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Diff for /imach/src/imach.c between versions 1.144 and 1.213

-version 1.144, 2014/02/10 22:17:31
+version 1.213, 2015/12/11 18:22:17
  Line 1
  /* $Id$
    $State$
    $Log$
-   Revision 1.144  2014/02/10 22:17:31  brouard
+   Revision 1.213  2015/12/11 18:22:17  brouard
+   Summary: 0.98r4
+   Revision 1.212  2015/11/21 12:47:24  brouard
+   Summary: minor typo
+   Revision 1.211  2015/11/21 12:41:11  brouard
+   Summary: 0.98r3 with some graph of projected cross-sectional
+   Author: Nicolas Brouard
+   Revision 1.210  2015/11/18 17:41:20  brouard
+   Summary: Start working on projected prevalences
+   Revision 1.209  2015/11/17 22:12:03  brouard
+   Summary: Adding ftolpl parameter
+   Author: N Brouard
+   We had difficulties to get smoothed confidence intervals. It was due
+   to the period prevalence which wasn't computed accurately. The inner
+   parameter ftolpl is now an outer parameter of the .imach parameter
+   file after estepm. If ftolpl is small 1.e-4 and estepm too,
+   computation are long.
+   Revision 1.208  2015/11/17 14:31:57  brouard
+   Summary: temporary
+   Revision 1.207  2015/10/27 17:36:57  brouard
+   *** empty log message ***
+   Revision 1.206  2015/10/24 07:14:11  brouard
+   *** empty log message ***
+   Revision 1.205  2015/10/23 15:50:53  brouard
+   Summary: 0.98r3 some clarification for graphs on likelihood contributions
+   Revision 1.204  2015/10/01 16:20:26  brouard
+   Summary: Some new graphs of contribution to likelihood
+   Revision 1.203  2015/09/30 17:45:14  brouard
+   Summary: looking at better estimation of the hessian
+   Also a better criteria for convergence to the period prevalence And
+   therefore adding the number of years needed to converge. (The
+   prevalence in any alive state shold sum to one
+   Revision 1.202  2015/09/22 19:45:16  brouard
+   Summary: Adding some overall graph on contribution to likelihood. Might change
+   Revision 1.201  2015/09/15 17:34:58  brouard
+   Summary: 0.98r0
+   - Some new graphs like suvival functions
+   - Some bugs fixed like model=1+age+V2.
+   Revision 1.200  2015/09/09 16:53:55  brouard
+   Summary: Big bug thanks to Flavia
+   Even model=1+age+V2. did not work anymore
+   Revision 1.199  2015/09/07 14:09:23  brouard
+   Summary: 0.98q6 changing default small png format for graph to vectorized svg.
+   Revision 1.198  2015/09/03 07:14:39  brouard
+   Summary: 0.98q5 Flavia
+   Revision 1.197  2015/09/01 18:24:39  brouard
    *** empty log message ***
+   Revision 1.196  2015/08/18 23:17:52  brouard
+   Summary: 0.98q5
+   Revision 1.195  2015/08/18 16:28:39  brouard
+   Summary: Adding a hack for testing purpose
+   After reading the title, ftol and model lines, if the comment line has
+   a q, starting with #q, the answer at the end of the run is quit. It
+   permits to run test files in batch with ctest. The former workaround was
+   $ echo q | imach foo.imach
+   Revision 1.194  2015/08/18 13:32:00  brouard
+   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
+   Revision 1.193  2015/08/04 07:17:42  brouard
+   Summary: 0.98q4
+   Revision 1.192  2015/07/16 16:49:02  brouard
+   Summary: Fixing some outputs
+   Revision 1.191  2015/07/14 10:00:33  brouard
+   Summary: Some fixes
+   Revision 1.190  2015/05/05 08:51:13  brouard
+   Summary: Adding digits in output parameters (7 digits instead of 6)
+   Fix 1+age+.
+   Revision 1.189  2015/04/30 14:45:16  brouard
+   Summary: 0.98q2
+   Revision 1.188  2015/04/30 08:27:53  brouard
+   *** empty log message ***
+   Revision 1.187  2015/04/29 09:11:15  brouard
+   *** empty log message ***
+   Revision 1.186  2015/04/23 12:01:52  brouard
+   Summary: V1*age is working now, version 0.98q1
+   Some codes had been disabled in order to simplify and Vn*age was
+   working in the optimization phase, ie, giving correct MLE parameters,
+   but, as usual, outputs were not correct and program core dumped.
+   Revision 1.185  2015/03/11 13:26:42  brouard
+   Summary: Inclusion of compile and links command line for Intel Compiler
+   Revision 1.184  2015/03/11 11:52:39  brouard
+   Summary: Back from Windows 8. Intel Compiler
+   Revision 1.183  2015/03/10 20:34:32  brouard
+   Summary: 0.98q0, trying with directest, mnbrak fixed
+   We use directest instead of original Powell test; probably no
+   incidence on the results, but better justifications;
+   We fixed Numerical Recipes mnbrak routine which was wrong and gave
+   wrong results.
+   Revision 1.182  2015/02/12 08:19:57  brouard
+   Summary: Trying to keep directest which seems simpler and more general
+   Author: Nicolas Brouard
+   Revision 1.181  2015/02/11 23:22:24  brouard
+   Summary: Comments on Powell added
+   Author:
+   Revision 1.180  2015/02/11 17:33:45  brouard
+   Summary: Finishing move from main to function (hpijx and prevalence_limit)
+   Revision 1.179  2015/01/04 09:57:06  brouard
+   Summary: back to OS/X
+   Revision 1.178  2015/01/04 09:35:48  brouard
+   *** empty log message ***
+   Revision 1.177  2015/01/03 18:40:56  brouard
+   Summary: Still testing ilc32 on OSX
+   Revision 1.176  2015/01/03 16:45:04  brouard
+   *** empty log message ***
+   Revision 1.175  2015/01/03 16:33:42  brouard
+   *** empty log message ***
+   Revision 1.174  2015/01/03 16:15:49  brouard
+   Summary: Still in cross-compilation
+   Revision 1.173  2015/01/03 12:06:26  brouard
+   Summary: trying to detect cross-compilation
+   Revision 1.172  2014/12/27 12:07:47  brouard
+   Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
+   Revision 1.171  2014/12/23 13:26:59  brouard
+   Summary: Back from Visual C
+   Still problem with utsname.h on Windows
+   Revision 1.170  2014/12/23 11:17:12  brouard
+   Summary: Cleaning some \%% back to %%
+   The escape was mandatory for a specific compiler (which one?), but too many warnings.
+   Revision 1.169  2014/12/22 23:08:31  brouard
+   Summary: 0.98p
+   Outputs some informations on compiler used, OS etc. Testing on different platforms.
+   Revision 1.168  2014/12/22 15:17:42  brouard
+   Summary: update
+   Revision 1.167  2014/12/22 13:50:56  brouard
+   Summary: Testing uname and compiler version and if compiled 32 or 64
+   Testing on Linux 64
+   Revision 1.166  2014/12/22 11:40:47  brouard
+   *** empty log message ***
+   Revision 1.165  2014/12/16 11:20:36  brouard
+   Summary: After compiling on Visual C
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.164  2014/12/16 10:52:11  brouard
+   Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.163  2014/12/16 10:30:11  brouard
+   * imach.c (Module): Merging 1.61 to 1.162
+   Revision 1.162  2014/09/25 11:43:39  brouard
+   Summary: temporary backup 0.99!
+   Revision 1.1  2014/09/16 11:06:58  brouard
+   Summary: With some code (wrong) for nlopt
+   Author:
+   Revision 1.161  2014/09/15 20:41:41  brouard
+   Summary: Problem with macro SQR on Intel compiler
+   Revision 1.160  2014/09/02 09:24:05  brouard
+   *** empty log message ***
+   Revision 1.159  2014/09/01 10:34:10  brouard
+   Summary: WIN32
+   Author: Brouard
+   Revision 1.158  2014/08/27 17:11:51  brouard
+   *** empty log message ***
+   Revision 1.157  2014/08/27 16:26:55  brouard
+   Summary: Preparing windows Visual studio version
+   Author: Brouard
+   In order to compile on Visual studio, time.h is now correct and time_t
+   and tm struct should be used. difftime should be used but sometimes I
+   just make the differences in raw time format (time(&now).
+   Trying to suppress #ifdef LINUX
+   Add xdg-open for __linux in order to open default browser.
+   Revision 1.156  2014/08/25 20:10:10  brouard
+   *** empty log message ***
+   Revision 1.155  2014/08/25 18:32:34  brouard
+   Summary: New compile, minor changes
+   Author: Brouard
+   Revision 1.154  2014/06/20 17:32:08  brouard
+   Summary: Outputs now all graphs of convergence to period prevalence
+   Revision 1.153  2014/06/20 16:45:46  brouard
+   Summary: If 3 live state, convergence to period prevalence on same graph
+   Author: Brouard
+   Revision 1.152  2014/06/18 17:54:09  brouard
+   Summary: open browser, use gnuplot on same dir than imach if not found in the path
+   Revision 1.151  2014/06/18 16:43:30  brouard
+   *** empty log message ***
+   Revision 1.150  2014/06/18 16:42:35  brouard
+   Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
+   Author: brouard
+   Revision 1.149  2014/06/18 15:51:14  brouard
+   Summary: Some fixes in parameter files errors
+   Author: Nicolas Brouard
+   Revision 1.148  2014/06/17 17:38:48  brouard
+   Summary: Nothing new
+   Author: Brouard
+   Just a new packaging for OS/X version 0.98nS
+   Revision 1.147  2014/06/16 10:33:11  brouard
+   *** empty log message ***
+   Revision 1.146  2014/06/16 10:20:28  brouard
+   Summary: Merge
+   Author: Brouard
+   Merge, before building revised version.
+   Revision 1.145  2014/06/10 21:23:15  brouard
+   Summary: Debugging with valgrind
+   Author: Nicolas Brouard
+   Lot of changes in order to output the results with some covariates
+   After the Edimburgh REVES conference 2014, it seems mandatory to
+   improve the code.
+   No more memory valgrind error but a lot has to be done in order to
+   continue the work of splitting the code into subroutines.
+   Also, decodemodel has been improved. Tricode is still not
+   optimal. nbcode should be improved. Documentation has been added in
+   the source code.
    Revision 1.143  2014/01/26 09:45:38  brouard
    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
- Line 377
+ Line 663
        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 393
+ Line 691
   end
  */
+ /* #define DEBUG */
+ /* #define DEBUGBRENT */
+ /* #define DEBUGLINMIN */
+ /* #define DEBUGHESS */
+ #define DEBUGHESSIJ
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
+ #define POWELL /* Instead of NLOPT */
+ #define POWELLF1F3 /* Skip test */
+ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
+ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
  #include <math.h>
  #include <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 */
- #ifdef LINUX
  #include <time.h>
- #include "timeval.h"
- #else
- #include <sys/time.h>
- #endif
  #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) */
- Line 439  extern int errno;
+ Line 767  extern int errno;
  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+ /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
+ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
  #define MAXN 20000
  #define YEARM 12. /**< Number of months per year */
  #define AGESUP 130
  #define AGEBASE 40
- #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
+ #define AGEOVERFLOW 1.e20
- #ifdef UNIX
+ #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- #define DIRSEPARATOR '/'
+ #ifdef _WIN32
- #define CHARSEPARATOR "/"
- #define ODIRSEPARATOR '\\'
- #else
  #define DIRSEPARATOR '\\'
  #define CHARSEPARATOR "\\"
  #define ODIRSEPARATOR '/'
+ #else
+ #define DIRSEPARATOR '/'
+ #define CHARSEPARATOR "/"
+ #define ODIRSEPARATOR '\\'
  #endif
  /* $Id$ */
  /* $State$ */
+ #include "version.h"
- char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+ char version[]=__IMACH_VERSION__;
+ char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
  char fullversion[]="$Revision$ $Date$";
  char strstart[80];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
- int nvar=0, nforce=0; /* Number of variables, number of forces */
+ int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
+ /* 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 */
- Line 481  int **mw; /* mw[mi][i] is number of the
+ Line 821  int **mw; /* mw[mi][i] is number of the
  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. */
+ 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 ; */ /* Used in readdata only */
- FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- Line 515  char command[FILENAMELENGTH];
+ Line 857  char command[FILENAMELENGTH];
  int  outcmd=0;
  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileresu[FILENAMELENGTH]; /* fileres without r in front */
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
  char fileregp[FILENAMELENGTH];
- Line 523  char popfile[FILENAMELENGTH];
+ Line 865  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 558  static double maxarg1,maxarg2;
+ Line 905  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 573  int estepm;
+ Line 925  int estepm;
  int m,nb;
  long *num;
- int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
+ int firstpass=0, lastpass=4,*cod, *cens;
+ int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
+                    covariate for which somebody answered excluding
+                    undefined. Usually 2: 0 and 1. */
+ int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs;
  double *ageexmed,*agecens;
- Line 582  double dateintmean=0;
+ Line 940  double dateintmean=0;
  double *weight;
  int **s; /* Status */
  double *agedc;
- double  **covar; /**< covar[i,j], value of jth covariate for individual i,
+ 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]; */
+                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ int *Tage;
+ int *Ndum; /** Freq of modality (tricode */
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double *lsurv, *lpop, *tpop;
- Line 601  static int split( char *path, char *dirc
+ Line 961  static int split( char *path, char *dirc
       the name of the file (name), its extension only (ext) and its first part of the name (finame)
    */
    char  *ss;                            /* pointer */
-   int   l1, l2;                         /* length counters */
+   int   l1=0, l2=0;                             /* length counters */
    l1 = strlen(path );                   /* length of path */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- Line 612  static int split( char *path, char *dirc
+ Line 972  static int split( char *path, char *dirc
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* get current working directory */
      /*    extern  char* getcwd ( char *buf , int len);*/
-     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #ifdef WIN32
+     if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
+ #else
+         if (getcwd(dirc, FILENAME_MAX) == NULL) {
+ #endif
        return( GLOCK_ERROR_GETCWD );
      }
      /* got dirc from getcwd*/
      printf(" DIRC = %s \n",dirc);
-   } else {                              /* strip direcotry from path */
+   } else {                              /* strip directory from path */
      ss++;                               /* after this, the filename */
      l2 = strlen( ss );                  /* length of filename */
      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
      strcpy( name, ss );         /* save file name */
      strncpy( dirc, path, l1 - l2 );     /* now the directory */
-     dirc[l1-l2] = 0;                    /* add zero */
+     dirc[l1-l2] = '\0';                 /* add zero */
      printf(" DIRC2 = %s \n",dirc);
    }
    /* We add a separator at the end of dirc if not exists */
- Line 675  char *trimbb(char *out, char *in)
+ Line 1039  char *trimbb(char *out, char *in)
    return s;
  }
+ /* char *substrchaine(char *out, char *in, char *chain) */
+ /* { */
+ /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
+ /*   char *s, *t; */
+ /*   t=in;s=out; */
+ /*   while ((*in != *chain) && (*in != '\0')){ */
+ /*     *out++ = *in++; */
+ /*   } */
+ /*   /\* *in matches *chain *\/ */
+ /*   while ((*in++ == *chain++) && (*in != '\0')){ */
+ /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   in--; chain--; */
+ /*   while ( (*in != '\0')){ */
+ /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*     *out++ = *in++; */
+ /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
+ /*   } */
+ /*   *out='\0'; */
+ /*   out=s; */
+ /*   return out; */
+ /* } */
+ char *substrchaine(char *out, char *in, char *chain)
+ {
+   /* Substract chain 'chain' from 'in', return and output 'out' */
+   /* in="V1+V1*age+age*age+V2", chain="age*age" */
+   char *strloc;
+   strcpy (out, in);
+   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
+   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
+   if(strloc != NULL){
+     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
+     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
+     /* strcpy (strloc, strloc +strlen(chain));*/
+   }
+   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
+   return out;
+ }
+ 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="abcdef" and alocc="ghi2j".
+      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'
+   /* 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
- Line 738  int nbocc(char *s, char occ)
+ Line 1173  int nbocc(char *s, char occ)
  /*   } */
  /* } */
+ #ifdef _WIN32
+ char * strsep(char **pp, const char *delim)
+ {
+   char *p, *q;
+   if ((p = *pp) == NULL)
+     return 0;
+   if ((q = strpbrk (p, delim)) != NULL)
+   {
+     *pp = q + 1;
+     *q = '\0';
+   }
+   else
+     *pp = 0;
+   return p;
+ }
+ #endif
  /********************** nrerror ********************/
  void nrerror(char error_text[])
- Line 845  double **matrix(long nrl, long nrh, long
+ Line 1298  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 934  char *subdirf3(char fileres[], char *pre
+ Line 1389  char *subdirf3(char fileres[], char *pre
    strcat(tmpout,fileres);
    return tmpout;
  }
+ /*************** function subdirfext ***********/
+ char *subdirfext(char fileres[], char *preop, char *postop)
+ {
+   strcpy(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   return tmpout;
+ }
+ /*************** function subdirfext3 ***********/
+ char *subdirfext3(char fileres[], char *preop, char *postop)
+ {
+   /* Caution optionfilefiname is hidden */
+   strcpy(tmpout,optionfilefiname);
+   strcat(tmpout,"/");
+   strcat(tmpout,preop);
+   strcat(tmpout,fileres);
+   strcat(tmpout,postop);
+   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;
- Line 955  double f1dim(double x)
+ Line 1446  double f1dim(double x)
  /*****************brent *************************/
  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)
  {
+   /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
+    * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
+    * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
+    * the minimum is returned as xmin, and the minimum function value is returned as brent , the
+    * returned function value.
+   */
    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 973  double brent(double ax, double bx, doubl
+ Line 1470  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 1008  double brent(double ax, double bx, doubl
+ Line 1505  double brent(double ax, double bx, doubl
      if (fu <= fx) {
        if (u >= x) a=x; else b=x;
        SHFT(v,w,x,u)
-         SHFT(fv,fw,fx,fu)
+       SHFT(fv,fw,fx,fu)
-         } else {
+     } else {
-           if (u < x) a=u; else b=u;
+       if (u < x) a=u; else b=u;
-           if (fu <= fw || w == x) {
+       if (fu <= fw || w == x) {
-             v=w;
+         v=w;
-             w=u;
+         w=u;
-             fv=fw;
+         fv=fw;
-             fw=fu;
+         fw=fu;
-           } else if (fu <= fv || v == x || v == w) {
+       } else if (fu <= fv || v == x || v == w) {
-             v=u;
+         v=u;
-             fv=fu;
+         fv=fu;
-           }
+       }
-         }
+     }
    }
    nrerror("Too many iterations in brent");
    *xmin=x;
- Line 1031  double brent(double ax, double bx, doubl
+ Line 1528  double brent(double ax, double bx, doubl
  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
              double (*func)(double))
- {
+ { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
+ the downhill direction (defined by the function as evaluated at the initial points) and returns
+ new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
+ values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
+    */
    double ulim,u,r,q, dum;
    double fu;
-   *fa=(*func)(*ax);
+   double scale=10.;
-   *fb=(*func)(*bx);
+   int iterscale=0;
+   *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
+   *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
+   /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
+   /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
+   /*   *bx = *ax - (*ax - *bx)/scale; */
+   /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
+   /* } */
    if (*fb > *fa) {
      SHFT(dum,*ax,*bx,dum)
-       SHFT(dum,*fb,*fa,dum)
+     SHFT(dum,*fb,*fa,dum)
-       }
+   }
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
-   while (*fb > *fc) {
+ #ifdef DEBUG
+   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+ #endif
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
      r=(*bx-*ax)*(*fb-*fc);
      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 abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
-     ulim=(*bx)+GLIMIT*(*cx-*bx);
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-     if ((*bx-u)*(u-*cx) > 0.0) {
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
        fu=(*func)(u);
-     } else if ((*cx-u)*(u-ulim) > 0.0) {
+ #ifdef DEBUG
+       /* f(x)=A(x-u)**2+f(u) */
+       double A, fparabu;
+       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+       fparabu= *fa - A*(*ax-u)*(*ax-u);
+       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       /* And thus,it can be that fu > *fc even if fparabu < *fc */
+       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
+         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
+       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
+ #endif
+ #ifdef MNBRAKORIGINAL
+ #else
+ /*       if (fu > *fc) { */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak4  fu > fc \n"); */
+ /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
+ /* #endif */
+ /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
+ /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } else { /\* end *\/ */
+ /* #ifdef DEBUG */
+ /*       printf("mnbrak3  fu < fc \n"); */
+ /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
+ /* #endif */
+ /*      dum=u; /\* Shifting c and u *\/ */
+ /*      u = *cx; */
+ /*      *cx = dum; */
+ /*      dum = fu; */
+ /*      fu = *fc; */
+ /*      *fc =dum; */
+ /*       } */
+ #ifdef DEBUG
+       printf("mnbrak34  fu < or >= fc \n");
+       fprintf(ficlog, "mnbrak34 fu < fc\n");
+ #endif
+       dum=u; /* Shifting c and u */
+       u = *cx;
+       *cx = dum;
+       dum = fu;
+       fu = *fc;
+       *fc =dum;
+ #endif
+     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
+ #ifdef DEBUG
+       printf("mnbrak2  u after c but before ulim\n");
+       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
+ #endif
        fu=(*func)(u);
        if (fu < *fc) {
+ #ifdef DEBUG
+       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
+       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
+ #endif
          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-           SHFT(*fb,*fc,fu,(*func)(u))
+         SHFT(*fb,*fc,fu,(*func)(u))
-           }
+       }
-     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
+ #ifdef DEBUG
+       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
+       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
+ #endif
        u=ulim;
        fu=(*func)(u);
-     } else {
+     } else { /* u could be left to b (if r > q parabola has a maximum) */
+ #ifdef DEBUG
+       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+ #endif
        u=(*cx)+GOLD*(*cx-*bx);
        fu=(*func)(u);
-     }
+     } /* end tests */
      SHFT(*ax,*bx,*cx,u)
-       SHFT(*fa,*fb,*fc,fu)
+     SHFT(*fa,*fb,*fc,fu)
-       }
+ #ifdef DEBUG
+       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+ #endif
+   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
  }
  /*************** linmin ************************/
+ /* 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 1085  void linmin(double p[], double xi[], int
+ Line 1675  void linmin(double p[], double xi[], int
    int j;
    double xx,xmin,bx,ax;
    double fx,fb,fa;
+ #ifdef LINMINORIGINAL
+ #else
+   double scale=10., axs, xxs; /* Scale added for infinity */
+ #endif
    ncom=n;
    pcom=vector(1,n);
    xicom=vector(1,n);
    nrfunc=func;
    for (j=1;j<=n;j++) {
      pcom[j]=p[j];
-     xicom[j]=xi[j];
+     xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
    }
-   ax=0.0;
-   xx=1.0;
+ #ifdef LINMINORIGINAL
-   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+   xx=1.;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+ #else
+   axs=0.0;
+   xxs=1.;
+   do{
+     xx= xxs;
+ #endif
+     ax=0.;
+     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
+     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
+     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
+     /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
+     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
+     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
+     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
+ #ifdef LINMINORIGINAL
+ #else
+     if (fx != fx){
+         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+         printf("|");
+         fprintf(ficlog,"|");
+ #ifdef DEBUGLINMIN
+         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
+ #endif
+     }
+   }while(fx != fx);
+ #endif
+ #ifdef DEBUGLINMIN
+   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+   fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
+ #endif
+   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
+   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
+   /* fmin = f(p[j] + xmin * xi[j]) */
+   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
+   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
  #ifdef DEBUG
    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  #endif
+ #ifdef DEBUGLINMIN
+   printf("linmin end ");
+   fprintf(ficlog,"linmin end ");
+ #endif
    for (j=1;j<=n;j++) {
+ #ifdef LINMINORIGINAL
      xi[j] *= xmin;
-     p[j] += xi[j];
+ #else
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" before xi[%d]=%12.8f", j,xi[j]);
+ #endif
+     xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
+ #ifdef DEBUGLINMIN
+     if(xxs <1.0)
+       printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
+ #endif
+ #endif
+     p[j] += xi[j]; /* Parameters values are updated accordingly */
    }
+ #ifdef DEBUGLINMIN
+   printf("\n");
+   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
+   for (j=1;j<=n;j++) {
+     printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
+     if(j % ncovmodel == 0){
+       printf("\n");
+       fprintf(ficlog,"\n");
+     }
+   }
+ #else
+ #endif
    free_vector(xicom,1,n);
    free_vector(pcom,1,n);
  }
- char *asc_diff_time(long time_sec, char ascdiff[])
- {
-   long sec_left, days, hours, minutes;
-   days = (time_sec) / (60*60*24);
-   sec_left = (time_sec) % (60*60*24);
-   hours = (sec_left) / (60*60) ;
-   sec_left = (sec_left) %(60*60);
-   minutes = (sec_left) /60;
-   sec_left = (sec_left) % (60);
-   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld 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 1131  void powell(double p[], double **xi, int
+ Line 1787  void powell(double p[], double **xi, int
                double (*func)(double []));
    int i,ibig,j;
    double del,t,*pt,*ptt,*xit;
+   double directest;
    double fp,fptt;
    double *xits;
    int niterf, itmp;
- Line 1141  void powell(double p[], double **xi, int
+ Line 1798  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);
+     fp=(*fret); /* From former iteration or initial value */
      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);
-    for (i=1;i<=n;i++) {
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+ /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
- Line 1159  void powell(double p[], double **xi, int
+ Line 1819  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 (i=1;i<=n;i++) { /* For each direction i */
-       for (j=1;j<=n;j++) xit[j]=xi[j][i];
+       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
        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);
+       printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        fprintf(ficlog,"%d",i);fflush(ficlog);
-       linmin(p,xit,n,fret,func);
+       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-       if (fabs(fptt-(*fret)) > del) {
+                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
+       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
+         /* because that direction will be replaced unless the gain del is small */
+         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
+         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
+         /* with the new direction. */
          del=fabs(fptt-(*fret));
          ibig=i;
        }
- Line 1203  void powell(double p[], double **xi, int
+ Line 1866  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 loop on each direction i */
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
+     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
+     /* New value of last point Pn is not computed, P(n-1) */
+     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
+       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
+       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
+       /* decreased of more than 3.84  */
+       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
+       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
+       /* By adding 10 parameters more the gain should be 18.31 */
+       /* Starting the program with initial values given by a former maximization will simply change */
+       /* the scales of the directions and the directions, because the are reset to canonical directions */
+       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
+       /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
  #ifdef DEBUG
        int k[2],l;
        k[0]=1;
- Line 1240  void powell(double p[], double **xi, int
+ Line 1918  void powell(double p[], double **xi, int
        free_vector(ptt,1,n);
        free_vector(pt,1,n);
        return;
-     }
+     } /* enough precision */
      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
-     for (j=1;j<=n;j++) {
+     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
        pt[j]=p[j];
      }
-     fptt=(*func)(ptt);
+     fptt=(*func)(ptt); /* f_3 */
-     if (fptt < fp) {
+ #ifdef POWELLF1F3
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ #else
-       if (t < 0.0) {
+     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
-         linmin(p,xit,n,fret,func);
+ #endif
+       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
+       /* From x1 (P0) distance of x2 is at h and x3 is 2h */
+       /* Let f"(x2) be the 2nd derivative equal everywhere.  */
+       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
+       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
+       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+ #ifdef NRCORIGINAL
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
+ #else
+       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
+       t= t- del*SQR(fp-fptt);
+ #endif
+       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
+ #ifdef DEBUG
+       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
+       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
+       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
+              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
+       printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+       fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
+ #endif
+ #ifdef POWELLORIGINAL
+       if (t < 0.0) { /* Then we use it for new direction */
+ #else
+       if (directest*t < 0.0) { /* Contradiction between both tests */
+         printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+         fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
+         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
+       }
+       if (directest < 0.0) { /* Then we use it for new direction */
+ #endif
+ #ifdef DEBUGLINMIN
+         printf("Before linmin in direction P%d-P0\n",n);
          for (j=1;j<=n;j++) {
-           xi[j][ibig]=xi[j][n];
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-           xi[j][n]=xit[j];
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
          }
+ #endif
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+ #ifdef DEBUGLINMIN
+         for (j=1;j<=n;j++) {
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           if(j % ncovmodel == 0){
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+ #endif
+         for (j=1;j<=n;j++) {
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
+         }
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          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 1266  void powell(double p[], double **xi, int
+ Line 2004  void powell(double p[], double **xi, int
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
-       }
+       } /* end of t or directest negative */
-     }
+ #ifdef POWELLF1F3
-   }
+ #else
+     } /* end if (fptt < fp)  */
+ #endif
+   } /* loop iteration */
  }
  /**** Prevalence limit (stable or period prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
  {
    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-      matrix by transitions matrix until convergence is reached */
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
+   /* or prevalence in state 1, prevalence in state 2, 0 */
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
+   /* Initial matrix pimij */
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
+   /*  0,                   0                  , 1} */
+   /*
+    * and after some iteration: */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
+   /*  0,                   0                  , 1} */
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
    int i, ii,j,k;
-   double min, max, maxmin, maxmax,sumnew=0.;
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-   double **matprod2();
+   /* double **matprod2(); */ /* test */
    double **out, cov[NCOVMAX+1], **pmij();
    double **newm;
-   double agefin, delaymax=50 ; /* Max number of years to converge */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
+   int ncvloop=0;
+   min=vector(1,nlstate);
+   max=vector(1,nlstate);
+   meandiff=vector(1,nlstate);
    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 */
+   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+     ncvloop++;
      newm=savm;
      /* Covariates have to be included here again */
      cov[2]=agefin;
+     if(nagesqr==1)
+       cov[3]= agefin*agefin;;
      for (k=1; k<=cptcovn;k++) {
-       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(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]]);*/
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-     }
+       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(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++)
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+     for (k=1; k<=cptcovprod;k++) /* Useless */
+       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
      /*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 \n",ij, cov[3]);*/
+     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
-     maxmax=0.;
-     for(j=1;j<=nlstate;j++){
+     for(j=1; j<=nlstate; j++){
-       min=1.;
+       max[j]=0.;
-       max=0.;
+       min[j]=1.;
-       for(i=1; i<=nlstate; i++) {
+     }
-         sumnew=0;
+     for(i=1;i<=nlstate;i++){
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       sumnew=0;
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       for(j=1; j<=nlstate; j++){
          prlim[i][j]= newm[i][j]/(1-sumnew);
-         max=FMAX(max,prlim[i][j]);
+         max[j]=FMAX(max[j],prlim[i][j]);
-         min=FMIN(min,prlim[i][j]);
+         min[j]=FMIN(min[j],prlim[i][j]);
        }
-       maxmin=max-min;
-       maxmax=FMAX(maxmax,maxmin);
      }
+     maxmax=0.;
+     for(j=1; j<=nlstate; j++){
+       meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
+       maxmax=FMAX(maxmax,meandiff[j]);
+       /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
+     } /* j loop */
+     *ncvyear= (int)age- (int)agefin;
+     /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
      if(maxmax < ftolpl){
+       /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+       free_vector(min,1,nlstate);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
+   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+ Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
+   free_vector(min,1,nlstate);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return prlim; /* should not reach here */
  }
  /*************** transition probabilities ***************/
- Line 1352  double **pmij(double **ps, double *cov,
+ Line 2146  double **pmij(double **ps, double *cov,
    */
    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++){
- Line 1401  double **pmij(double **ps, double *cov,
+ Line 2195  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 1417  double **pmij(double **ps, double *cov,
+ Line 2211  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 1453  double ***hpxij(double ***po, int nhstep
+ Line 2248  double ***hpxij(double ***po, int nhstep
    int i, j, d, h, k;
    double **out, cov[NCOVMAX+1];
    double **newm;
+   double agexact;
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
- Line 1466  double ***hpxij(double ***po, int nhstep
+ Line 2262  double ***hpxij(double ***po, int nhstep
        newm=savm;
        /* Covariates have to be included here again */
        cov[1]=1.;
-       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+       cov[2]=agexact;
+       if(nagesqr==1)
+         cov[3]= agexact*agexact;
        for (k=1; k<=cptcovn;k++)
-         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-       for (k=1; k<=cptcovage;k++)
+         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
-         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
-       for (k=1; k<=cptcovprod;k++)
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
- Line 1493  double ***hpxij(double ***po, int nhstep
+ Line 2296  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)
- Line 1505  double func( double *x)
+ Line 2327  double func( double *x)
    int s1, s2;
    double bbh, survp;
    long ipmx;
+   double agexact;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    /*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.;
- Line 1522  double func( double *x)
+ Line 2348  double func( double *x)
           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++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+           cov[2+nagesqr+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 */
- Line 1534  double func( double *x)
+ Line 2362  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* 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 1588  double func( double *x)
+ Line 2419  double func( double *x)
          which slows down the processing. The difference can be up to 10%
          lower mortality.
            */
-           lli=log(out[s1][s2] - savm[s1][s2]);
+         /* If, at the beginning of the maximization mostly, the
+            cumulative probability or probability to be dead is
+            constant (ie = 1) over time d, the difference is equal to
+.  out[s1][3] = savm[s1][3]: probability, being at state
+            s1 at precedent wave, to be dead a month before current
+            wave is equal to probability, being at state s1 at
+            precedent wave, to be dead at mont of the current
+            wave. Then the observed probability (that this person died)
+            is null according to current estimated parameter. In fact,
+            it should be very low but not zero otherwise the log go to
+            infinity.
+         */
+ /* #ifdef INFINITYORIGINAL */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #else */
+ /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
+ /*          lli=log(mytinydouble); */
+ /*        else */
+ /*          lli=log(out[s1][s2] - savm[s1][s2]); */
+ /* #endif */
+             lli=log(out[s1][s2] - savm[s1][s2]);
          } else if  (s2==-2) {
            for (j=1,survp=0. ; j<=nlstate; j++)
- Line 1620  double func( double *x)
+ Line 2470  double func( double *x)
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+         /* if (lli < log(mytinydouble)){ */
+         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
+         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
+         /* } */
        } /* end of wave */
      } /* end of individual */
    }  else if(mle==2){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1633  double func( double *x)
+ Line 2487  double func( double *x)
            }
          for(d=0; d<=dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1654  double func( double *x)
+ Line 2511  double func( double *x)
      } /* end of individual */
    }  else if(mle==3){  /* exponential inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1663  double func( double *x)
+ Line 2520  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 1684  double func( double *x)
+ Line 2544  double func( double *x)
      } /* end of individual */
    }else if (mle==4){  /* ml=4 no inter-extrapolation */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1693  double func( double *x)
+ Line 2553  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 1719  double func( double *x)
+ Line 2582  double func( double *x)
      } /* end of individual */
    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 1728  double func( double *x)
+ Line 2591  double func( double *x)
            }
          for(d=0; d<dh[mi][i]; d++){
            newm=savm;
-           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           cov[2]=agexact;
+           if(nagesqr==1)
+             cov[3]= agexact*agexact;
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- Line 1766  double funcone( double *x)
+ Line 2632  double funcone( double *x)
    double llt;
    int s1, s2;
    double bbh, survp;
+   double agexact;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 1777  double funcone( double *x)
+ Line 2644  double funcone( double *x)
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
      for(mi=1; mi<= wav[i]-1; mi++){
        for (ii=1;ii<=nlstate+ndeath;ii++)
          for (j=1;j<=nlstate+ndeath;j++){
- Line 1786  double funcone( double *x)
+ Line 2653  double funcone( double *x)
          }
        for(d=0; d<dh[mi][i]; d++){
          newm=savm;
-         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         cov[2]=agexact;
+         if(nagesqr==1)
+           cov[3]= agexact*agexact;
          for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
          }
+         /* 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 1825  double funcone( double *x)
+ Line 2699  double funcone( double *x)
        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]); */
        if(globpr){
-         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+         fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
   %11.6f %11.6f %11.6f ", \
-                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
+                 num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
            llt +=ll[k]*gipmx/gsw;
- Line 1859  void likelione(FILE *ficres,double p[],
+ Line 2733  void likelione(FILE *ficres,double p[],
    int k;
    if(*globpri !=0){ /* Just counts and sums, no printings */
-     strcpy(fileresilk,"ilk");
+     strcpy(fileresilk,"ILK_");
-     strcat(fileresilk,fileres);
+     strcat(fileresilk,fileresu);
      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresilk);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      }
-     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
+     fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
-     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
+     fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
      for(k=1; k<=nlstate; k++)
        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
- Line 1876  void likelione(FILE *ficres,double p[],
+ Line 2750  void likelione(FILE *ficres,double p[],
    *fretone=(*funcone)(p);
    if(*globpri !=0){
      fclose(ficresilk);
-     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     if (mle ==0)
-     fflush(fichtm);
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
-   }
+     else if(mle >=1)
+       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
+     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     for (k=1; k<= nlstate ; k++) {
+       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
+ <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
+     }
+     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
+ <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
+ <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
+     fflush(fichtm);
+   }
    return;
  }
- Line 1887  void likelione(FILE *ficres,double p[],
+ Line 2775  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++)
        xi[i][j]=(i==j ? 1.0 : 0.0);
    printf("Powell\n");  fprintf(ficlog,"Powell\n");
-   strcpy(filerespow,"pow");
+   strcpy(filerespow,"POW_");
    strcat(filerespow,fileres);
    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", filerespow);
- Line 1908  void mlikeli(FILE *ficres,double p[], in
+ Line 2808  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,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  }
  /**** Computes Hessian and covariance matrix ***/
- void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+ void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  {
    double  **a,**y,*x,pd;
-   double **hess;
+   /* 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);
-   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
+   double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
    void lubksb(double **a, int npar, int *indx, double b[]) ;
    void ludcmp(double **a, int npar, int *indx, double *d) ;
    double gompertz(double p[]);
-   hess=matrix(1,npar,1,npar);
+   /* hess=matrix(1,npar,1,npar); */
    printf("\nCalculation of the hessian matrix. Wait...\n");
    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    for (i=1;i<=npar;i++){
-     printf("%d",i);fflush(stdout);
+     printf("%d-",i);fflush(stdout);
-     fprintf(ficlog,"%d",i);fflush(ficlog);
+     fprintf(ficlog,"%d-",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
- Line 1949  void hesscov(double **matcov, double p[]
+ Line 2876  void hesscov(double **matcov, double p[]
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++)  {
        if (j>i) {
-         printf(".%d%d",i,j);fflush(stdout);
+         printf(".%d-%d",i,j);fflush(stdout);
-         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+         fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
-         hess[i][j]=hessij(p,delti,i,j,func,npar);
+         hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
          hess[j][i]=hess[i][j];
          /*printf(" %lf ",hess[i][j]);*/
- Line 1985  void hesscov(double **matcov, double p[]
+ Line 2912  void hesscov(double **matcov, double p[]
    fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
-       printf("%.3e ",hess[i][j]);
+       printf("%.6e ",hess[i][j]);
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.6e ",hess[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
+   /*   for (j=1;j<=npar;j++) {  */
+   /*     printf("%.6e ",matcov[i][j]); */
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
    /* Recompute Inverse */
-   for (i=1;i<=npar;i++)
+   /* for (i=1;i<=npar;i++) */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   ludcmp(a,npar,indx,&pd);
+   /* ludcmp(a,npar,indx,&pd); */
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
+   /*   lubksb(a,npar,indx,x); */
+   /*   for (i=1;i<=npar;i++){  */
+   /*     y[i][j]=x[i]; */
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
    for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
-     x[j]=1;
-     lubksb(a,npar,indx,x);
      for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+       printf("%.2f ",y[i][j]);
-       printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
-   */
+ #endif
    free_matrix(a,1,npar,1,npar);
    free_matrix(y,1,npar,1,npar);
    free_vector(x,1,npar);
    free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
  }
  /*************** hessian matrix ****************/
  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
    int i;
    int l=1, lmax=20;
-   double k1,k2;
+   double k1,k2, res, fx;
    double p2[MAXPARM+1]; /* identical to x */
-   double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
    int k=0,kmax=10;
    double l1;
    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 */
+       res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
- #ifdef DEBUGHESS
+ #ifdef DEBUGHESSII
        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 2058  double hessii(double x[], double delta,
+ Line 3010  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;
        }
-     }
+     } /* End loop k */
    }
    delti[theta]=delts;
    return res;
  }
- double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
+ double hessij( double x[], double **hess, 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[MAXPARM+1];
-   int k;
+   int k, kmax=1;
+   double v1, v2, cv12, lc1, lc2;
+   int firstime=0;
    fx=func(x);
-   for (k=1; k<=2; k++) {
+   for (k=1; k<=kmax; k=k+10) {
      for (i=1;i<=npar;i++) p2[i]=x[i];
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k1=func(p2)-fx;
-     p2[thetai]=x[thetai]+delti[thetai]/k;
+     p2[thetai]=x[thetai]+delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k2=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]+delti[thetaj]*k;
      k3=func(p2)-fx;
-     p2[thetai]=x[thetai]-delti[thetai]/k;
+     p2[thetai]=x[thetai]-delti[thetai]*k;
-     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+     p2[thetaj]=x[thetaj]-delti[thetaj]*k;
      k4=func(p2)-fx;
-     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
- #ifdef DEBUG
+     if(k1*k2*k3*k4 <0.){
-     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       firstime=1;
-     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       kmax=kmax+10;
+     }
+     if(kmax >=10 || firstime ==1){
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     }
+ #ifdef DEBUGHESSIJ
+     v1=hess[thetai][thetai];
+     v2=hess[thetaj][thetaj];
+     cv12=res;
+     /* Computing eigen value of Hessian matrix */
+     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) ){
+       printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
+       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+     }
  #endif
    }
    return res;
  }
+     /* Not done yet: Was supposed to fix if not exactly at the maximum */
+ /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
+ /* { */
+ /*   int i; */
+ /*   int l=1, lmax=20; */
+ /*   double k1,k2,k3,k4,res,fx; */
+ /*   double p2[MAXPARM+1]; */
+ /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
+ /*   int k=0,kmax=10; */
+ /*   double l1; */
+ /*   fx=func(x); */
+ /*   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 = delti*(l1*k); */
+ /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k1=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k2=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
+ /*       k3=func(p2)-fx; */
+ /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
+ /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
+ /*       k4=func(p2)-fx; */
+ /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
+ /* #ifdef DEBUGHESSIJ */
+ /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+ /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
+ /* #endif */
+ /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
+ /*      k=kmax; */
+ /*       } */
+ /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
+ /*      k=kmax; l=lmax*10; */
+ /*       } */
+ /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
+ /*      delts=delt; */
+ /*       } */
+ /*     } /\* End loop k *\/ */
+ /*   } */
+ /*   delti[theta]=delts; */
+ /*   return res;  */
+ /* } */
  /************** Inverse of matrix **************/
  void ludcmp(double **a, int n, int *indx, double *d)
  {
- Line 2181  void lubksb(double **a, int n, int *indx
+ Line 3210  void lubksb(double **a, int n, int *indx
  void pstamp(FILE *fichier)
  {
-   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
  /************ Frequencies ********************/
  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
  {  /* Some frequencies */
-   int i, m, jk, k1,i1, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j;
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   char fileresp[FILENAMELENGTH];
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH];
    pp=vector(1,nlstate);
    prop=matrix(1,nlstate,iagemin,iagemax+3);
-   strcpy(fileresp,"p");
+   strcpy(fileresp,"P_");
-   strcat(fileresp,fileres);
+   strcat(fileresp,fileresu);
+   /*strcat(fileresphtm,fileresu);*/
    if((ficresp=fopen(fileresp,"w"))==NULL) {
      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
+   printf("Problem with prevalence resultfile: %s\n", fileresp);
+   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
+   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
+     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   }
    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
- Line 2212  void  freqsummary(char fileres[], int ia
+ Line 3250  void  freqsummary(char fileres[], int ia
    first=1;
-   for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
+   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
-     for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
+   /*  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++)
- Line 2230  void  freqsummary(char fileres[], int ia
+ Line 3269  void  freqsummary(char fileres[], int ia
        k2cpt=0;
        for (i=1; i<=imx; i++) {
          bool=1;
-         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+         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]][codtabm(j1,z1)]){
+                 /* 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, i1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
-                 bool,i,z1, i1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);
+                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
              }
-         }
+         } /* cptcovn > 0 */
          if (bool==1){
            for(m=firstpass; m<=lastpass; m++){
- Line 2247  void  freqsummary(char fileres[], int ia
+ Line 3287  void  freqsummary(char fileres[], int ia
              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+               if (s[m][i]>0 && s[m][i]<=nlstate)
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
                if (m<lastpass) {
                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                }
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
                  dateintsum=dateintsum+k2;
                  k2cpt++;
+                 /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                }
                /*}*/
-           }
+           } /* end m */
-         }
+         } /* end bool */
-       }
+       } /* end i = 1 to imx */
        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        pstamp(ficresp);
        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         fprintf(ficresphtm, "\n<h3>********** Variable ");
-         fprintf(ficresp, "**********\n#");
+         for (z1=1; z1<=cptcoveff; z1++){
+           fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         }
+           fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtm, "**********</h3>\n#");
          fprintf(ficlog, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficlog, "**********\n#");
        }
-       for(i=1; i<=nlstate;i++)
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\"><th></th>");
+       for(i=1; i<=nlstate;i++) {
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
+       }
        fprintf(ficresp, "\n");
+       fprintf(ficresphtm, "\n");
        for(i=iagemin; i <= iagemax+3; i++){
+         fprintf(ficresphtm,"<tr>");
          if(i==iagemax+3){
            fprintf(ficlog,"Total");
          }else{
- Line 2326  void  freqsummary(char fileres[], int ia
+ Line 3378  void  freqsummary(char fileres[], int ia
            if( i <= iagemax){
              if(pos>=1.e-5){
                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                /*probs[i][jk][j1]= pp[jk]/pos;*/
                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
              }
-             else
+             else{
                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
+             }
            }
          }
- Line 2341  void  freqsummary(char fileres[], int ia
+ Line 3396  void  freqsummary(char fileres[], int ia
                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
              }
-         if(i <= iagemax)
+         if(i <= iagemax){
            fprintf(ficresp,"\n");
+           fprintf(ficresphtm,"</tr>\n");
+         }
          if(first==1)
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
-       }
+       } /* end loop i */
-     }
+       fprintf(ficresphtm,"</table>\n");
-   }
+       /*}*/
+   } /* end j1 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
+   fclose(ficresphtm);
    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    free_vector(pp,1,nlstate);
    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
- Line 2366  void prevalence(double ***probs, double
+ Line 3425  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, k1, i1, j1, bool, z1,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 2380  void prevalence(double ***probs, double
+ Line 3440  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 2395  void prevalence(double ***probs, double
+ Line 3456  void prevalence(double ***probs, double
          bool=1;
          if  (cptcovn>0) {
            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]][codtabm(j1,z1)])
                bool=0;
          }
          if (bool==1) {
- Line 2415  void prevalence(double ***probs, double
+ Line 3476  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 2455  void  concatwav(int wav[], int **dh, int
+ Line 3519  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 2580  void  concatwav(int wav[], int **dh, int
+ Line 3644  void  concatwav(int wav[], int **dh, int
   }
  /*********** 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 */
    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-   /* Boring subroutine which should only output nbcode[Tvar[j]][k]
+    * Boring subroutine which should only output nbcode[Tvar[j]][k]
-   /* nbcode[Tvar[j][1]=
+    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
+    * nbcode[Tvar[j]][1]=
    */
-   int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+   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++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
-   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
+   /* Loop on covariates without age and products */
-     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
+     for (k=-1; k < maxncov; k++) Ndum[k]=0;
+     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
                                 modality of this covariate Vj*/
-       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
+       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 > modmaxcovj) modmaxcovj=ij;
        /* getting the maximum value of the modality of the covariate
           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           female is 1, then modmaxcovj=1.*/
-     }
+     } /* end for loop on individuals i */
+     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+     cptcode=modmaxcovj;
      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-     for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
+    /*for (i=0; i<=cptcode; i++) {*/
-       if( Ndum[i] != 0 )
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-         ncodemax[j]++;
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-       /* Number of modalities of the j th covariate. In fact
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-          ncodemax[j]=2 (dichotom. variables only) but it could be more for
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
-          historical reasons */
+         if( k != -1){
+           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered excluding
+                              undefined. Usually 2: 0 and 1. */
+         }
+         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
+                              covariate for which somebody answered including
+                              undefined. Usually 3: -1, 0 and 1. */
+       }
+       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
+          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 */
-     ij=1;
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
-       for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
+        modmincovj=3; modmaxcovj = 7;
-         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-                                      k is a modality. If we have model=V1+V1*sex
+        defining two dummy variables: variables V1_1 and V1_2.
-                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+        nbcode[Tvar[j]][ij]=k;
-           ij++;
+        nbcode[Tvar[j]][1]=0;
-         }
+        nbcode[Tvar[j]][2]=1;
-         if (ij > ncodemax[j]) break;
+        nbcode[Tvar[j]][3]=2;
-       }  /* end of loop on */
+        To be continued (not working yet).
-     } /* end of loop on modality */
+     */
+     ij=0; /* ij is similar to i but can jump over null modalities */
+     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+           break;
+         }
+         ij++;
+         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
+         cptcode = ij; /* New max modality for covar j */
+     } /* end of loop on modality i=-1 to 1 or more */
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+     /*  /\*recode from 0 *\/ */
+     /*                               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; */
+     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+     /*  } */
+     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+     /*  if (ij > ncodemax[j]) { */
+     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+     /*    break; */
+     /*  } */
+     /*   }  /\* end of loop on modality k *\/ */
    } /* 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++) { /* -2, cste and age */
+   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
-    Ndum[ij]++;
+    Ndum[ij]++; /* Might be supersed V1 + V1*age */
   }
-  ij=1;
+  ij=0;
-  for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+  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 */
       ij++;
+      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+      Tvaraff[ij]=i; /*For printing (unclear) */
+    }else{
+        /* Tvaraff[ij]=0; */
     }
   }
-  ij--;
+  /* ij--; */
   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 2970  void cvevsij(double ***eij, double x[],
+ Line 4094  void cvevsij(double ***eij, double x[],
  }
  /************ Variance ******************/
- void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
  {
    /* 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 2996  void varevsij(char optionfilefiname[], d
+ Line 4123  void varevsij(char optionfilefiname[], d
    if(popbased==1){
      if(mobilav!=0)
-       strcpy(digitp,"-populbased-mobilav-");
+       strcpy(digitp,"-POPULBASED-MOBILAV_");
-     else strcpy(digitp,"-populbased-nomobil-");
+     else strcpy(digitp,"-POPULBASED-NOMOBIL_");
    }
    else
-     strcpy(digitp,"-stablbased-");
+     strcpy(digitp,"-STABLBASED_");
    if (mobilav!=0) {
      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- Line 3010  void varevsij(char optionfilefiname[], d
+ Line 4137  void varevsij(char optionfilefiname[], d
      }
    }
-   strcpy(fileresprobmorprev,"prmorprev");
+   strcpy(fileresprobmorprev,"PRMORPREV-");
    sprintf(digit,"%-d",ij);
    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileres);
+   strcat(fileresprobmorprev,fileresu);
    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprobmorprev);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    }
    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
- Line 3032  void varevsij(char optionfilefiname[], d
+ Line 4158  void varevsij(char optionfilefiname[], d
        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    }
    fprintf(ficresprobmorprev,"\n");
    fprintf(ficgp,"\n# Routine varevsij");
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+   fprintf(ficgp,"\nunset title \n");
+ /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  /*   } */
- Line 3068  void varevsij(char optionfilefiname[], d
+ Line 4196  void varevsij(char optionfilefiname[], d
    /* For example we decided to compute the life expectancy with the smallest unit */
    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
       nhstepm is the number of hstepm from age to agelim
-      nstepm is the number of stepm from age to agelin.
+      nstepm is the number of stepm from age to agelim.
-      Look at function hpijx to understand why (it is linked to memory size questions) */
+      Look at function hpijx to understand why because of memory size limitations,
-   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+      we decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
       means that if the survival funtion is printed every two years of age and if
       you sum them up and add 1 year (area under the trapezoids) you won't get the same
- Line 3091  void varevsij(char optionfilefiname[], d
+ Line 4219  void varevsij(char optionfilefiname[], d
        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
        if (popbased==1) {
          if(mobilav ==0){
- Line 3104  void varevsij(char optionfilefiname[], d
+ Line 4232  void varevsij(char optionfilefiname[], d
          }
        }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
        for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }
        }
-       /* This for computing probability of death (h=1 means
+       /* Next for computing probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)
           as a weighted average of prlim.
        */
- Line 3122  void varevsij(char optionfilefiname[], d
+ Line 4251  void varevsij(char optionfilefiname[], d
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
        if (popbased==1) {
          if(mobilav ==0){
- Line 3135  void varevsij(char optionfilefiname[], d
+ Line 4264  void varevsij(char optionfilefiname[], d
          }
        }
+       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
- Line 3197  void varevsij(char optionfilefiname[], d
+ Line 4328  void varevsij(char optionfilefiname[], d
          varppt[j][i]=doldmp[j][i];
      /* end ppptj */
      /*  x centered again */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
      if (popbased==1) {
        if(mobilav ==0){
- Line 3214  void varevsij(char optionfilefiname[], d
+ Line 4345  void varevsij(char optionfilefiname[], d
         computed over hstepm (estepm) matrices product = hstepm*stepm months)
         as a weighted average of prlim.
      */
+     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
      for(j=nlstate+1;j<=nlstate+ndeath;j++){
        for(i=1,gmp[j]=0.;i<= nlstate; i++)
          gmp[j] += prlim[i][i]*p3mat[i][j][1];
- Line 3245  void varevsij(char optionfilefiname[], d
+ Line 4377  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,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
+   /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
+   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+   fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
  /*   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 lt 2 ",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 lt 3 ",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 lt 3 ",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. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
  */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
+ /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,nlstate);
- Line 3274  void varevsij(char optionfilefiname[], d
+ Line 4408  void varevsij(char optionfilefiname[], d
  }  /* end varevsij */
  /************ Variance of prevlim ******************/
- void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
+  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
  {
-   /* Variance of prevalence limit */
+   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  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;
+   double **mgm, **mgp;
    double age,agelim;
    int theta;
- Line 3307  void varprevlim(char fileres[], double *
+ Line 4441  void varprevlim(char fileres[], double *
      if (stepm >= YEARM) hstepm=1;
      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      gradg=matrix(1,npar,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
      gp=vector(1,nlstate);
      gm=vector(1,nlstate);
- Line 3314  void varprevlim(char fileres[], double *
+ Line 4450  void varprevlim(char fileres[], double *
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       for(i=1;i<=nlstate;i++)
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
+         mgp[theta][i] = prlim[i][i];
+       }
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-       for(i=1;i<=nlstate;i++)
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       else
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
+         mgm[theta][i] = prlim[i][i];
+       }
        for(i=1;i<=nlstate;i++)
          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
      } /* End theta */
      trgradg =matrix(1,nlstate,1,npar);
- Line 3333  void varprevlim(char fileres[], double *
+ Line 4478  void varprevlim(char fileres[], double *
      for(j=1; j<=nlstate;j++)
        for(theta=1; theta <=npar; theta++)
          trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     }else{
      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     }
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
- Line 3347  void varprevlim(char fileres[], double *
+ Line 4515  void varprevlim(char fileres[], double *
      fprintf(ficresvpl,"\n");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
      free_matrix(gradg,1,npar,1,nlstate);
      free_matrix(trgradg,1,nlstate,1,npar);
    } /* End age */
- Line 3360  void varprevlim(char fileres[], double *
+ Line 4530  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");
+   strcpy(fileresprob,"PROB_");
    strcat(fileresprob,fileres);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
    }
-   strcpy(fileresprobcov,"probcov");
+   strcpy(fileresprobcov,"PROBCOV_");
-   strcat(fileresprobcov,fileres);
+   strcat(fileresprobcov,fileresu);
    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprobcov);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    }
-   strcpy(fileresprobcor,"probcor");
+   strcpy(fileresprobcor,"PROBCOR_");
-   strcat(fileresprobcor,fileres);
+   strcat(fileresprobcor,fileresu);
    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprobcor);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- Line 3434  void varprob(char optionfilefiname[], do
+ Line 4603  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
+   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
-   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
+   fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
-   file %s<br>\n",optionfilehtmcov);
+   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
-   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
  and drawn. It helps understanding how is the covariance between two incidences.\
   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
- Line 3449  standard deviations wide on each axis. <
+ Line 4617  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]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprob, "**********\n#\n");
          fprintf(ficresprobcov, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprobcov, "**********\n#\n");
          fprintf(ficgp, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficgp, "**********\n#\n");
          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
          fprintf(ficresprobcor, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          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;
+         if(nagesqr==1)
+           cov[3]= age*age;
          for (k=1; k<=cptcovn;k++) {
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
+                                                          * 1  1 1 1 1
+                                                          * 2  2 1 1 1
+                                                          * 3  1 2 1 1
+                                                          */
+           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,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]]];
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-         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 3527  To be simple, these graphs help to under
+ Line 4705  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 3564  To be simple, these graphs help to under
+ Line 4738  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,"\nunset parametric;unset label");
- Line 3587  To be simple, these graphs help to under
+ Line 4766  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 3609  To be simple, these graphs help to under
+ Line 4788  To be simple, these graphs help to under
                    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) ){
-                     printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                     if(first2==1){
-                     fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
+                       first1=0;
-                     lc1=fabs(lc1);
+                     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);
-                     lc2=fabs(lc2);
+                     }
+                     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 */
- Line 3632  To be simple, these graphs help to under
+ Line 4814  To be simple, these graphs help to under
                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                    if(first==1){
                      first=0;
+                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                      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 svg size 640, 480");
                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+ %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
- Line 3659  To be simple, these graphs help to under
+ Line 4842  To be simple, these graphs help to under
                    }/* if first */
                  } /* age mod 5 */
                } /* end loop age */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* 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 3681  To be simple, these graphs help to under
+ Line 4864  To be simple, these graphs help to under
  /******************* Printing html file ***********/
- void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int estepm ,\
+                   int popforecast, int prevfcast, int estepm ,          \
-                   double jprev1, double mprev1,double anprev1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, \
-                   double jprev2, double mprev2,double anprev2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2){
    int jj1, k1, i1, cpt;
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
-  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
+  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
+    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     fprintf(fichtm,"\
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
-            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
+            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
     fprintf(fichtm,"\
   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
+            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
     fprintf(fichtm,"\
-  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
+  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
     <a href=\"%s\">%s</a> <br>\n",
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
-    fprintf(fichtm,"\
+    if(prevfcast==1){
-  - Population projections by age and states: \
+      fprintf(fichtm,"\
-    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+  - Prevalence projections by age and states:                            \
+    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
+    }
  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;
   for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        for (cpt=1; cpt<=cptcoveff;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
+        }
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
+      /* aij, bij */
+      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+ <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
       /* 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>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
- <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ <img src=\"%s_%d-2.svg\">",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\
+      fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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,\
- <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
-        /* Period (stable) prevalence in each health state */
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
-        for(cpt=1; cpt<nlstate;cpt++){
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
-          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+      /* Survival functions (period) in state j */
- <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+      for(cpt=1; cpt<=nlstate;cpt++){
-        }
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+      }
+      /* State specific survival functions (period) */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
+  Or probability to survive in various states (1 to %d) being in state %d at different ages.\
+  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+      }
+      /* Period (stable) prevalence in each health state */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- 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.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+      }
+     if(prevfcast==1){
+       /* Projection of prevalence up to period (stable) prevalence in each health state */
+       for(cpt=1; cpt<=nlstate;cpt++){
+         fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %f to %f) up 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.svg\">%s%d_%d.svg</a><br> \
+ <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),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) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</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.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
       }
-    } /* end i1 */
+    /* } /\* end i1 *\/ */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
   fprintf(fichtm,"\
  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
-  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
+  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
+ But because parameters are usually highly correlated (a higher incidence of disability \
+ and a higher incidence of recovery can give very close observed transition) it might \
+ be very useful to look not only at linear confidence intervals estimated from the \
+ variances but at the covariance matrix. And instead of looking at the estimated coefficients \
+ (parameters) of the logistic regression, it might be more meaningful to visualize the \
+ covariance matrix of the one-step probabilities. \
+ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
+          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
   fprintf(fichtm,"\
   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
+          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   fprintf(fichtm,"\
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
+          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
   fprintf(fichtm,"\
   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
     <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
   fprintf(fichtm,"\
   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
     <a href=\"%s\">%s</a> <br>\n</li>",
-            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
   fprintf(fichtm,"\
   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
-          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
+          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
   fprintf(fichtm,"\
   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
-          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
+          estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
   fprintf(fichtm,"\
   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
+          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 3785  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 5004  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;
   for(k1=1; k1<=m;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         for (cpt=1; cpt<=cptcoveff;cpt++)
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       }
       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): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
- <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+ <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,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) \
  true period expectancies (those weighted with period prevalences are also\
   drawn in addition to the population based expectancies computed using\
-  observed and cahotic prevalences: %s%d.png<br>\
+  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg<br>\
- <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
+ <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
-    } /* end i1 */
+    /* } /\* end i1 *\/ */
   }/* End k1 */
   fprintf(fichtm,"</ul>");
   fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+     void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int lv=0, vlv=0, kl=0;
    int ng=0;
+   int vpopbased;
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 3831  void printinggnuplot(char fileres[], cha
+ Line 5052  void printinggnuplot(char fileres[], cha
      /*#endif */
    m=pow(2,cptcoveff);
+   /* Contribution to likelihood */
+   /* Plot the probability implied in the likelihood */
+     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
+     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+ /* nice for mle=4 plot by number of matrix products.
+    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
+ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
+     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
+     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+     for (i=1; i<= nlstate ; i ++) {
+       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
+       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
+       fprintf(ficgp,"  u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+       for (j=2; j<= nlstate+ndeath ; j ++) {
+         fprintf(ficgp,",\\\n \"\" u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
+       }
+       fprintf(ficgp,";\nset out; unset ylabel;\n");
+     }
+     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+     fprintf(ficgp,"\nset out;unset log\n");
+     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
   /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-    for (k1=1; k1<= m ; k1 ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
-      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+      fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \n\
  set ylabel \"Probability\" \n\
- set ter png small\n\
+ set ter svg size 640, 480\n\
- set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"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 lt 1,\"%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(fileresu,"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 lt 2,\"%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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else fprintf(ficgp," %%*lf (%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",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(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-    }
+      fprintf(ficgp,"\nset out \n");
-   }
+     } /* k1 */
+   } /* cpt */
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-     for (i=1; i<= nlstate+1 ; i ++) {
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       k=2*i;
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       for (j=1; j<= nlstate+1 ; j ++) {
+         vlv= nbcode[Tvaraff[lv]][lv];
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp," V%d=%d ",k,vlv);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       }
-       }
+       fprintf(ficgp,"\n#\n");
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       for (j=1; j<= nlstate+1 ; j ++) {
+       if(vpopbased==0)
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+       else
-       }
+         fprintf(ficgp,"\nreplot ");
-       fprintf(ficgp,"\" t\"\" w l lt 1,");
+       for (i=1; i<= nlstate+1 ; i ++) {
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+         k=2*i;
-       for (j=1; j<= nlstate+1 ; j ++) {
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+         for (j=1; j<= nlstate+1 ; j ++) {
-         else fprintf(ficgp," \%%*lf (\%%*lf)");
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-       }
+           else fprintf(ficgp," %%*lf (%%*lf)");
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
+         }
-       else fprintf(ficgp,"\" t\"\" w l lt 1,");
+         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-     }
+         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-   }
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"\" w l lt 0,");
+         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+       } /* state */
+     } /* vpopbased */
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+   } /* k1 */
    /*3eme*/
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
+       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
+       fprintf(ficgp,"\n#\n");
        /*       k=2+nlstate*(2*cpt-2); */
        k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-       fprintf(ficgp,"set ter png small\n\
+       fprintf(ficgp,"set ter svg size 640, 480\n\
- set size 0.65,0.65\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- Line 3911  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 5198  plot [%.f:%.f] \"%s\" every :::%d::%d u
        */
        for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
        }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
+       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
      }
    }
-   /* CV preval stable (period) */
+   /* Survival functions (period) from state i in state j by initial state i */
-   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 */
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\n\
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3;
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+       for (i=1; i<= nlstate ; i ++){
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         if(i==1)
- set ter png small\nset size 0.65,0.65\n\
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate+ndeath ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+   /* Survival functions (period) from state i in state j by final state j */
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\n\
  unset log y\n\
- plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3;
-       for (i=1; i< nlstate ; i ++)
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-         fprintf(ficgp,"+$%d",k+i+1);
+         if(j==1)
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
-       l=3+(nlstate+ndeath)*cpt;
+           fprintf(ficgp,", '' ");
-       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
+         l=(nlstate+ndeath)*(cpt-1) +j;
-       for (i=1; i< nlstate ; i ++) {
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-         l=3+(nlstate+ndeath)*cpt;
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
-         fprintf(ficgp,"+$%d",l+i+1);
+         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+       } /* nlstate */
+       fprintf(ficgp,", '' ");
+       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+         l=(nlstate+ndeath)*(cpt-1) +j;
+         if(j < nlstate)
+           fprintf(ficgp,"$%d +",k+l);
+         else
+           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+       }
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+   /* CV preval stable (period) for each covariate */
+   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
        }
-       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+       fprintf(ficgp,"\n#\n");
-     }
-   }
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\n\
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+       k=3; /* Offset */
+       for (i=1; i<= nlstate ; i ++){
+         if(i==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate ; j ++)
+           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+       } /* nlstate */
+       fprintf(ficgp,"\nset out\n");
+     } /* end cpt state*/
+   } /* end covariate */
+   if(prevfcast==1){
+   /* Projection from cross-sectional to stable (period) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[lv]][lv];
+           fprintf(ficgp," V%d=%d ",k,vlv);
+         }
+         fprintf(ficgp,"\n#\n");
+         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\n\
+ unset log y\n\
+ plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             fprintf(ficgp," u 2:("); /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             if(i==nlstate+1)
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
++(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
++(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+           }else{
+             fprintf(ficgp,"u 6:(("); /* Age is in 6 */
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             kl=0;
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate  */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               vlv= nbcode[Tvaraff[lv]][lv];
+               kl++;
+               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+               if(k==cptcoveff)
+                 if(i==nlstate+1)
+                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
++(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                 else
+                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
++(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+               else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevfcast */
    /* proba elementaires */
+   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
+     fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) {
+         fprintf(ficgp,"#   current state %d\n",k);
          for(j=1; j <=ncovmodel; j++){
-           fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
            jk++;
-           fprintf(ficgp,"\n");
          }
+         fprintf(ficgp,"\n");
        }
      }
     }
+   fprintf(ficgp,"##############\n#\n");
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   /*goto avoid;*/
+   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
+   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
+   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
+   fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
+   fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+   fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
+   fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
+   fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
+   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
+   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
+   fprintf(ficgp,"#\n");
+    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
+      fprintf(ficgp,"# ng=%d\n",ng);
+      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
       for(jk=1; jk <=m; jk++) {
-        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+        fprintf(ficgp,"#    jk=%d\n",jk);
-        if (ng==2)
+        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+        fprintf(ficgp,"\nset ter svg size 640, 480 ");
+        if (ng==1){
+          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
+          fprintf(ficgp,"\nunset log y");
+        }else if (ng==2){
+          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
+          fprintf(ficgp,"\nset log y");
+        }else if (ng==3){
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-        else
+          fprintf(ficgp,"\nset log y");
-          fprintf(ficgp,"\nset title \"Probability\"\n");
+        }else
-        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+          fprintf(ficgp,"\nunset title ");
+        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
           for(k=1; k<=(nlstate+ndeath); k++) {
             if (k != k2){
-              if(ng==2)
+              switch( ng) {
-                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+              case 1:
-              else
+                if(nagesqr==0)
-                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+                  fprintf(ficgp," p%d+p%d*x",i,i+1);
+                else /* nagesqr =1 */
+                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+                break;
+              case 2: /* ng=2 */
+                if(nagesqr==0)
+                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+                else /* nagesqr =1 */
+                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+                break;
+              case 3:
+                if(nagesqr==0)
+                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+                else /* nagesqr =1 */
+                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
+                break;
+              }
               ij=1;/* To be checked else nbcode[0][0] wrong */
-              for(j=3; j <=ncovmodel; j++) {
+              for(j=3; j <=ncovmodel-nagesqr; j++) {
-                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
+                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                if(ij <=cptcovage) { /* Bug valgrind */
-                  ij++;
+                  if((j-2)==Tage[ij]) { /* Bug valgrind */
+                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                    ij++;
+                  }
                 }
                 else
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
               }
-              fprintf(ficgp,")/(1");
+              if(ng != 1){
+                fprintf(ficgp,")/(1");
-              for(k1=1; k1 <=nlstate; k1++){
+                for(k1=1; k1 <=nlstate; k1++){
-                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                  if(nagesqr==0)
-                ij=1;
+                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-                for(j=3; j <=ncovmodel; j++){
+                  else /* nagesqr =1 */
-                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-                    ij++;
+                  ij=1;
+                  for(j=3; j <=ncovmodel-nagesqr; j++){
+                    if(ij <=cptcovage) { /* Bug valgrind */
+                      if((j-2)==Tage[ij]) { /* Bug valgrind */
+                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                        /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                        ij++;
+                      }
+                    }
+                    else
+                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                   }
-                  else
+                  fprintf(ficgp,")");
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
                 fprintf(ficgp,")");
+                if(ng ==2)
+                  fprintf(ficgp," t \"p%d%d\" ", k2,k);
+                else /* ng= 3 */
+                  fprintf(ficgp," t \"i%d%d\" ", k2,k);
+              }else{ /* end ng <> 1 */
+                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
               }
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
               i=i+ncovmodel;
             }
           } /* end k */
         } /* end k2 */
+        fprintf(ficgp,"\n set out\n");
       } /* end jk */
     } /* end ng */
+  /* avoid: */
     fflush(ficgp);
  }  /* end gnuplot */
- Line 4052  int movingaverage(double ***probs, doubl
+ Line 5574  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 4068  prevforecast(char fileres[], double anpr
+ Line 5589  prevforecast(char fileres[], double anpr
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   strcpy(fileresf,"f");
+   strcpy(fileresf,"F_");
-   strcat(fileresf,fileres);
+   strcat(fileresf,fileresu);
    if((ficresf=fopen(fileresf,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
- Line 4118  prevforecast(char fileres[], double anpr
+ Line 5643  prevforecast(char fileres[], double anpr
    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        k=k+1;
-       fprintf(ficresf,"\n#******");
+       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
-       fprintf(ficresf,"******\n");
+       fprintf(ficresf," yearproj age");
-       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
        for(j=1; j<=nlstate+ndeath;j++){
          for(i=1; i<=nlstate;i++)
            fprintf(ficresf," p%d%d",i,j);
- Line 4144  prevforecast(char fileres[], double anpr
+ Line 5668  prevforecast(char fileres[], double anpr
              if (h*hstepm/YEARM*stepm ==yearp) {
                fprintf(ficresf,"\n");
                for(j=1;j<=cptcoveff;j++)
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
              }
              for(j=1; j<=nlstate+ndeath;j++) {
- Line 4176  prevforecast(char fileres[], double anpr
+ Line 5700  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 4194  populforecast(char fileres[], double anp
+ Line 5718  populforecast(char fileres[], double anp
    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-   strcpy(filerespop,"pop");
+   strcpy(filerespop,"POP_");
-   strcat(filerespop,fileres);
+   strcat(filerespop,fileresu);
    if((ficrespop=fopen(filerespop,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", filerespop);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
- Line 4242  populforecast(char fileres[], double anp
+ Line 5766  populforecast(char fileres[], double anp
        k=k+1;
        fprintf(ficrespop,"\n#******");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
        fprintf(ficrespop,"******\n");
        fprintf(ficrespop,"# Age");
- Line 4353  void prwizard(int ncovmodel, int nlstate
+ Line 5877  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 4548  double gompertz_f(const gsl_vector *v, v
+ Line 6072  double gompertz_f(const gsl_vector *v, v
  #endif
  /******************* Printing html file ***********/
- void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
+ void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,  double p[],double **matcov,double agemortsup){
    int i,k;
- Line 4557  void printinghtmlmort(char fileres[], ch
+ Line 6081  void printinghtmlmort(char fileres[], ch
    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
    for (i=1;i<=2;i++)
      fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
+   fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
    fprintf(fichtm,"</ul>");
  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
- Line 4572  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 6096  fprintf(fichtm,"<ul><li><h4>Life table</
  }
  /******************* Gnuplot file **************/
- void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+ void printinggnuplotmort(char fileresu[], 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 4586  void printinggnuplotmort(char fileres[],
+ Line 6110  void printinggnuplotmort(char fileres[],
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-   fprintf(ficgp,"set out \"graphmort.png\"\n ");
+   fprintf(ficgp,"set out \"graphmort.svg\"\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 svg size 640, 480\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);
  }
- Line 4600  int readdata(char datafile[], int firsto
+ Line 6124  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i, j, n;
+   int i=0, j=0, n=0;
    int linei, month, year,iout;
    char line[MAXLINE], linetmp[MAXLINE];
-   char stra[80], strb[80];
+   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;
+     printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
    }
    i=1;
- Line 4631  int readdata(char datafile[], int firsto
+ Line 6155  int readdata(char datafile[], int firsto
        continue;
      }
      trimbb(linetmp,line); /* Trims multiple blanks in line */
-     for (j=0; line[j]!='\0';j++){
+     strcpy(line, linetmp);
-       line[j]=linetmp[j];
-     }
      for (j=maxwav;j>=1;j--){
- Line 4654  int readdata(char datafile[], int firsto
+ Line 6176  int readdata(char datafile[], int firsto
        strcpy(line,stra);
        cutv(stra, strb,line,' ');
-       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
        }
-       else  if(iout=sscanf(strb,"%s.") != 0){
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
          month=99;
          year=9999;
        }else{
- Line 4670  int readdata(char datafile[], int firsto
+ Line 6192  int readdata(char datafile[], int firsto
      } /* ENd Waves */
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.",dummy) != 0){
+     else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
        month=99;
        year=9999;
      }else{
- Line 4685  int readdata(char datafile[], int firsto
+ Line 6207  int readdata(char datafile[], int firsto
      strcpy(line,stra);
      cutv(stra, strb,line,' ');
-     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
-     else  if(iout=sscanf(strb,"%s.") != 0){
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
        month=99;
        year=9999;
      }else{
- Line 4772  int readdata(char datafile[], int firsto
+ Line 6294  int readdata(char datafile[], int firsto
    fclose(fic);
    return (0);
-   endread:
+   /* endread: */
      printf("Exiting readdata: ");
      fclose(fic);
      return (1);
- Line 4780  int readdata(char datafile[], int firsto
+ Line 6302  int readdata(char datafile[], int firsto
  }
+ void removespace(char *str) {
- int decodemodel ( char model[], int lastobs)
+   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+age*age
+    * - nagesqr = 1 if age*age in the model, otherwise 0.
+    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
+    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+    * - 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;
+   int i, j, k, ks;
-   int i1, j1, k1, k2;
+   int  j1, k1, k2;
    char modelsav[80];
-    char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   char *strpt;
+   /*removespace(model);*/
    if (strlen(model) >1){ /* If there is at least 1 covariate */
-     j=0, j1=0, k1=1, k2=1;
+     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
-     j=nbocc(model,'+'); /* j=Number of '+' */
-     j1=nbocc(model,'*'); /* j1=Number of '*' */
-     cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
-                   but the covariates which are product must be computed and stored. */
-     cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
-     strcpy(modelsav,model);
      if (strstr(model,"AGE") !=0){
-       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
-       fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
        return 1;
      }
      if (strstr(model,"v") !=0){
- Line 4807  int decodemodel ( char model[], int last
+ Line 6344  int decodemodel ( char model[], int last
        fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
        return 1;
      }
+     strcpy(modelsav,model);
-     /* This loop fills the array Tvar from the string 'model'.*/
+     if ((strpt=strstr(model,"age*age")) !=0){
-     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       printf(" strpt=%s, model=%s\n",strpt, model);
-     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       if(strpt != model){
-     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+  corresponding column of parameters.\n",model);
-     /*  k=1 Tvar[1]=2 (from V2) */
+       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-     /*  k=5 Tvar[5] */
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-     /* for (k=1; k<=cptcovn;k++) { */
+  corresponding column of parameters.\n",model); fflush(ficlog);
-     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+       return 1;
-     /*  } */
+     }
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     for(k=cptcovn; k>=1;k--){
+       nagesqr=1;
-       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+       if (strstr(model,"+age*age") !=0)
-                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
+         substrchaine(modelsav, model, "+age*age");
-                                     */
+       else if (strstr(model,"age*age+") !=0)
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         substrchaine(modelsav, model, "age*age+");
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+       else
-       /*scanf("%d",i);*/
+         substrchaine(modelsav, model, "age*age");
-       if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
+     }else
-         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+       nagesqr=0;
-         if (strcmp(strc,"age")==0) { /* Vn*age */
+     if (strlen(modelsav) >1){
-           cptcovprod--;
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-           cutv(strb,stre,strd,'V'); /* stre="V3" */
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
-           cptcovage++; /* Sums the number of covariates which include age as a product */
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+                    * cst, age and age*age
-           /*printf("stre=%s ", stre);*/
+                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
-         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+                   /* including age products which are counted in cptcovage.
-           cptcovprod--;
+                   * but the covariates which are products must be treated
-           cutv(strb,stre,strc,'V');
+                   * separately: ncovn=4- 2=2 (V1+V3). */
-           Tvar[k]=atoi(stre);
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-           cptcovage++;
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-           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 */
+       /*   Design
-           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
-           Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
+        *  <          ncovcol=8                >
-                                   because this model-covariate is a construction we invent a new column
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
-                                   ncovcol + k1
+        *   k=  1    2      3       4     5       6      7        8
-                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
-                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+        *  covar[k,i], value of kth covariate if not including age for individual i:
-           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
-           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
-           Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
-           Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
+        *  Tage[++cptcovage]=k
-           Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
+        *       if products, new covar are created after ncovcol with k1
-           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-           for (i=1; i<=lastobs;i++){
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-             /* Computes the new covariate which is a product of
+        *  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
-                covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+        *  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
-           k1++;
+        *  <          ncovcol=8                >
-           k2=k2+2;
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-         } /* End age is not in the model */
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-       } /* End if model includes a product */
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-       else { /* no more sum */
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+        * p Tprod[1]@2={                         6, 5}
-        /*  scanf("%d",i);*/
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
-         cutv(strd,strc,strb,'V');
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-         Tvar[k]=atoi(strc);
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-       }
+        *How to reorganize?
-       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-         scanf("%d",i);*/
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
-     } /* end of loop + */
+        * Struct []
-   } /* end model */
+        */
+       /* 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]][codtabm(ij,Tvar[k])]; */
+       /*        } */
+       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
+       /*
+        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+         Tvar[k]=0;
+       cptcovage=0;
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*scanf("%d",i);*/
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+             /* covar is not filled and then is empty */
+             cptcovprod--;
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             /*printf("stre=%s ", stre);*/
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+             cptcovprod--;
+             cutl(stre,strb,strc,'V');
+             Tvar[k]=atoi(stre);
+             cptcovage++;
+             Tage[cptcovage]=k;
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             cptcovn++;
+             cptcovprodnoage++;k1++;
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+                                    because this model-covariate is a construction we invent a new column
+                                    ncovcol + k1
+                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             k2=k2+2;
+             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+             for (i=1; i<=lastobs;i++){
+               /* Computes the new covariate which is a product of
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+             }
+           } /* End age is not in the model */
+         } /* End if model includes a product */
+         else { /* no more sum */
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*  scanf("%d",i);*/
+           cutl(strd,strc,strb,'V');
+           ks++; /**< Number of simple covariates */
+           cptcovn++;
+           Tvar[k]=atoi(strd);
+         }
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+           scanf("%d",i);*/
+       } /* end of loop + on total covariates */
+     } /* end if strlen(modelsave == 0) age*age might exist */
+   } /* end if strlen(model == 0) */
    /*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*/
- Line 4888  int decodemodel ( char model[], int last
+ Line 6503  int decodemodel ( char model[], int last
    return (0); /* with covar[new additional covariate if product] and Tage if age */
-   endread:
+   /*endread:*/
      printf("Exiting decodemodel: ");
      return (1);
  }
- calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+ int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
  {
    int i, m;
- Line 4904  calandcheckages(int imx, int maxwav, dou
+ Line 6519  calandcheckages(int imx, int maxwav, dou
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         *nberr++;
+         *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\n",(int)moisdc[i],(int)andc[i],num[i],i);
+         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%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\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 (%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++;
+         (*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 */
- Line 4923  calandcheckages(int imx, int maxwav, dou
+ Line 6538  calandcheckages(int imx, int maxwav, dou
      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(agedc[i]>0){
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+             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 {
+             }else {
                if ((int)andc[i]!=9999){
                  nbwarn++;
                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- Line 4935  calandcheckages(int imx, int maxwav, dou
+ Line 6550  calandcheckages(int imx, int maxwav, dou
                  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 */
- Line 4947  calandcheckages(int imx, int maxwav, dou
+ Line 6563  calandcheckages(int imx, int maxwav, dou
            }
            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);
+             /* 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;*/
- Line 4965  calandcheckages(int imx, int maxwav, dou
+ Line 6581  calandcheckages(int imx, int maxwav, dou
    for (i=1; i<=imx; i++)  {
      for(m=firstpass; (m<=lastpass); m++){
        if (s[m][i] > (nlstate+ndeath)) {
-         *nberr++;
+         (*nberr)++;
          printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
          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;
- Line 4985  calandcheckages(int imx, int maxwav, dou
+ Line 6601  calandcheckages(int imx, int maxwav, dou
    fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
    return (0);
-   endread:
+  /* 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(int logged)
+  {
+    /* #include "syscompilerinfo.h"*/
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
+ #endif
+ #include <stdint.h>
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
+ #if defined(__clang__)
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
+ #endif
+ #if defined(__ICC) || defined(__INTEL_COMPILER)
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+ #endif
+ #if defined(__GNUC__) || defined(__GNUG__)
+    printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+ #endif
+ #if defined(__HP_cc) || defined(__HP_aCC)
+    printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+ #endif
+ #if defined(__IBMC__) || defined(__IBMCPP__)
+    printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+ #endif
+ #if defined(_MSC_VER)
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+ #endif
+ #if defined(__PGI)
+    printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+ #endif
+ #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+ #endif
+    printf(" for "); if (logged) 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) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
+ #elif __unix__ // all unices, not all compilers
+     // Unix
+    printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
+ #elif __linux__
+     // linux
+    printf("linux ");if(logged) fprintf(ficlog,"linux ");
+ #elif __APPLE__
+     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
+    printf("Mac OS ");if(logged) 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"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
+ #elif UINTPTR_MAX == 0xffffffffffffffff
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
+ #else
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
+ #endif
+ #if defined(__GNUC__)
+ # if defined(__GNUC_PATCHLEVEL__)
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100 \
+                             + __GNUC_PATCHLEVEL__)
+ # else
+ #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+                             + __GNUC_MINOR__ * 100)
+ # endif
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+    if (uname(&sysInfo) != -1) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
+ #endif
+ #endif
+    //   void main()
+    //   {
+ #if defined(_MSC_VER)
+    if (IsWow64()){
+            printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+            if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
+    }
+    else{
+            printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+            if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
+    }
+    //      printf("\nPress Enter to continue...");
+    //      getchar();
+    //   }
+ #endif
+  }
+  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   int i, j, k, i1 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(filerespl,"PL_");
+   strcat(filerespl,fileresu);
+   if((ficrespl=fopen(filerespl,"w"))==NULL) {
+     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+   }
+   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   pstamp(ficrespl);
+   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+   fprintf(ficrespl,"\n");
+     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+     agebase=ageminpar;
+     agelim=agemaxpar;
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         k=k+1;
+         /* to clean */
+         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+         fprintf(ficrespl,"#******");
+         printf("#******");
+         fprintf(ficlog,"#******");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         fprintf(ficrespl,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         fprintf(ficrespl,"#Age ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+         fprintf(ficrespl,"Total Years_to_converge\n");
+         for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+           fprintf(ficrespl,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           tot=0.;
+           for(i=1; i<=nlstate;i++){
+             tot +=  prlim[i][i];
+             fprintf(ficrespl," %.5f", prlim[i][i]);
+           }
+           fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         } /* Age */
+         /* was end of cptcod */
+     } /* cptcov */
+         return 0;
+ }
+ int hPijx(double *p, int bage, int fage){
+     /*------------- h Pij x at various ages ------------*/
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k;
+   double agedeb;
+   double ***p3mat;
+     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
+     if((ficrespij=fopen(filerespij,"w"))==NULL) {
+       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
+       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
+     }
+     printf("Computing pij: result on file '%s' \n", filerespij);
+     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+     stepsize=(int) (stepm+YEARM-1)/YEARM;
+     /*if (stepm<=24) stepsize=2;*/
+     agelim=AGESUP;
+     hstepm=stepsize*YEARM; /* Every year of age */
+     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+     /* hstepm=1;   aff par mois*/
+     pstamp(ficrespij);
+     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
+     i1= pow(2,cptcoveff);
+    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+    /*   k=k+1;  */
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+       fprintf(ficrespij,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrespij,"******\n");
+       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespij," %1d-%1d",i,j);
+         fprintf(ficrespij,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
+           for(i=1; i<=nlstate;i++)
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespij,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespij,"\n");
+       }
+       /*}*/
+     }
+         return 0;
+ }
  /***********************************************/
  /**************** Main Program *****************/
- Line 5005  int main(int argc, char *argv[])
+ Line 6960  int main(int argc, char *argv[])
    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 ncvyear=0; /* Number of years needed for the period prevalence to converge */
-   int jj, ll, li, lj, lk, imk;
+   int jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
+   int num_filled;
    int itimes;
    int NDIM=2;
    int vpopbased=0;
-   char ca[32], cb[32], cc[32];
+   char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    struct stat info;
-   double agedeb, agefin,hf;
+   double agedeb=0.;
-   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
    double fret;
-   double **xi,tmp,delta;
+   double dum=0.; /* Dummy variable */
-   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 path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
+   char model[MAXLINE], modeltemp[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, c2;
-   int c,  h , cpt,l;
+   int jl=0;
-   int ju,jl, mi;
+   int i1, j1, jk, stepsize=0;
-   int i1,j1, jk,aa,bb, stepsize, ij;
+   int count=0;
-   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
+   int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
    int mobilav=0,popforecast=0;
-   int hstepm, nhstepm;
+   int hstepm=0, nhstepm=0;
    int agemortsup;
    float  sumlpop=0.;
    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-   double bage, fage, age, agelim, agebase;
+   double bage=0, fage=110., age, agelim=0., agebase=0.;
    double ftolpl=FTOL;
    double **prlim;
    double ***param; /* Matrix of parameters */
    double  *p;
    double **matcov; /* Matrix of covariance */
+   double **hess; /* Hessian matrix */
    double ***delti3; /* Scale */
    double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double kk1, kk2;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
    double **ximort;
-   char *alph[]={"a","a","b","c","d","e"}, str[4];
+   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];
-   long total_usecs;
  /*   setlocale (LC_ALL, ""); */
  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
  /*   textdomain (PACKAGE); */
- Line 5076  int main(int argc, char *argv[])
+ Line 7034  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 5100  int main(int argc, char *argv[])
+ Line 7060  int main(int argc, char *argv[])
    nberr=0; /* Number of errors and warnings */
    nbwarn=0;
+ #ifdef WIN32
+   _getcwd(pathcd, size);
+ #else
    getcwd(pathcd, size);
+ #endif
-   printf("\n%s\n%s",version,fullversion);
+   syscompilerinfo(0);
+   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
    if(argc <=1){
      printf("\nEnter the parameter file name: ");
-     fgets(pathr,FILENAMELENGTH,stdin);
+     if(!fgets(pathr,FILENAMELENGTH,stdin)){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
      i=strlen(pathr);
      if(pathr[i-1]=='\n')
        pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+     i=strlen(pathr);
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
+       pathr[i-1]='\0';
+     }
+     i=strlen(pathr);
+     if( i==0 ){
+       printf("ERROR Empty parameter file name\n");
+       goto end;
+     }
+     for (tok = pathr; tok != NULL; ){
        printf("Pathr |%s|\n",pathr);
        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
        printf("val= |%s| pathr=%s\n",val,pathr);
- Line 5133  int main(int argc, char *argv[])
+ Line 7109  int main(int argc, char *argv[])
    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
    printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ #ifdef WIN32
+   _chdir(path); /* Can be a relative path */
+   if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ #else
    chdir(path); /* Can be a relative path */
-   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+   if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
-     printf("Current directory %s!\n",pathcd);
+ #endif
+   printf("Current directory %s!\n",pathcd);
    strcpy(command,"mkdir ");
    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 5150  int main(int argc, char *argv[])
+ Line 7131  int main(int argc, char *argv[])
    /*-------- arguments in the command line --------*/
-   /* Log file */
+   /* Main Log file */
    strcat(filelog, optionfilefiname);
    strcat(filelog,".log");    /* */
    if((ficlog=fopen(filelog,"w"))==NULL)    {
- Line 5158  int main(int argc, char *argv[])
+ Line 7139  int main(int argc, char *argv[])
      goto end;
    }
    fprintf(ficlog,"Log filename:%s\n",filelog);
-   fprintf(ficlog,"\n%s\n%s",version,fullversion);
+   fprintf(ficlog,"Version %s %s",version,fullversion);
    fprintf(ficlog,"\nEnter the parameter file name: \n");
    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
   path=%s \n\
   optionfile=%s\n\
   optionfilext=%s\n\
-  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
+   syscompilerinfo(1);
    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");
    strcat(fileres, optionfilefiname);
+   strcat(fileresu, optionfilefiname); /* Without r in front */
    strcat(fileres,".txt");    /* Other files have txt extension */
+   strcat(fileresu,".txt");    /* Other files have txt extension */
-   /*---------arguments file --------*/
+   /* Main ---------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);
    }
    strcpy(filereso,"o");
-   strcat(filereso,fileres);
+   strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
      printf("Problem with Output resultfile: %s\n", filereso);
      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
- Line 5199  int main(int argc, char *argv[])
+ Line 7185  int main(int argc, char *argv[])
    /* Reads comments: lines beginning with '#' */
    numlinepar=0;
-   while((c=getc(ficpar))=='#' && c!= EOF){
-     ungetc(c,ficpar);
+     /* First parameter line */
-     fgets(line, MAXLINE, ficpar);
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
+                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
+     if (num_filled != 5) {
+       printf("Should be 5 parameters\n");
+     }
      numlinepar++;
-     fputs(line,stdout);
+     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
-     fputs(line,ficparo);
-     fputs(line,ficlog);
    }
-   ungetc(c,ficpar);
+   /* Second parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
-   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+     /* If line starts with a # it is a comment */
-   numlinepar++;
+     if (line[0] == '#') {
-   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+       numlinepar++;
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       fputs(line,stdout);
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+     if (num_filled != 8) {
+       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       printf("but line=%s\n",line);
+     }
+     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+   /* Third parameter line */
+   while(fgets(line, MAXLINE, ficpar)) {
+     /* If line starts with a # it is a comment */
+     if (line[0] == '#') {
+       numlinepar++;
+       fputs(line,stdout);
+       fputs(line,ficparo);
+       fputs(line,ficlog);
+       continue;
+     }else
+       break;
+   }
+   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
+     if (num_filled == 0)
+             model[0]='\0';
+     else if (num_filled != 1){
+       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     }
+     else{
+       if (model[0]=='+'){
+         for(i=1; i<=strlen(model);i++)
+           modeltemp[i-1]=model[i];
+         strcpy(model,modeltemp);
+       }
+     }
+     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
+     printf("model=1+age+%s\n",model);fflush(stdout);
+   }
+   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
+   /* numlinepar=numlinepar+3; /\* In general *\/ */
+   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
+   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
    fflush(ficlog);
+   /* if(model[0]=='#'|| model[0]== '\0'){ */
+   if(model[0]=='#'){
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+     if(mle != -1){
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       exit(1);
+     }
+   }
    while((c=getc(ficpar))=='#' && c!= EOF){
      ungetc(c,ficpar);
      fgets(line, MAXLINE, ficpar);
      numlinepar++;
+     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
+       z[0]=line[1];
+     }
+     /* printf("****line [1] = %c \n",line[1]); */
      fputs(line, stdout);
      //puts(line);
      fputs(line,ficparo);
- Line 5227  int main(int argc, char *argv[])
+ Line 7291  int main(int argc, char *argv[])
    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 plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
       v1+v2*age+v2*v3 makes cptcovn = 3
    */
    if (strlen(model)>1)
-     cptcovn=nbocc(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,age*age makes 3*/
-   /* ncovprod */
+   else
-   ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+     ncovmodel=2; /* Constant and age */
-   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
    npar= nforce*ncovmodel; /* Number of parameters like aij*/
    if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
- Line 5251  int main(int argc, char *argv[])
+ Line 7314  int main(int argc, char *argv[])
    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      fclose (ficparo);
      fclose (ficlog);
      goto end;
      exit(0);
    }
-   else if(mle==-3) {
+   else if(mle==-3) { /* Main Wizard */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      matcov=matrix(1,npar,1,npar);
+     hess=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);
- Line 5286  int main(int argc, char *argv[])
+ Line 7350  int main(int argc, char *argv[])
          if(jj==i) continue;
          j++;
          fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ((i1 != i) && (j1 != j)){
+         if ((i1 != i) || (j1 != jj)){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
  It might be a problem of design; if ncovcol and the model are correct\n \
  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
- Line 5294  run imach with mle=-1 to get a correct t
+ Line 7358  run imach with mle=-1 to get a correct t
          }
          fprintf(ficparo,"%1d%1d",i1,j1);
          if(mle==1)
-           printf("%1d%1d",i,j);
+           printf("%1d%1d",i,jj);
-         fprintf(ficlog,"%1d%1d",i,j);
+         fprintf(ficlog,"%1d%1d",i,jj);
          for(k=1; k<=ncovmodel;k++){
            fscanf(ficpar," %lf",&param[i][j][k]);
            if(mle==1){
- Line 5316  run imach with mle=-1 to get a correct t
+ Line 7380  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 5332  run imach with mle=-1 to get a correct t
+ Line 7397  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 5354  run imach with mle=-1 to get a correct t
+ Line 7419  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
+     /* Reads covariance matrix */
      delti=delti3[1][1];
- Line 5371  run imach with mle=-1 to get a correct t
+ Line 7437  run imach with mle=-1 to get a correct t
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
+     hess=matrix(1,npar,1,npar);
      for(i=1; i <=npar; i++)
        for(j=1; j <=npar; j++) matcov[i][j]=0.;
+     /* Scans npar lines */
      for(i=1; i <=npar; i++){
-       fscanf(ficpar,"%s",&str);
+       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+       if(count != 3){
+         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
+         exit(1);
+       }else
        if(mle==1)
-         printf("%s",str);
+         printf("%1d%1d%1d",i1,j1,jk);
-       fprintf(ficlog,"%s",str);
+       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
-       fprintf(ficparo,"%s",str);
+       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
- Line 5395  run imach with mle=-1 to get a correct t
+ Line 7472  run imach with mle=-1 to get a correct t
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
+     /* End of read covariance matrix npar lines */
      for(i=1; i <=npar; i++)
        for(j=i+1;j<=npar;j++)
          matcov[i][j]=matcov[j][i];
- Line 5411  run imach with mle=-1 to get a correct t
+ Line 7489  run imach with mle=-1 to get a correct t
      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;
+       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
      }
      fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
+   /*  Main data
+    */
    n= lastobs;
    num=lvector(1,n);
    moisnais=vector(1,n);
- Line 5433  run imach with mle=-1 to get a correct t
+ Line 7512  run imach with mle=-1 to get a correct t
    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 */
+   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
    /* Reads data from file datafile */
    if (readdata(datafile, firstobs, lastobs, &imx)==1)
- Line 5455  run imach with mle=-1 to get a correct t
+ Line 7535  run imach with mle=-1 to get a correct t
      ncovcol + k1
      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
      Tvar[3=V1*V4]=4+1 etc */
-   Tprod=ivector(1,15); /* Gives the position of a product */
+   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(1,15);
+   Tvaraff=ivector(1,NCOVMAX); /* Unclear */
-   Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
+   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(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
+   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
                        */
+ /* Main decodemodel */
    if(decodemodel(model, lastobs) == 1)
      goto end;
- Line 5495  run imach with mle=-1 to get a correct t
+ Line 7578  run imach with mle=-1 to get a correct t
       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 5504  run imach with mle=-1 to get a correct t
+ Line 7587  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 */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+   Ndum =ivector(-1,NCOVMAX);
+   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
-   codtab=imatrix(1,100,1,10); /**< codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1)
+     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-                                */
+   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
+      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
+   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
+   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
+   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
+   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
+   /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
+    * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
+    * (currently 0 or 1) in the data.
+    * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
+    * corresponding modality (h,j).
+    */
    h=0;
+   /*if (cptcovn > 0) */
    m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     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 each modality of this covariate ncodemax=2*/
-         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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-            *     h     1     2     3     4
+            * For k=4 covariates, h goes from 1 to m=2**k
+            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
+            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+            *     h\k   1     2     3     4
             *______________________________
             *     1 i=1 1 i=1 1 i=1 1 i=1 1
             *     2     2     1     1     1
- Line 5534  run imach with mle=-1 to get a correct t
+ Line 7632  run imach with mle=-1 to get a correct t
             *     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
+            *     9 i=5 1 i=3 1 i=2 1     2
-            *    10     2     1     1     1
+            *    10     2     1     1     2
-            *    11 i=6 1     2     1     1
+            *    11 i=6 1     2     1     2
-            *    12     2     2     1     1
+            *    12     2     2     1     2
-            *    13 i=7 1 i=4 1     2     1
+            *    13 i=7 1 i=4 1     2     2
-            *    14     2     1     2     1
+            *    14     2     1     2     2
-            *    15 i=8 1     2     2     1
+            *    15 i=8 1     2     2     2
-            *    16     2     2     2     1
+            *    16     2     2     2     2
             */
-           codtab[h][k]=j;
+   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
-           codtab[h][Tvar[k]]=j;
+      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
-           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]]);
+      * and the value of each covariate?
-         }
+      * V1=1, V2=1, V3=2, V4=1 ?
-       }
+      * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
-     }
+      * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
-   }
+      * In order to get the real value in the data, we use nbcode
+      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
+      * We are keeping this crazy system in order to be able (in the future?)
+      * to have more than 2 values (0 or 1) for a covariate.
+      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
+      *              bbbbbbbb
+      *              76543210
+      *   h-1        00000101 (6-1=5)
+      *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
+      *           &
+      *     1        00000001 (1)
+      *              00000001        = 1 & ((h-1) >> (k-1))
+      *          +1= 00000010 =2
+      *
+      * h=14, k=3 => h'=h-1=13, k'=k-1=2
+      *          h'      1101 =2^3+2^2+0x2^1+2^0
+      *    >>k'            11
+      *          &   00000001
+      *            = 00000001
+      *      +1    = 00000010=2    =  codtabm(14,3)
+      * Reverse h=6 and m=16?
+      * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
+      * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
+      * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
+      * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
+      * V3=decodtabm(14,3,2**4)=2
+      *          h'=13   1101 =2^3+2^2+0x2^1+2^0
+      *(h-1) >> (j-1)    0011 =13 >> 2
+      *          &1 000000001
+      *           = 000000001
+      *         +1= 000000010 =2
+      *                  2211
+      *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
+      *                  V3=2
+      */
+   /* /\* for(h=1; h <=100 ;h++){  *\/ */
+   /*   /\* printf("h=%2d ", h); *\/ */
+   /*    /\* for(k=1; k <=10; k++){ *\/ */
+   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
+   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
+   /*    /\* } *\/ */
+   /*    /\* printf("\n"); *\/ */
+   /* } */
+   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
+   /*   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 each modality of this covariate ncodemax=2*\/ */
+   /*    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[12][3]=1; *\/ */
+   /*      /\*codtab[h][Tvar[k]]=j;*\/ */
+   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
+   /*    }  */
+   /*     } */
+   /*   } */
+   /* }  */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
       codtab[1][2]=1;codtab[2][2]=2; */
-   /* for(i=1; i <=m ;i++){
+   /* for(i=1; i <=m ;i++){  */
-      for(k=1; k <=cptcovn; k++){
+   /*    for(k=1; k <=cptcovn; k++){ */
-        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
-      }
+   /*    } */
-      printf("\n");
+   /*    printf("\n"); */
-      }
+   /* } */
-      scanf("%d",i);*/
+   /*   scanf("%d",i);*/
+  free_ivector(Ndum,-1,NCOVMAX);
-   /*------------ gnuplot -------------*/
+   /* Initialisation of ----------- gnuplot -------------*/
    strcpy(optionfilegnuplot,optionfilefiname);
    if(mle==-3)
-     strcat(optionfilegnuplot,"-mort");
+     strcat(optionfilegnuplot,"-MORT_");
    strcat(optionfilegnuplot,".gp");
    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
      printf("Problem with file %s",optionfilegnuplot);
    }
    else{
-     fprintf(ficgp,"\n# %s\n", version);
+     fprintf(ficgp,"\n# IMaCh-%s\n", version);
      fprintf(ficgp,"# %s\n", optionfilegnuplot);
      //fprintf(ficgp,"set missing 'NaNq'\n");
      fprintf(ficgp,"set datafile missing 'NaNq'\n");
    }
    /*  fclose(ficgp);*/
-   /*--------- index.htm --------*/
+   /* Initialisation of --------- index.htm --------*/
    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
    if(mle==-3)
-     strcat(optionfilehtm,"-mort");
+     strcat(optionfilehtm,"-MORT_");
    strcat(optionfilehtm,".htm");
    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
      printf("Problem with %s \n",optionfilehtm);
- Line 5595  run imach with mle=-1 to get a correct t
+ Line 7758  run imach with mle=-1 to get a correct t
    else{
    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
+   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
+ <font size=\"2\">IMaCh-%s <br> %s</font> \
+ <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
  \n\
  <hr  size=\"2\" color=\"#EC5E5E\">\
   <ul><li><h4>Parameter files</h4>\n\
- Line 5618  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 7783  Title=%s <br>Datafile=%s Firstpass=%d La
    strcpy(pathr,path);
    strcat(pathr,optionfilefiname);
+ #ifdef WIN32
+   _chdir(optionfilefiname); /* Move to directory named optionfile */
+ #else
    chdir(optionfilefiname); /* Move to directory named optionfile */
+ #endif
    /* Calculates basic frequencies. Computes observed prevalence at single age
       and prints on file fileres'p'. */
- Line 5641  Interval (in months) between two waves:
+ Line 7811  Interval (in months) between two waves:
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+   /* For mortality only */
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
- /*     ximort=gsl_matrix_alloc(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 5682  Interval (in months) between two waves:
+ Line 7852  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");
- #elsedef
+ #else
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
  #endif
-     strcpy(filerespow,"pow-mort");
+     strcpy(filerespow,"POW-MORT_");
-     strcat(filerespow,fileres);
+     strcat(filerespow,fileresu);
      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");
- #elsedef
+ #else
      fprintf(ficrespow,"# Powell\n# iter -2*LL");
  #endif
      /*  for (i=1;i<=nlstate;i++)
- Line 5734  Interval (in months) between two waves:
+ Line 7904  Interval (in months) between two waves:
      /* Initialize method and iterate */
      /*     p[1]=0.0268; p[NDIM]=0.083; */
- /*     gsl_vector_set(x, 0, 0.0268); */
+     /*     gsl_vector_set(x, 0, 0.0268); */
- /*     gsl_vector_set(x, 1, 0.083); */
+     /*     gsl_vector_set(x, 1, 0.083); */
      gsl_vector_set(x, 0, p[1]);
      gsl_vector_set(x, 1, p[2]);
- Line 5788  Interval (in months) between two waves:
+ Line 7958  Interval (in months) between two waves:
  #endif
      fclose(ficrespow);
-     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
+     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
          matcov[i][j]=matcov[j][i];
      printf("\nCovariance matrix\n ");
+     fprintf(ficlog,"\nCovariance matrix\n ");
      for(i=1; i <=NDIM; i++) {
        for(j=1;j<=NDIM;j++){
          printf("%f ",matcov[i][j]);
+         fprintf(ficlog,"%f ",matcov[i][j]);
        }
-       printf("\n ");
+       printf("\n ");  fprintf(ficlog,"\n ");
      }
      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-     for (i=1;i<=NDIM;i++)
+     for (i=1;i<=NDIM;i++) {
        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+     }
      lsurv=vector(1,AGESUP);
      lpop=vector(1,AGESUP);
      tpop=vector(1,AGESUP);
- Line 5837  Interval (in months) between two waves:
+ Line 8010  Interval (in months) between two waves:
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else
+       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
- Line 5852  Interval (in months) between two waves:
+ Line 8032  Interval (in months) between two waves:
      free_ivector(dcwave,1,n);
      free_matrix(ximort,1,NDIM,1,NDIM);
  #endif
-   } /* Endof if mle==-3 */
+   } /* Endof if mle==-3 mortality only */
+   /* Standard  */
-   else{ /* For mle >=1 */
+   else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
-     globpr=0;/* debug */
+     globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+     /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
-     globpr=1; /* to print the contributions */
+     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
+       /* mlikeli uses func not funcone */
+       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+     }
+     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
+       globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
+       /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
+       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
+     }
+     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
      for (k=1; k<=npar;k++)
        printf(" %d %8.5f",k,p[k]);
      printf("\n");
-     if(mle>=1){ /* Could be 1 or 2 */
-       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
-     }
      /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- Line 5885  Interval (in months) between two waves:
+ Line 8072  Interval (in months) between two waves:
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
            for(j=1; j <=ncovmodel; j++){
-             printf("%lf ",p[jk]);
+             printf("%12.7f ",p[jk]);
-             fprintf(ficlog,"%lf ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
-             fprintf(ficres,"%lf ",p[jk]);
+             fprintf(ficres,"%12.7f ",p[jk]);
              jk++;
            }
            printf("\n");
- Line 5896  Interval (in months) between two waves:
+ Line 8083  Interval (in months) between two waves:
          }
        }
      }
-     if(mle!=0){
+     if(mle != 0){
-       /* Computing hessian and covariance matrix */
+       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
        ftolhess=ftol; /* Usually correct */
-       hesscov(matcov, p, npar, delti, ftolhess, func);
+       hesscov(matcov, hess, p, npar, delti, ftolhess, func);
-     }
+       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       for(i=1,jk=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(j=1; j <=ncovmodel; j++){
+               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+     } /* end of hesscov and Wald tests */
+     /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
- Line 5924  Interval (in months) between two waves:
+ Line 8130  Interval (in months) between two waves:
      }
      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
-     if(mle>=1)
+     if(mle >= 1) /* To big for the screen */
        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
      /* # 121 Var(a12)\n\ */
- Line 5987  Interval (in months) between two waves:
+ Line 8193  Interval (in months) between two waves:
                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                        }else{
                          if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+                           printf(" %.7e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                         fprintf(ficlog," %.7e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                         fprintf(ficres," %.7e",matcov[jj][ll]);
                        }
                      }
                    }
- Line 6008  Interval (in months) between two waves:
+ Line 8214  Interval (in months) between two waves:
      fflush(ficlog);
      fflush(ficres);
+       while(fgets(line, MAXLINE, ficpar)) {
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     /* If line starts with a # it is a comment */
-       ungetc(c,ficpar);
+     if (line[0] == '#') {
-       fgets(line, MAXLINE, ficpar);
+       numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
-     }
+       fputs(line,ficlog);
-     ungetc(c,ficpar);
+       continue;
+     }else
+       break;
+   }
+     /* while((c=getc(ficpar))=='#' && c!= EOF){ */
+     /*   ungetc(c,ficpar); */
+     /*   fgets(line, MAXLINE, ficpar); */
+     /*   fputs(line,stdout); */
+     /*   fputs(line,ficparo); */
+     /* } */
+     /* ungetc(c,ficpar); */
      estepm=0;
-     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+     if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
+     if (num_filled != 6) {
+       printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
+       printf("but line=%s\n",line);
+       goto end;
+     }
+     printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
+   }
+   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
+   /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
+     /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
      if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
        bage = ageminpar;
- Line 6026  Interval (in months) between two waves:
+ Line 8255  Interval (in months) between two waves:
      }
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
-     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
-     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
+     /* Other stuffs, more or less useful */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
- Line 6056  Interval (in months) between two waves:
+ Line 8286  Interval (in months) between two waves:
      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
      fscanf(ficpar,"pop_based=%d\n",&popbased);
+     fprintf(ficlog,"pop_based=%d\n",popbased);
      fprintf(ficparo,"pop_based=%d\n",popbased);
      fprintf(ficres,"pop_based=%d\n",popbased);
- Line 6076  Interval (in months) between two waves:
+ Line 8307  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);
+     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
+         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
+     }else
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
- Line 6101  Interval (in months) between two waves:
+ Line 8340  Interval (in months) between two waves:
      fclose(ficres);
-     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+     /* Other results (useful)*/
-     strcpy(filerespl,"pl");
-     strcat(filerespl,fileres);
-     if((ficrespl=fopen(filerespl,"w"))==NULL) {
-       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
-     }
-     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
-     pstamp(ficrespl);
-     fprintf(ficrespl,"# Period (stable) prevalence \n");
-     fprintf(ficrespl,"#Age ");
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
-     fprintf(ficrespl,"\n");
-     prlim=matrix(1,nlstate,1,nlstate);
-     agebase=ageminpar;
-     agelim=agemaxpar;
-     ftolpl=1.e-10;
-     i1=pow(2,cptcoveff);
-     if (cptcovn < 1){i1=1;}
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
-         k=k+1;
+     prlim=matrix(1,nlstate,1,nlstate);
-         /* to clean */
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
-         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
-         fprintf(ficrespl,"\n#******");
-         printf("\n#******");
-         fprintf(ficlog,"\n#******");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficrespl,"******\n");
-         printf("******\n");
-         fprintf(ficlog,"******\n");
-         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");
-         } /* Age */
-         /* was end of cptcod */
-     } /* cptcov */
      fclose(ficrespl);
-     /*------------- h Pij x at various ages ------------*/
+ #ifdef FREEEXIT2
+ #include "freeexit2.h"
-     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
+ #endif
-     if((ficrespij=fopen(filerespij,"w"))==NULL) {
-       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
-       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
-     }
-     printf("Computing pij: result on file '%s' \n", filerespij);
-     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-     stepsize=(int) (stepm+YEARM-1)/YEARM;
-     /*if (stepm<=24) stepsize=2;*/
-     agelim=AGESUP;
-     hstepm=stepsize*YEARM; /* Every year of age */
-     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-     /* hstepm=1;   aff par mois*/
-     pstamp(ficrespij);
-     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficrespij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrespij,"******\n");
-         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-           /*      nhstepm=nhstepm*YEARM; aff par mois*/
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     /*------------- h Pij x at various ages ------------*/
-           oldm=oldms;savm=savms;
+     /*#include "hpijx.h"*/
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+     hPijx(p, bage, fage);
-           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
+     fclose(ficrespij);
-           for(i=1; i<=nlstate;i++)
-             for(j=1; j<=nlstate+ndeath;j++)
-               fprintf(ficrespij," %1d-%1d",i,j);
-           fprintf(ficrespij,"\n");
-           for (h=0; h<=nhstepm; h++){
-             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
-             for(i=1; i<=nlstate;i++)
-               for(j=1; j<=nlstate+ndeath;j++)
-                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
-             fprintf(ficrespij,"\n");
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           fprintf(ficrespij,"\n");
-         }
-       }
-     }
+   /*-------------- Variance of one-step probabilities---*/
+     k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     fclose(ficrespij);
      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1;i<=AGESUP;i++)
- Line 6224  Interval (in months) between two waves:
+ Line 8373  Interval (in months) between two waves:
      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
        /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
        /*      }  */
        /*      else{ */
- Line 6233  Interval (in months) between two waves:
+ Line 8382  Interval (in months) between two waves:
        /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
        /*      } */
      }
+     /* ------ Other prevalence ratios------------ */
      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- Line 6253  Interval (in months) between two waves:
+ Line 8403  Interval (in months) between two waves:
      /*---------- Health expectancies, no variances ------------*/
-     strcpy(filerese,"e");
+     strcpy(filerese,"E_");
-     strcat(filerese,fileres);
+     strcat(filerese,fileresu);
      if((ficreseij=fopen(filerese,"w"))==NULL) {
        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
      }
-     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
-     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
-     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]]);
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          fprintf(ficreseij,"******\n");
- Line 6275  Interval (in months) between two waves:
+ Line 8426  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);
+     printf("done evsij\n");fflush(stdout);
+     fprintf(ficlog,"done evsij\n");fflush(ficlog);
      /*---------- Health expectancies and variances ------------*/
-     strcpy(filerest,"t");
+     strcpy(filerest,"T_");
-     strcat(filerest,fileres);
+     strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
      }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
-     strcpy(fileresstde,"stde");
+     strcpy(fileresstde,"STDE_");
-     strcat(fileresstde,fileres);
+     strcat(fileresstde,fileresu);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
        printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
        fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
      }
-     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     strcpy(filerescve,"cve");
+     strcpy(filerescve,"CVE_");
-     strcat(filerescve,fileres);
+     strcat(filerescve,fileresu);
      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
        printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
        fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
      }
-     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
-     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
-     strcpy(fileresv,"v");
+     strcpy(fileresv,"V_");
-     strcat(fileresv,fileres);
+     strcat(fileresv,fileresu);
      if((ficresvij=fopen(fileresv,"w"))==NULL) {
        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
      }
-     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
-         fprintf(ficrest,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficrest,"******\n");
-         fprintf(ficresstdeij,"\n#****** ");
-         fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         }
-         fprintf(ficresstdeij,"******\n");
-         fprintf(ficrescveij,"******\n");
-         fprintf(ficresvij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficresvij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
-         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         pstamp(ficrest);
-         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-           oldm=oldms;savm=savms;
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
-           if(vpopbased==1)
-             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
-           else
-             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-           fprintf(ficrest,"# Age e.. (std) ");
-           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-           fprintf(ficrest,"\n");
-           epj=vector(1,nlstate+1);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-           for(age=bage; age <=fage ;age++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
-             if (vpopbased==1) {
+     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-               if(mobilav ==0){
+       fprintf(ficrest,"\n#****** ");
-                 for(i=1; i<=nlstate;i++)
+       for(j=1;j<=cptcoveff;j++)
-                   prlim[i][i]=probs[(int)age][i][k];
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-               }else{ /* mobilav */
+       fprintf(ficrest,"******\n");
-                 for(i=1; i<=nlstate;i++)
-                   prlim[i][i]=mobaverage[(int)age][i][k];
+       fprintf(ficresstdeij,"\n#****** ");
-               }
+       fprintf(ficrescveij,"\n#****** ");
-             }
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-             fprintf(ficrest," %4.0f",age);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+       }
-               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+       fprintf(ficresstdeij,"******\n");
-                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+       fprintf(ficrescveij,"******\n");
-                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-               }
+       fprintf(ficresvij,"\n#****** ");
-               epj[nlstate+1] +=epj[j];
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresvij,"******\n");
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       printf(" cvevsij %d, ",k);
+       fprintf(ficlog, " cvevsij %d, ",k);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       printf(" end cvevsij \n ");
+       fprintf(ficlog, " end cvevsij \n ");
+       /*
+        */
+       /* 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; /* ZZ Segmentation fault */
+         cptcod= 0; /* To be deleted */
+         printf("varevsij %d \n",vpopbased);
+         fprintf(ficlog, "varevsij %d \n",vpopbased);
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, 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
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         fprintf(ficrest,"\n");
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+         epj=vector(1,nlstate+1);
+         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
+         for(age=bage; age <=fage ;age++){
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           if (vpopbased==1) {
+             if(mobilav ==0){
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=probs[(int)age][i][k];
+             }else{ /* mobilav */
+               for(i=1; i<=nlstate;i++)
+                 prlim[i][i]=mobaverage[(int)age][i][k];
              }
+           }
-             for(i=1, vepp=0.;i <=nlstate;i++)
-               for(j=1;j <=nlstate;j++)
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-                 vepp += vareij[i][j][(int)age];
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           /* printf(" age %4.0f ",age); */
-             for(j=1;j <=nlstate;j++){
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
              }
-             fprintf(ficrest,"\n");
+             epj[nlstate+1] +=epj[j];
            }
+           /* printf(" age %4.0f \n",age); */
+           for(i=1, vepp=0.;i <=nlstate;i++)
+             for(j=1;j <=nlstate;j++)
+               vepp += vareij[i][j][(int)age];
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           for(j=1;j <=nlstate;j++){
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+           }
+           fprintf(ficrest,"\n");
          }
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       } /* End vpopbased */
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-         free_vector(epj,1,nlstate+1);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       }
+       free_vector(epj,1,nlstate+1);
-     }
+       printf("done \n");fflush(stdout);
+       fprintf(ficlog,"done\n");fflush(ficlog);
+       /*}*/
+     } /* End k */
      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 6407  Interval (in months) between two waves:
+ Line 8583  Interval (in months) between two waves:
      fclose(ficrescveij);
      fclose(ficresvij);
      fclose(ficrest);
+     printf("done Health expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
      fclose(ficpar);
      /*------- Variance of period (stable) prevalence------*/
-     strcpy(fileresvpl,"vpl");
+     strcpy(fileresvpl,"VPL_");
-     strcat(fileresvpl,fileres);
+     strcat(fileresvpl,fileresu);
      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
        exit(0);
      }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
+     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
-     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,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficresvpl,"******\n");
          varpl=matrix(1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
+         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       }
+       /*}*/
      }
      fclose(ficresvpl);
+     printf("done variance-covariance of period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
      /*---------- End : free ----------------*/
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }  /* mle==-3 arrives here for freeing */
-  endfree:
+  /* 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);
- Line 6448  Interval (in months) between two waves:
+ Line 8630  Interval (in months) between two waves:
      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
      free_matrix(covar,0,NCOVMAX,1,n);
      free_matrix(matcov,1,npar,1,npar);
+     free_matrix(hess,1,npar,1,npar);
      /*free_vector(delti,1,npar);*/
      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
      free_matrix(agev,1,maxwav,1,imx);
      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(ncodemax,1,8);
+     free_ivector(ncodemax,1,NCOVMAX);
-     free_ivector(Tvar,1,15);
+     free_ivector(ncodemaxwundef,1,NCOVMAX);
-     free_ivector(Tprod,1,15);
+     free_ivector(Tvar,1,NCOVMAX);
-     free_ivector(Tvaraff,1,15);
+     free_ivector(Tprod,1,NCOVMAX);
-     free_ivector(Tage,1,15);
+     free_ivector(Tvaraff,1,NCOVMAX);
+     free_ivector(Tage,1,NCOVMAX);
      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
-     free_imatrix(codtab,1,100,1,10);
+     /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
    fflush(ficgp);
- Line 6474  Interval (in months) between two waves:
+ Line 8658  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 %ld 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 %ld 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 6497  Interval (in months) between two waves:
+ Line 8682  Interval (in months) between two waves:
     printf("Before Current directory %s!\n",pathcd);
+ #ifdef WIN32
+    if (_chdir(pathcd) != 0)
+            printf("Can't move to directory %s!\n",path);
+    if(_getcwd(pathcd,MAXLINE) > 0)
+ #else
     if(chdir(pathcd) != 0)
-     printf("Can't move to directory %s!\n",path);
+            printf("Can't move to directory %s!\n", path);
-   if(getcwd(pathcd,MAXLINE) > 0)
+    if (getcwd(pathcd, MAXLINE) > 0)
+ #endif
      printf("Current directory %s!\n",pathcd);
    /*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 6523  Interval (in months) between two waves:
+ Line 8714  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);
    }
    end:
    while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
+     printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
  }

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