   num=lvector(1,n);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+   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
+covariates (3 plus signs)
+                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
+                       */
-   for (i=1; i<=imx; i++) {
+   if(decodemodel(model, lastobs) == 1)
-     for(m=2; (m<= maxwav); m++) {
+     goto end;
-       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((double)(lastobs-imx)/(double)imx > 1.10){
-     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+     nbwarn++;
-     for(m=firstpass; (m<= lastpass); m++){
+     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(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+     fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx);
-         if (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;
-               }
-             }
-         }
-         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;
-   free_vector(severity,1,maxwav);
-   free_imatrix(outcome,1,maxwav+1,1,n);
    free_vector(moisnais,1,n);
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
    free_vector(moisdc,1,n);
    free_vector(andc,1,n);
+   /* */
    wav=ivector(1,imx);
    dh=imatrix(1,lastpass-firstpass+1,1,imx);
    bh=imatrix(1,lastpass-firstpass+1,1,imx);
- Line 5148  run imach with mle=-1 to get a correct t
+ Line 6138  run imach with mle=-1 to get a correct t
    /* Concatenates waves */
    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 */
-   Tcode=ivector(1,100);
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel > 2)
-   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-                                  the estimations*/
+   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
    h=0;
+   /*if (cptcovn > 0) */
    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++;
-           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+           if (h>m)
-           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+             h=1;
+           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
+            *     h     1     2     3     4
+            *______________________________
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     2     2     1     1     1
+            *     3 i=2 1     2     1     1
+            *     4     2     2     1     1
+            *     5 i=3 1 i=2 1     2     1
+            *     6     2     1     2     1
+            *     7 i=4 1     2     2     1
+            *     8     2     2     2     1
+            *     9 i=5 1 i=3 1 i=2 1     1
+            *    10     2     1     1     1
+            *    11 i=6 1     2     1     1
+            *    12     2     2     1     1
+            *    13 i=7 1 i=4 1     2     1
+            *    14     2     1     2     1
+            *    15 i=8 1     2     2     1
+            *    16     2     2     2     1
+            */
+           codtab[h][k]=j;
+           /*codtab[h][Tvar[k]]=j;*/
+           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
          }
        }
      }
- Line 5176  run imach with mle=-1 to get a correct t
+ Line 6196  run imach with mle=-1 to get a correct t
       codtab[1][2]=1;codtab[2][2]=2; */
    /* for(i=1; i <=m ;i++){
       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");
       }
       scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
    /*------------ gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
- Line 5194  run imach with mle=-1 to get a correct t
+ Line 6218  run imach with mle=-1 to get a correct t
    else{
      fprintf(ficgp,"\n# %s\n", version);
      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);*/
    /*--------- index.htm --------*/
- Line 5204  run imach with mle=-1 to get a correct t
+ Line 6229  run imach with mle=-1 to get a correct t
      strcat(optionfilehtm,"-mort");
    strcat(optionfilehtm,".htm");
    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 */
- Line 5263  Interval (in months) between two waves:
+ Line 6289  Interval (in months) between two waves:
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
+ /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
- Line 5301  Interval (in months) between two waves:
+ Line 6328  Interval (in months) between two waves:
          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]);*/
+ #ifdef GSL
+     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
+ #else
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
+ #endif
      strcpy(filerespow,"pow-mort");
      strcat(filerespow,fileres);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
+ #ifdef GSL
+     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+ #else
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ #endif
      /*  for (i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      */
      fprintf(ficrespow,"\n");
+ #ifdef GSL
+     /* gsl starts here */
+     T = gsl_multimin_fminimizer_nmsimplex;
+     gsl_multimin_fminimizer *sfm = NULL;
+     gsl_vector *ss, *x;
+     gsl_multimin_function minex_func;
+     /* Initial vertex size vector */
+     ss = gsl_vector_alloc (NDIM);
+     if (ss == NULL){
+       GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+     }
+     /* Set all step sizes to 1 */
+     gsl_vector_set_all (ss, 0.001);
+     /* Starting point */
+     x = gsl_vector_alloc (NDIM);
+     if (x == NULL){
+       gsl_vector_free(ss);
+       GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+     }
+     /* Initialize method and iterate */
+     /*     p[1]=0.0268; p[NDIM]=0.083; */
+ /*     gsl_vector_set(x, 0, 0.0268); */
+ /*     gsl_vector_set(x, 1, 0.083); */
+     gsl_vector_set(x, 0, p[1]);
+     gsl_vector_set(x, 1, p[2]);
+     minex_func.f = &gompertz_f;
+     minex_func.n = NDIM;
+     minex_func.params = (void *)&p; /* ??? */
+     sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+     gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+     printf("Iterations beginning .....\n\n");
+     printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
+     iteri=0;
+     while (rval == GSL_CONTINUE){
+       iteri++;
+       status = gsl_multimin_fminimizer_iterate(sfm);
+       if (status) printf("error: %s\n", gsl_strerror (status));
+       fflush(0);
+       if (status)
+         break;
+       rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+       ssval = gsl_multimin_fminimizer_size (sfm);
+       if (rval == GSL_SUCCESS)
+         printf ("converged to a local maximum at\n");
+       printf("%5d ", iteri);
+       for (it = 0; it < NDIM; it++){
+         printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+       }
+       printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+     }
-     powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+     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);
      hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
- Line 5380  Interval (in months) between two waves:
+ Line 6492  Interval (in months) between two waves:
      free_vector(lsurv,1,AGESUP);
      free_vector(lpop,1,AGESUP);
      free_vector(tpop,1,AGESUP);
+ #ifdef GSL
+     free_ivector(cens,1,n);
+     free_vector(agecens,1,n);
+     free_ivector(dcwave,1,n);
+     free_matrix(ximort,1,NDIM,1,NDIM);
+ #endif
    } /* Endof if mle==-3 */
    else{ /* For mle >=1 */
+     globpr=0;/* debug */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
- Line 5540  Interval (in months) between two waves:
+ Line 6658  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5560  Interval (in months) between two waves:
+ Line 6678  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5574  Interval (in months) between two waves:
+ Line 6692  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5590  Interval (in months) between two waves:
+ Line 6708  Interval (in months) between two waves:
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
-       puts(line);
+       fputs(line,stdout);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 5604  Interval (in months) between two waves:
+ Line 6722  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 / */
      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
- Line 5630  Interval (in months) between two waves:
+ Line 6748  Interval (in months) between two waves:
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+ #include "prevlim.h"  /* Use ficrespl, ficlog */
-     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++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
-         fprintf(ficlog,"******\n");
-         for (age=agebase; age<=agelim; age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-           fprintf(ficrespl,"%.0f ",age );
-           for(j=1;j<=cptcoveff;j++)
-             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           for(i=1; i<=nlstate;i++)
-             fprintf(ficrespl," %.5f", prlim[i][i]);
-           fprintf(ficrespl,"\n");
-         }
-       }
-     }
      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);
+     fclose(ficrespij);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
-         }
-       }
-     }
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     fclose(ficrespij);
      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1;i<=AGESUP;i++)
- Line 5788  Interval (in months) between two waves:
+ Line 6811  Interval (in months) between two waves:
      }
      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /*for(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#****** ");
          for(j=1;j<=cptcoveff;j++) {
            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- Line 5802  Interval (in months) between two waves:
+ Line 6826  Interval (in months) between two waves:
          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       }
+       /*}*/
      }
      fclose(ficreseij);
- Line 5847  Interval (in months) between two waves:
+ Line 6871  Interval (in months) between two waves:
      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /*for(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++)
            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          fprintf(ficrest,"******\n");
- Line 5872  Interval (in months) between two waves:
+ Line 6897  Interval (in months) between two waves:
          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
          cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+         /*
+          */
+         /* goto endfree; */
          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
          pstamp(ficrest);
          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-           oldm=oldms;savm=savms;
+           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)
              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
- Line 5921  Interval (in months) between two waves:
+ Line 6953  Interval (in months) between two waves:
          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
          free_vector(epj,1,nlstate+1);
-       }
+       /*}*/
      }
      free_vector(weight,1,n);
-     free_imatrix(Tvard,1,15,1,2);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
      free_imatrix(s,1,maxwav+1,1,n);
      free_matrix(anint,1,maxwav,1,n);
      free_matrix(mint,1,maxwav,1,n);
- Line 5946  Interval (in months) between two waves:
+ Line 6978  Interval (in months) between two waves:
      }
      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++)
            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          fprintf(ficresvpl,"******\n");
- Line 5958  Interval (in months) between two waves:
+ Line 6991  Interval (in months) between two waves:
          oldm=oldms;savm=savms;
          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       }
+       /*}*/
      }
      fclose(ficresvpl);
- Line 5966  Interval (in months) between two waves:
+ Line 6999  Interval (in months) between two waves:
      /*---------- End : free ----------------*/
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }  /* mle==-3 arrives here for freeing */
-   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(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
- Line 5980  Interval (in months) between two waves:
+ Line 7013  Interval (in months) between two waves:
      free_matrix(agev,1,maxwav,1,imx);
      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(ncodemax,1,8);
+     free_ivector(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(codtab,1,100,1,10);
- Line 6002  Interval (in months) between two waves:
+ Line 7034  Interval (in months) between two waves:
    }
    printf("See log file on %s\n",filelog);
    /*  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);
    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);*/
  /*   if(fileappend(fichtm,optionfilehtm)){ */
    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
- Line 6031  Interval (in months) between two waves:
+ Line 7064  Interval (in months) between two waves:
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
    sprintf(plotcmd,"gnuplot");
- #ifndef UNIX
+ #ifdef _WIN32
    sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
  #endif
    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)){
-       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
        strcpy(pplotcmd,plotcmd);
- #ifdef UNIX
+ #ifdef __unix
      strcpy(plotcmd,GNUPLOTPROGRAM);
      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
        strcpy(pplotcmd,plotcmd);
  #endif
- Line 6051  Interval (in months) between two waves:
+ Line 7084  Interval (in months) between two waves:
      strcpy(pplotcmd,plotcmd);
    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){
-     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') {
      /* 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);
  /*     if (z[0] == 'c') system("./imach"); */
      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] == 'q') exit(0);
- Line 6075  Interval (in months) between two waves:
+ Line 7119  Interval (in months) between two waves:
      scanf("%s",z);
    }
  }

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Removed from v.1.129
changed lines
	Added in v.1.175