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Diff for /imach/src/imach.c between versions 1.167 and 1.217

-version 1.167, 2014/12/22 13:50:56
+version 1.217, 2015/12/23 17:18:31
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.217  2015/12/23 17:18:31  brouard
+   Summary: Experimental backcast
+   Revision 1.216  2015/12/18 17:32:11  brouard
+   Summary: 0.98r4 Warning and status=-2
+   Version 0.98r4 is now:
+    - displaying an error when status is -1, date of interview unknown and date of death known;
+    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+   Older changes concerning s=-2, dating from 2005 have been supersed.
+   Revision 1.215  2015/12/16 08:52:24  brouard
+   Summary: 0.98r4 working
+   Revision 1.214  2015/12/16 06:57:54  brouard
+   Summary: temporary not working
+   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
- Line 510
+ Line 708
   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>
- Line 519
+ Line 726
  #ifdef _WIN32
  #include <io.h>
+ #include <windows.h>
+ #include <tchar.h>
  #else
  #include <unistd.h>
  #endif
  #include <limits.h>
  #include <sys/types.h>
- #include <sys/utsname.h>
+ #if defined(__GNUC__)
+ #include <sys/utsname.h> /* Doesn't work on Windows */
+ #endif
  #include <sys/stat.h>
  #include <errno.h>
  /* extern int errno; */
- Line 571  typedef struct {
+ Line 784  typedef struct {
  #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) ;
+ #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 AGEOVERFLOW 1.e20
  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
  #ifdef _WIN32
  #define DIRSEPARATOR '\\'
- Line 589  typedef struct {
+ Line 805  typedef struct {
  /* $Id$ */
  /* $State$ */
+ #include "version.h"
- char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+ char 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 */
  /* 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) */
- Line 627  double **matprod2(); /* test */
+ Line 844  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, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- Line 650  char fileresv[FILENAMELENGTH];
+ Line 867  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[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 706  static double maxarg1,maxarg2;
+ Line 923  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 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; */
- Line 725  int estepm;
+ Line 942  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 736  int **s; /* Status */
+ Line 959  int **s; /* Status */
  double *agedc;
  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 *Tage;
  int *Ndum; /** Freq of modality (tricode */
- int **codtab; /**< codtab=imatrix(1,100,1,10); */
+ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
  double *lsurv, *lpop, *tpop;
- Line 754  static int split( char *path, char *dirc
+ Line 978  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 765  static int split( char *path, char *dirc
+ Line 989  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 828  char *trimbb(char *out, char *in)
+ Line 1056  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'
+   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-      gives blocc="abcdef2ghi" and alocc="j".
+      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;
- Line 858  char *cutl(char *blocc, char *alocc, cha
+ Line 1129  char *cutl(char *blocc, char *alocc, cha
  }
  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 1135  char *subdirf3(char fileres[], char *pre
+ Line 1406  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;
- Line 1169  double f1dim(double x)
+ Line 1463  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=0,fv,fw,fx;
- Line 1222  double brent(double ax, double bx, doubl
+ Line 1522  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 1245  double brent(double ax, double bx, doubl
+ Line 1545  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) { /* Declining fa, 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)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
+       (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); /* Maximum abscisse where function can be evaluated */
+     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
-     if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
+     if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
        fu=(*func)(u);
  #ifdef DEBUG
        /* f(x)=A(x-u)**2+f(u) */
- Line 1272  void mnbrak(double *ax, double *bx, doub
+ Line 1591  void mnbrak(double *ax, double *bx, doub
        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) { /* 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 ************************/
- Line 1311  void linmin(double p[], double xi[], int
+ Line 1692  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); /* Find a bracket a,x,b in direction n=xi ie xicom */
+   xx=1.;
-   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
+ #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);
  }
- Line 1353  void powell(double p[], double **xi, int
+ Line 1804  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 1363  void powell(double p[], double **xi, int
+ Line 1815  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);
+   rcurr_time = time(NULL);
    for (*iter=1;;++(*iter)) {
-     fp=(*fret);
+     fp=(*fret); /* From former iteration or initial value */
      ibig=0;
      del=0.0;
      rlast_time=rcurr_time;
- Line 1375  void powell(double p[], double **xi, int
+ Line 1827  void powell(double p[], double **xi, int
      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
-    for (i=1;i<=n;i++) {
+     for (i=1;i<=n;i++) {
        printf(" %d %.12f",i, p[i]);
        fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
- Line 1403  void powell(double p[], double **xi, int
+ Line 1855  void powell(double p[], double **xi, int
          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, %lf, %lf \n", *fret, *fret, *fret);
+       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
-           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *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 1432  void powell(double p[], double **xi, int
+ Line 1889  void powell(double p[], double **xi, int
        printf("\n");
        fprintf(ficlog,"\n");
  #endif
-     } /* end i */
+     } /* 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 1463  void powell(double p[], double **xi, int
+ Line 1935  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++) { /* Computes an extrapolated point */
+     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 */
+ #ifdef POWELLF1F3
+ #else
      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
+ #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 */
-       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
-       /* Thus we compare delta(2h) with observed f1-f3 */
-       /* or best gain on one ancient line 'del' with total  */
-       /* gain f1-f2 = f1 - f2 - 'del' with del  */
        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+ #ifdef NRCORIGINAL
-       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
+       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);
-       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+ #endif
-       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
+       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),
- Line 1495  void powell(double p[], double **xi, int
+ Line 1971  void powell(double p[], double **xi, int
        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
  #endif
-       if (t < 0.0) { /* Then we use it for last direction */
+ #ifdef POWELLORIGINAL
-         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
+       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++) {
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[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 the direction with biggest decrease by n */
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
          }
-         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         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 average direction of P0 P%d instead of biggest increase direction :\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);
- Line 1514  void powell(double p[], double **xi, int
+ Line 2021  void powell(double p[], double **xi, int
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
-       } /* end of t negative */
+       } /* 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(); */ /* 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("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
+       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++) /\* Useless *\/ */
+     /*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]);*/
- Line 1563  double **prevalim(double **prlim, int nl
+ Line 2102  double **prevalim(double **prlim, int nl
      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);
-         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
+         max[j]=FMAX(max[j],prlim[i][j]);
-         max=FMAX(max,prlim[i][j]);
+         min[j]=FMIN(min[j],prlim[i][j]);
-         min=FMIN(min,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 ***************/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
+ double **bprevalim(double **bprlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
  {
-   /* According to parameters values stored in x and the covariate's values stored in cov,
+   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
-      computes the probability to be observed in state j being in state i by appying the
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-      model to the ncovmodel covariates (including constant and age).
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-      ncth covariate in the global vector x is given by the formula:
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+   /* Initial matrix pimij */
-      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+   /*  0,                   0                  , 1} */
-      Outputs ps[i][j] the probability to be observed in j being in j according to
+   /*
-      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+    * and after some iteration: */
-   */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-   double s1, lnpijopii;
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-   /*double t34;*/
+   /*  0,                   0                  , 1} */
-   int i,j, nc, ii, jj;
+   /* 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 */
-     for(i=1; i<= nlstate; i++){
+   int i, ii,j,k;
-       for(j=1; j<i;j++){
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+   /* double **matprod2(); */ /* test */
-           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+   double **out, cov[NCOVMAX+1], **bmij();
-           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+   double **newm;
- /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-         }
+   int ncvloop=0;
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+   min=vector(1,nlstate);
-       }
+   max=vector(1,nlstate);
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   meandiff=vector(1,nlstate);
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+     for (j=1;j<=nlstate+ndeath;j++){
- /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-         }
+     }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       }
+   cov[1]=1.;
+   /* 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+nagesqr+k]=nbcode[Tvar[k]][codtabm(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])]); */
+     }
+     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[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, oldm ,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate)); /* Bug Valgrind */
+     savm=oldm;
+     oldm=newm;
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
+       min[j]=1.;
+     }
+       /* sumnew=0; */
+       /* for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; */
+     for(j=1; j<=nlstate; j++){
+       for(i=1;i<=nlstate;i++){
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         bprlim[i][j]= newm[i][j];
+         max[i]=FMAX(max[i],bprlim[i][j]);
+         min[i]=FMIN(min[i],bprlim[i][j]);
+       }
+     }
+     maxmax=0.;
+     for(i=1; i<=nlstate; i++){
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
+       maxmax=FMAX(maxmax,meandiff[i]);
+       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
+     } /* j loop */
+     *ncvyear= -( (int)age- (int)agefin);
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
+     if(maxmax < ftolpl){
+       printf("OK Back maxmax=%lf ncvloop=%d, 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 bprlim;
+     }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
+   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+ Oldest 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 bprlim; /* should not reach here */
+ }
+ /*************** transition probabilities ***************/
+ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
+     for(i=1; i<= nlstate; i++){
+       for(j=1; j<i;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       }
      }
      for(i=1; i<= nlstate; i++){
- Line 1666  double **pmij(double **ps, double *cov,
+ Line 2343  double **pmij(double **ps, double *cov,
      return ps;
  }
+ /*************** transition probabilities ***************/
+ double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+ {
+   /* According to parameters values stored in x and the covariate's values stored in cov,
+      computes the probability to be observed in state j being in state i by appying the
+      model to the ncovmodel covariates (including constant and age).
+      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+      Outputs ps[i][j] the probability to be observed in j being in j according to
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
+     for(i=1; i<= nlstate; i++){
+       for(j=1; j<i;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+ /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+ /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       }
+       for(j=i+1; j<=nlstate+ndeath;j++){
+         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+ /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+         }
+         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       }
+     }
+     for(i=1; i<= nlstate; i++){
+       s1=0;
+       for(j=1; j<i; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       for(j=i+1; j<=nlstate+ndeath; j++){
+         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       }
+       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+       ps[i][i]=1./(s1+1.);
+       /* Computing other pijs */
+       for(j=1; j<i; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       for(j=i+1; j<=nlstate+ndeath; j++)
+         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     } /* end i */
+     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+       for(jj=1; jj<= nlstate+ndeath; jj++){
+         ps[ii][jj]=0;
+         ps[ii][ii]=1;
+       }
+     }
+     /* Added for backcast */
+     for(jj=1; jj<= nlstate; jj++){
+       s1=0.;
+       for(ii=1; ii<= nlstate; ii++){
+         s1+=ps[ii][jj];
+       }
+       for(ii=1; ii<= nlstate; ii++){
+         ps[ii][jj]=ps[ii][jj]/s1;
+       }
+     }
+     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+     /*   } */
+     /*   printf("\n "); */
+     /* } */
+     /* printf("\n ");printf("%lf ",cov[2]);*/
+     /*
+       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+       goto end;*/
+     return ps;
+ }
  /**************** Product of 2 matrices ******************/
  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
- Line 1705  double ***hpxij(double ***po, int nhstep
+ Line 2474  double ***hpxij(double ***po, int nhstep
    int i, j, d, h, k;
    double **out, cov[NCOVMAX+1];
    double **newm;
+   double agexact;
+   double agebegin, ageend;
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
- Line 1718  double ***hpxij(double ***po, int nhstep
+ Line 2489  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; /* age just before transition */
+       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 */
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[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+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)];
+         /* 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);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                     pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* if((int)age == 70){ */
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
+       savm=oldm;
+       oldm=newm;
+     }
+     for(i=1; i<=nlstate+ndeath; i++)
+       for(j=1;j<=nlstate+ndeath;j++) {
+         po[i][j][h]=newm[i][j];
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+       }
+     /*printf("h=%d ",h);*/
+   } /* end h */
+ /*     printf("\n H=%d \n",h); */
+   return po;
+ }
+ /************* Higher Back Matrix Product ***************/
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ {
+   /* Computes the transition matrix starting at age 'age' over
+      'nhstepm*hstepm*stepm' months (i.e. until
+      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
+      nhstepm*hstepm matrices.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+      (typically every 2 years instead of every month which is too big
+      for the memory).
+      Model is determined by parameters x and covariates have to be
+      included manually here.
+      */
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
+   double **newm;
+   double agexact;
+   double agebegin, ageend;
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
+     for(d=1; d <=hstepm; d++){
+       newm=savm;
+       /* Covariates have to be included here again */
+       cov[1]=1.;
+       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
+       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
+       cov[2]=agexact;
+       if(nagesqr==1)
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++)
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[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);*/
+       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+                   oldm);
+       /* if((int)age == 70){ */
+       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
        savm=oldm;
        oldm=newm;
      }
- Line 1745  double ***hpxij(double ***po, int nhstep
+ Line 2620  double ***hpxij(double ***po, int nhstep
    return po;
  }
  #ifdef NLOPT
    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    double fret;
- Line 1776  double func( double *x)
+ Line 2652  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]);*/
- Line 1797  double func( double *x)
+ Line 2674  double func( double *x)
           to be observed in j being in i according to the model.
         */
        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
-         cov[2+k]=covar[Tvar[k]][i];
+           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]
- Line 1810  double func( double *x)
+ Line 2687  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 1864  double func( double *x)
+ Line 2744  double func( double *x)
          which slows down the processing. The difference can be up to 10%
          lower mortality.
            */
+         /* 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==-1 ) { /* alive */
-         } else if  (s2==-2) {
            for (j=1,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            /*survp += out[s1][j]; */
            lli= log(survp);
          }
          else if  (s2==-4) {
            for (j=3,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
          else if  (s2==-5) {
            for (j=1,survp=0. ; j<=2; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
          else{
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
- Line 1896  double func( double *x)
+ Line 2792  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 1909  double func( double *x)
+ Line 2809  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 1930  double func( double *x)
+ Line 2833  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 1939  double func( double *x)
+ Line 2842  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 1960  double func( double *x)
+ Line 2866  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 1969  double func( double *x)
+ Line 2875  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 1984  double func( double *x)
+ Line 2893  double func( double *x)
          s2=s[mw[mi+1][i]][i];
          if( s2 > nlstate){
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += out[s1][j];
+           lli= log(survp);
          }else{
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }
- Line 1995  double func( double *x)
+ Line 2908  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 2004  double func( double *x)
+ Line 2917  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 2042  double funcone( double *x)
+ Line 2958  double funcone( double *x)
    double llt;
    int s1, s2;
    double bbh, survp;
+   double agexact;
+   double agebegin, ageend;
    /*extern weight */
    /* We are differentiating ll according to initial status */
    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- Line 2053  double funcone( double *x)
+ Line 2971  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++){
            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            savm[ii][j]=(ii==j ? 1.0 : 0.0);
          }
-       for(d=0; d<dh[mi][i]; d++){
+       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
+       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
+       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+           and mw[mi+1][i]. dh depends on stepm.*/
          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));
- Line 2077  double funcone( double *x)
+ Line 3004  double funcone( double *x)
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
+       /* if(s2==-1){ */
+       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
+       /*        /\* exit(1); *\/ */
+       /* } */
        bbh=(double)bh[mi][i]/(double)stepm;
        /* bias is positive if real duration
         * is higher than the multiple of stepm and negative otherwise.
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
          lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if  (s2==-2) {
+       } else if  ( s2==-1 ) { /* alive */
          for (j=1,survp=0. ; j<=nlstate; j++)
            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          lli= log(survp);
- Line 2104  double funcone( double *x)
+ Line 3035  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 %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], agebegin, ageend, 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 2138  void likelione(FILE *ficres,double p[],
+ Line 3069  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 ageb ageend 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 ageb agend 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 2155  void likelione(FILE *ficres,double p[],
+ Line 3086  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 2188  void mlikeli(FILE *ficres,double p[], in
+ Line 3133  void mlikeli(FILE *ficres,double p[], in
      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 2233  void mlikeli(FILE *ficres,double p[], in
+ Line 3178  void mlikeli(FILE *ficres,double p[], in
    fclose(ficrespow);
    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
-   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,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;
    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 2267  void hesscov(double **matcov, double p[]
+ Line 3212  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 2303  void hesscov(double **matcov, double p[]
+ Line 3248  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"); */
+   /* } */
-   /*  printf("\n#Hessian matrix recomputed#\n");
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
+    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;
- Line 2365  double hessii(double x[], double delta,
+ Line 3335  double hessii(double x[], double delta,
        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 2381  double hessii(double x[], double delta,
+ Line 3351  double hessii(double x[], double delta,
        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, 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 2499  void lubksb(double **a, int n, int *indx
+ Line 3546  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[])
+ 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[],\
+                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies */
    int i, m, jk, j1, bool, z1,j;
+   int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
    double *pp, **prop;
    double pos,posprop, k2, dateintsum=0,k2cpt=0;
-   char fileresp[FILENAMELENGTH];
+   char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
+   double agebegin, ageend;
    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);
    }
+   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);
+   }
+   else{
+     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %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=1+age+%s<br>\n",\
+           fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+     fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
+   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
+   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
+     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
+     fflush(ficlog);
+     exit(70);
+   }
+   else{
+     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %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=1+age+%s<br>\n",\
+           fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+   }
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    j1=0;
- Line 2530  void  freqsummary(char fileres[], int ia
+ Line 3613  void  freqsummary(char fileres[], int ia
    first=1;
-   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
+   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
-   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
-   /*    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 2548  void  freqsummary(char fileres[], int ia
+ Line 3627  void  freqsummary(char fileres[], int ia
        dateintsum=0;
        k2cpt=0;
-       for (i=1; i<=imx; i++) {
+       for (i=1; i<=imx; i++) { /* For each individual 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, 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, 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++){
+           /* for(m=firstpass; m<=lastpass; m++){ */
-             k2=anint[m][i]+(mint[m][i]/12.);
+           for(mi=1; mi<wav[i];mi++){
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+             m=mw[mi][i];
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+             /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+                and mw[mi+1][i]. dh depends on stepm. */
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
+             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+             ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
+             if(m >=firstpass && m <=lastpass){
+               k2=anint[m][i]+(mint[m][i]/12.);
+               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+               if (s[m][i]>0 && s[m][i]<=nlstate)  /* If status at wave m is known and a live state */
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];  /* At age of beginning of transition, where status is known */
                if (m<lastpass) {
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+                 /* if(s[m][i]==4 && s[m+1][i]==4) */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
+                 /*   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
-               }
+                 if(s[m][i]==-1)
+                   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
+                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
-                 dateintsum=dateintsum+k2;
+                 /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
-                 k2cpt++;
+                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                }
-               /*}*/
+             }
-           }
+             if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
-         }
+               dateintsum=dateintsum+k2;
-       } /* end i */
+               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<br/><br/><h3>********** Variable ");
-         fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+         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(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         }
+           fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtm, "**********</h3>\n");
+         fprintf(ficresphtmfr, "**********</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#");
+         fprintf(ficlog, "**********\n");
        }
-       for(i=1; i<=nlstate;i++)
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+       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");
+       /* Header of frequency table by age */
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(ficresphtmfr,"<th>Age</th> ");
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
+         for(m=-1; m <=nlstate+ndeath; m++){
+           if(jk!=0 && m!=0)
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
+         }
+       }
+       fprintf(ficresphtmfr, "\n");
+       /* For each age */
        for(i=iagemin; i <= iagemax+3; i++){
-         if(i==iagemax+3){
+         fprintf(ficresphtm,"<tr>");
+         if(i==iagemax+1){
+           fprintf(ficlog,"1");
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         }else if(i==iagemax+2){
+           fprintf(ficlog,"0");
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+         }else if(i==iagemax+3){
            fprintf(ficlog,"Total");
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
          }else{
            if(first==1){
              first=0;
              printf("See log file for details...\n");
            }
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
            fprintf(ficlog,"Age %d", i);
          }
          for(jk=1; jk <=nlstate ; jk++){
- Line 2647  void  freqsummary(char fileres[], int ia
+ Line 3773  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);
+             }
            }
          }
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+         for(jk=-1; jk <=nlstate+ndeath; jk++){
-           for(m=-1; m <=nlstate+ndeath; m++)
+           for(m=-1; m <=nlstate+ndeath; m++){
-             if(freq[jk][m][i] !=0 ) {
+             if(freq[jk][m][i] !=0 ) { /* minimizing output */
-             if(first==1)
+               if(first==1){
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+                 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(jk!=0 && m!=0)
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
+           }
+         }
+         fprintf(ficresphtmfr,"</tr>\n ");
+         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");
+       fprintf(ficresphtmfr,"</table>\n");
        /*}*/
-   }
+   } /* end j1 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
+   fclose(ficresphtm);
+   fclose(ficresphtmfr);
    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 2688  void prevalence(double ***probs, double
+ Line 3829  void prevalence(double ***probs, double
    */
    int i, m, jk, j1, bool, z1,j;
+   int mi; /* Effective wave */
+   int iage;
+   double agebegin, ageend;
    double **prop;
    double posprop;
- Line 2707  void prevalence(double ***probs, double
+ Line 3851  void prevalence(double ***probs, double
    first=1;
    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
-     /*for(i1=1; i1<=ncodemax[k1];i1++){
+     for (i=1; i<=nlstate; i++)
-       j1++;*/
+       for(iage=iagemin; iage <= iagemax+3; iage++)
+         prop[i][iage]=0.0;
-       for (i=1; i<=nlstate; i++)
-         for(m=iagemin; m <= iagemax+3; m++)
+     for (i=1; i<=imx; i++) { /* Each individual */
-           prop[i][m]=0.0;
+       bool=1;
+       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-       for (i=1; i<=imx; i++) { /* Each individual */
+         for (z1=1; z1<=cptcoveff; z1++)
-         bool=1;
+           if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
-         if  (cptcovn>0) {
+             bool=0;
-           for (z1=1; z1<=cptcoveff; z1++)
+       }
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+       if (bool==1) {
-               bool=0;
+         /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-         }
+         for(mi=1; mi<wav[i];mi++){
-         if (bool==1) {
+           m=mw[mi][i];
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+           if(m >=firstpass && m <=lastpass){
              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
                if (s[m][i]>0 && s[m][i]<=nlstate) {
                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                  prop[s[m][i]][iagemax+3] += weight[i];
-               }
+               } /* end valid statuses */
-             }
+             } /* end selection of dates */
            } /* end selection of waves */
-         }
+         } /* end effective waves */
-       }
+       } /* end bool */
-       for(i=iagemin; i <= iagemax+3; i++){
+     }
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+     for(i=iagemin; i <= iagemax+3; i++){
-           posprop += prop[jk][i];
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-         }
+         posprop += prop[jk][i];
+       }
-         for(jk=1; jk <=nlstate ; jk++){
-           if( i <=  iagemax){
+       for(jk=1; jk <=nlstate ; jk++){
-             if(posprop>=1.e-5){
+         if( i <=  iagemax){
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+           if(posprop>=1.e-5){
-             } else{
+             probs[i][jk][j1]= prop[jk][i]/posprop;
-               if(first==1){
+           } else{
-                 first=0;
+             if(first==1){
-                 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]);
+               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 jk */
+     }/* end i */
      /*} *//* end i1 */
    } /* end j1 */
- Line 2777  void  concatwav(int wav[], int **dh, int
+ Line 3924  void  concatwav(int wav[], int **dh, int
    int i, mi, m;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
-   int first;
+   int first, firstwo, firsthree;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
+   firstwo=0;
+   firsthree=0;
    jmin=100000;
    jmax=-1;
    jmean=0.;
-   for(i=1; i<=imx; i++){
+   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
      mi=0;
      m=firstpass;
-     while(s[m][i] <= nlstate){
+     while(s[m][i] <= nlstate){  /* a live state */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
          mw[++mi][i]=m;
-       if(m >=lastpass)
+       }
+       if(m >=lastpass){
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+           if(firsthree == 0){
+             printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             firsthree=1;
+           }else{
+             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+           }
+           mw[++mi][i]=m;
+         }
+         if(s[m][i]==-2){ /* Vital status is really unknown */
+           nbwarn++;
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+           }
+           break;
+         }
          break;
+       }
        else
          m++;
      }/* end while */
-     if (s[m][i] > nlstate){
+     /* After last pass */
+     if (s[m][i] > nlstate){  /* In a death state */
        mi++;     /* Death is another wave */
        /* if(mi==0)  never been interviewed correctly before death */
           /* Only death is a correct wave */
        mw[mi][i]=m;
+     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
+       /* m++; */
+       /* mi++; */
+       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
+       /* mw[mi][i]=m; */
+       nberr++;
+       if(firstwo==0){
+         printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         firstwo=1;
+       }else if(firstwo==1){
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+       }
      }
      wav[i]=mi;
      if(mi==0){
        nbwarn++;
- Line 2814  void  concatwav(int wav[], int **dh, int
+ Line 3997  void  concatwav(int wav[], int **dh, int
        }
      } /* end mi==0 */
    } /* End individuals */
+   /* wav and mw are no more changed */
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
- Line 2910  void tricode(int *Tvar, int **nbcode, in
+ Line 4095  void tricode(int *Tvar, int **nbcode, in
  {
    /**< 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]
     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-   /* nbcode[Tvar[j]][1]=
+    * nbcode[Tvar[j]][1]=
    */
    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
- Line 2923  void tricode(int *Tvar, int **nbcode, in
+ Line 4108  void tricode(int *Tvar, int **nbcode, in
    cptcoveff=0;
-   for (k=-1; k < maxncov; k++) Ndum[k]=0;
    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
    /* Loop on covariates without age and products */
-   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
+   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
+     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. Value of the covariate Tvar[j] for individual i
                                      * If product of Vn*Vm, still boolean *:
- Line 2950  void tricode(int *Tvar, int **nbcode, in
+ Line 4135  void tricode(int *Tvar, int **nbcode, in
        /* 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<=cptcode; i++) {*/
-     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
+     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
-       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
+       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
+       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
-         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
+       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
+         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 */
-     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
+     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
-     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
+        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
         modmincovj=3; modmaxcovj = 7;
-        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
+        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
-        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
+        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
-        variables V1_1 and V1_2.
+        defining two dummy variables: variables V1_1 and V1_2.
         nbcode[Tvar[j]][ij]=k;
         nbcode[Tvar[j]][1]=0;
         nbcode[Tvar[j]][2]=1;
         nbcode[Tvar[j]][3]=2;
+        To be continued (not working yet).
      */
-     ij=1; /* ij is similar to i but can jumps over null modalities */
+     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 */
+     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*/
-       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
+         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-         /*recode from 0 */
+           break;
-         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
+         }
-           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.
+         ij++;
-                                      k is a modality. If we have model=V1+V1*sex
+         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.*/
-                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+         cptcode = ij; /* New max modality for covar j */
-           ij++;
+     } /* end of loop on modality i=-1 to 1 or more */
-         }
-         if (ij > ncodemax[j]) break;
+     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-       }  /* end of loop on */
+     /*  /\*recode from 0 *\/ */
-     } /* end of loop on modality */
+     /*                               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=-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=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)){
+      ij++;
       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       Tvaraff[ij]=i; /*For printing (unclear) */
-      ij++;
+    }else{
-    }else
+        /* Tvaraff[ij]=0; */
-        Tvaraff[ij]=0;
+    }
   }
-  ij--;
+  /* ij--; */
   cptcoveff=ij; /*Number of total covariates*/
  }
- Line 3335  void cvevsij(double ***eij, double x[],
+ Line 4541  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 ;
- Line 3361  void varevsij(char optionfilefiname[], d
+ Line 4570  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 3375  void varevsij(char optionfilefiname[], d
+ Line 4584  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 3397  void varevsij(char optionfilefiname[], d
+ Line 4605  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 3433  void varevsij(char optionfilefiname[], d
+ Line 4643  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 3456  void varevsij(char optionfilefiname[], d
+ Line 4666  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 3469  void varevsij(char optionfilefiname[], d
+ Line 4679  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 3487  void varevsij(char optionfilefiname[], d
+ Line 4698  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 3500  void varevsij(char optionfilefiname[], d
+ Line 4711  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 3562  void varevsij(char optionfilefiname[], d
+ Line 4775  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 3579  void varevsij(char optionfilefiname[], d
+ Line 4792  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 3610  void varevsij(char optionfilefiname[], d
+ Line 4824  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 size 320, 240");
+   /* 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 1 ",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)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
+   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <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 3639  void varevsij(char optionfilefiname[], d
+ Line 4855  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 **dnewm,**doldm;
- Line 3649  void varprevlim(char fileres[], double *
+ Line 4865  void varprevlim(char fileres[], double *
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mgm, **mgp;
    double age,agelim;
    int theta;
- Line 3671  void varprevlim(char fileres[], double *
+ Line 4888  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 3678  void varprevlim(char fileres[], double *
+ Line 4897  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 3697  void varprevlim(char fileres[], double *
+ Line 4925  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 3711  void varprevlim(char fileres[], double *
+ Line 4962  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 3742  void varprob(char optionfilefiname[], do
+ Line 4995  void varprob(char optionfilefiname[], do
    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 3797  void varprob(char optionfilefiname[], do
+ Line 5050  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 3821  To be simple, these graphs help to under
+ Line 5073  To be simple, these graphs help to under
      /*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#");
        }
- Line 3847  To be simple, these graphs help to under
+ Line 5099  To be simple, these graphs help to under
        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]]];/* j1 1 2 3 4
+           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)];
          for(theta=1; theta <=npar; theta++){
- Line 4005  To be simple, these graphs help to under
+ Line 5261  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 size 320, 240");
+                     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 4032  To be simple, these graphs help to under
+ Line 5289  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 4054  To be simple, these graphs help to under
+ Line 5311  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 backcast, 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 \
+    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 ",
+    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
-            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
+            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
+    fprintf(fichtm,"<li> - 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,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,"\
+  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
+            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     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): \
+  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
-    <a href=\"%s\">%s</a> <br>\n",
+            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
-            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fprintf(fichtm,"\
-  - Population projections by age and states: \
+  - (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</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
+    <a href=\"%s\">%s</a> <br>\n",
+            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
+    if(prevfcast==1){
+      fprintf(fichtm,"\
+  - 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>");
- Line 4089  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 5357  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   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%d_1.png\">%s%d_1.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%d_1.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%d_2.png\">%s%d_2.png</a><br> \
+  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
- <img src=\"%s%d_2.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>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
+      /* Survival functions (period) in state j */
- <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+      for(cpt=1; cpt<=nlstate;cpt++){
-        }
+        fprintf(fichtm,"<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(backcast==1){
+      /* Period (stable) back prevalence in each health state */
+      for(cpt=1; cpt<=nlstate;cpt++){
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),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 %.1f to %.1f) 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 in each alive state (1 to %d) : <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,nlstate,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 4163  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 5471  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   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 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 4204  void printinggnuplot(char fileres[], cha
+ Line 5514  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:(-$13):6 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:(-$13):5 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:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 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:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 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*/
-   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
+   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
-   for (cpt=1; cpt<= nlstate ; cpt ++) {
+     for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
-      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
+       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 size 320, 240\n\
+ set ter svg size 640, 480\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(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\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      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 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
       for (i=1; i<= nlstate ; i ++) {
-        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-        else fprintf(ficgp," \%%*lf (\%%*lf)");
+        else fprintf(ficgp," %%*lf (%%*lf)");
       }
-      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+      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*/
-   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
    for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\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 0,");
+       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 0");
+         }
-       else fprintf(ficgp,"\" t\"\" w l lt 0,");
+         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+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+         for (j=1; j<= nlstate+1 ; j ++) {
+           if (j==i) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+       } /* state */
+     } /* vpopbased */
+     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
+   } /* k1 */
    /*3eme*/
    for (k1=1; k1<= m ; k1 ++) {
      for (cpt=1; cpt<= nlstate ; cpt ++) {
+       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         vlv= nbcode[Tvaraff[lv]][lv];
+         fprintf(ficgp," V%d=%d ",k,vlv);
+       }
+       fprintf(ficgp,"\n#\n");
        /*       k=2+nlstate*(2*cpt-2); */
        k=2+(nlstate+1)*(cpt-1);
-       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
-       fprintf(ficgp,"set ter png small size 320, 240\n\
+       fprintf(ficgp,"set ter svg size 640, 480\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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 4283  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 5660  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 each multivariate if any */
      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;
+       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/($%d",k1,k+l+(cpt-1),k+l);
+         for (j=2; j<= nlstate+ndeath ; j ++)
+           fprintf(ficgp,"+$%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]  ", ageminpar, agemaxpar);
        k=3;
-       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
+       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+         if(j==1)
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(cpt-1) +j;
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         /*   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,"\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 png small size 320, 240\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(fileres,"pij"));
+           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
          l=(nlstate+ndeath)*(i-1)+1;
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-         for (j=1; j<= (nlstate-1) ; j ++)
+         for (j=2; j<= nlstate ; j ++)
-           fprintf(ficgp,"+$%d",k+l+j);
+           fprintf(ficgp,"+$%d",k+l+j-1);
          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\n");
+       fprintf(ficgp,"\nset out\n");
      } /* end cpt state*/
    } /* end covariate */
+     /* CV back 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 Back 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,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),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,"PIJB_"));
+         else
+           fprintf(ficgp,", '' ");
+         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /* a vérifier */
+         for (j=2; j<= nlstate ; j ++)
+           fprintf(ficgp,"+$%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");
    /*goto avoid;*/
-    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+   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 size 320, 240\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)]);
-                /* else */
+                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                    ij++;
+                  }
+                }
+                else
+                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
               }
+            }else{
+              i=i-ncovmodel;
+              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+                fprintf(ficgp," (1.");
+            }
+            if(ng != 1){
               fprintf(ficgp,")/(1");
               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)
+                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                else /* nagesqr =1 */
+                  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);
                 ij=1;
-                for(j=3; j <=ncovmodel; j++){
+                for(j=3; j <=ncovmodel-nagesqr; j++){
-                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
+                  if(ij <=cptcovage) { /* Bug valgrind */
-                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
+                    if((j-2)==Tage[ij]) { /* Bug valgrind */
-                  /*   ij++; */
+                      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])]); */
-                  /* else */
+                      ij++;
-                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                    }
+                  }
+                  else
+                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                 }
                 fprintf(ficgp,")");
               }
-              fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+              fprintf(ficgp,")");
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+              if(ng ==2)
-              i=i+ncovmodel;
+                fprintf(ficgp," t \"p%d%d\" ", k2,k);
+              else /* ng= 3 */
+                fprintf(ficgp," t \"i%d%d\" ", k2,k);
+            }else{ /* end ng <> 1 */
+              if( k !=k2) /* logit p11 is hard to draw */
+                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
             }
+            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
+              fprintf(ficgp,",");
+            if (ng == 1 && k!=k2 && (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: */
- Line 4426  int movingaverage(double ***probs, doubl
+ Line 6081  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
- Line 4441  prevforecast(char fileres[], double anpr
+ Line 6096  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.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
    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);
    }
-   printf("Computing forecasting: result on file '%s' \n", fileresf);
+   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
- Line 4491  prevforecast(char fileres[], double anpr
+ Line 6152  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);
          fprintf(ficresf," p.%d",j);
        }
        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
          fprintf(ficresf,"\n");
          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
          for (agec=fage; agec>=(ageminpar-1); agec--){
            nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            oldm=oldms;savm=savms;
            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
            for (h=0; h<=nhstepm; h++){
              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 4546  prevforecast(char fileres[], double anpr
+ Line 6205  prevforecast(char fileres[], double anpr
    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficresf);
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
+ }
+ /************** Back Forecasting ******************/
+ void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
+   /* back1, year, month, day of starting backection
+      agemin, agemax range of age
+      dateprev1 dateprev2 range of dates during which prevalence is computed
+      anback2 year of en of backection (same day and month as back1).
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+   double agec; /* generic age */
+   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   double ***mobaverage;
+   char fileresfb[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.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
+   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   strcpy(fileresfb,"FB_");
+   strcat(fileresfb,fileresu);
+   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
+     printf("Problem with back forecast resultfile: %s\n", fileresfb);
+     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+   }
+   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   if (mobilav!=0) {
+     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+     }
+   }
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else  hstepm=estepm;
+   hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
+   anprojmean=yp;
+   yp2=modf((yp1*12),&yp);
+   mprojmean=yp;
+   yp1=modf((yp2*30.5),&yp);
+   jprojmean=yp;
+   if(jprojmean==0) jprojmean=1;
+   if(mprojmean==0) jprojmean=1;
+   i1=cptcoveff;
+   if (cptcovn < 1){i1=1;}
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
+ /*            if (h==(int)(YEARM*yearp)){ */
+   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+       k=k+1;
+       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       fprintf(ficresfb," yearbproj age");
+       for(j=1; j<=nlstate+ndeath;j++){
+         for(i=1; i<=nlstate;i++)
+           fprintf(ficresfb," p%d%d",i,j);
+         fprintf(ficresfb," p.%d",j);
+       }
+       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
+      /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
+         fprintf(ficresfb,"\n");
+         fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
+         for (agec=fage; agec>=(ageminpar-1); agec--){
+           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+           nhstepm = nhstepm/hstepm;
+           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           oldm=oldms;savm=savms;
+           hbxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+           for (h=0; h<=nhstepm; h++){
+             if (h*hstepm/YEARM*stepm ==yearp) {
+               fprintf(ficresfb,"\n");
+               for(j=1;j<=cptcoveff;j++)
+                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+               fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm);
+             }
+             for(j=1; j<=nlstate+ndeath;j++) {
+               ppij=0.;
+               for(i=1; i<=nlstate;i++) {
+                 if (mobilav==1)
+                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                 else {
+                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                 }
+                 if (h*hstepm/YEARM*stepm== yearp) {
+                   fprintf(ficresfb," %.3f", p3mat[i][j][h]);
+                 }
+               } /* end i */
+               if (h*hstepm/YEARM*stepm==yearp) {
+                 fprintf(ficresfb," %.3f", ppij);
+               }
+             }/* end j */
+           } /* end h */
+           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         } /* end agec */
+       } /* end yearp */
+     } /* end cptcod */
+   } /* end  cptcov */
+   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   fclose(ficresfb);
+   printf("End of Computing Back forecasting \n");
+   fprintf(ficlog,"End of Computing Back forecasting\n");
  }
  /************** 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 4567  populforecast(char fileres[], double anp
+ Line 6360  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 4615  populforecast(char fileres[], double anp
+ Line 6408  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 4921  double gompertz_f(const gsl_vector *v, v
+ Line 6714  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 4930  void printinghtmlmort(char fileres[], ch
+ Line 6723  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 4945  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 6738  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];
- Line 4959  void printinggnuplotmort(char fileres[],
+ Line 6752  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 size 320, 240\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,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
- Line 4982  int readdata(char datafile[], int firsto
+ Line 6775  int readdata(char datafile[], int firsto
    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 5025  int readdata(char datafile[], int firsto
+ Line 6818  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.",dummy) != 0){
+       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
          month=99;
          year=9999;
        }else{
- Line 5041  int readdata(char datafile[], int firsto
+ Line 6834  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 5056  int readdata(char datafile[], int firsto
+ Line 6849  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.", dummy) != 0){
+     else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
        month=99;
        year=9999;
      }else{
- Line 5156  void removespace(char *str) {
+ Line 6949  void removespace(char *str) {
    do
      while (*p2 == ' ')
        p2++;
-   while (*p1++ = *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
+    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
-    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+    * - nagesqr = 1 if age*age in the model, otherwise 0.
-    * - cptcovn or number of covariates k of the models excluding age*products =6
+    * - 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
- Line 5177  int decodemodel ( char model[], int last
+ Line 6971  int decodemodel ( char model[], int last
    int  j1, k1, k2;
    char modelsav[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=0, k2=-1, ks=0, cptcovn=0;
-     j=nbocc(model,'+'); /**< j=Number of '+' */
-     j1=nbocc(model,'*'); /**< j1=Number of '*' */
-     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
-     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
-                   /* including age products which are counted in cptcovage.
-                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
-     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
-     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
-     strcpy(modelsav,model);
      if (strstr(model,"AGE") !=0){
-       printf("Error. AGE must be in lower case 'age' model=%s ",model);
+       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 5200  int decodemodel ( char model[], int last
+ Line 6986  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);
-     /*   Design
+     if ((strpt=strstr(model,"age*age")) !=0){
-      *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+       printf(" strpt=%s, model=%s\n",strpt, model);
-      *  <          ncovcol=8                >
+       if(strpt != model){
-      * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-      *   k=  1    2      3       4     5       6      7        8
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-      *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+  corresponding column of parameters.\n",model);
-      *  covar[k,i], value of kth covariate if not including age for individual i:
+       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
-      *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
-      *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+  corresponding column of parameters.\n",model); fflush(ficlog);
-      *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+       return 1;
-      *  Tage[++cptcovage]=k
+     }
-      *       if products, new covar are created after ncovcol with k1
-      *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
-      *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
-      *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
-      *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
-      *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
-      *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
-      *  <          ncovcol=8                >
-      *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
-      *          k=  1    2      3       4     5       6      7        8    9   10   11  12
-      *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-      * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-      * p Tprod[1]@2={                         6, 5}
-      *p Tvard[1][1]@4= {7, 8, 5, 6}
-      * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
-      *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-      *How to reorganize?
-      * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
-      * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
-      *       {2,   1,     4,      8,    5,      6,     3,       7}
-      * Struct []
-      */
-     /* This loop fills the array Tvar from the string 'model'.*/
+       nagesqr=1;
-     /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       if (strstr(model,"+age*age") !=0)
-     /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+         substrchaine(modelsav, model, "+age*age");
-     /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       else if (strstr(model,"age*age+") !=0)
-     /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
+         substrchaine(modelsav, model, "age*age+");
-     /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
+       else
-     /*  k=1 Tvar[1]=2 (from V2) */
+         substrchaine(modelsav, model, "age*age");
-     /*  k=5 Tvar[5] */
+     }else
-     /* for (k=1; k<=cptcovn;k++) { */
+       nagesqr=0;
-     /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+     if (strlen(modelsav) >1){
-     /*  } */
+       j=nbocc(modelsav,'+'); /**< j=Number of '+' */
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-     /*
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
-      * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+       cptcovt= j+1; /* Number of total covariates in the model, not including
-     for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+                    * cst, age and age*age
+                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
+                   /* including age products which are counted in cptcovage.
+                   * but the covariates which are products must be treated
+                   * separately: ncovn=4- 2=2 (V1+V3). */
+       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
+       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
+       /*   Design
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
+        *  <          ncovcol=8                >
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+        *   k=  1    2      3       4     5       6      7        8
+        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+        *  covar[k,i], value of kth covariate if not including age for individual i:
+        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+        *  Tage[++cptcovage]=k
+        *       if products, new covar are created after ncovcol with k1
+        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
+        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
+        *  <          ncovcol=8                >
+        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
+        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
+        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
+        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tprod[1]@2={                         6, 5}
+        *p Tvard[1][1]@4= {7, 8, 5, 6}
+        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
+        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+        *How to reorganize?
+        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        *       {2,   1,     4,      8,    5,      6,     3,       7}
+        * Struct []
+        */
+       /* This loop fills the array Tvar from the string 'model'.*/
+       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
+       /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+       /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
+       /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
+       /*        k=1 Tvar[1]=2 (from V2) */
+       /*        k=5 Tvar[5] */
+       /* for (k=1; k<=cptcovn;k++) { */
+       /*        cov[2+k]=nbcode[Tvar[k]][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;
+       cptcovage=0;
-     for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
-       cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
-                                      modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-       /*scanf("%d",i);*/
+         /*scanf("%d",i);*/
-       if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         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 */
+           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 */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-           /* covar is not filled and then is empty */
+             /* covar is not filled and then is empty */
-           cptcovprod--;
+             cptcovprod--;
-           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             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 */
+             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 */
+             cptcovage++; /* Sums the number of covariates which include age as a product */
-           Tage[cptcovage]=k;  /* Tage[1] = 4 */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-           /*printf("stre=%s ", stre);*/
+             /*printf("stre=%s ", stre);*/
-         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-           cptcovprod--;
+             cptcovprod--;
-           cutl(stre,strb,strc,'V');
+             cutl(stre,strb,strc,'V');
-           Tvar[k]=atoi(stre);
+             Tvar[k]=atoi(stre);
-           cptcovage++;
+             cptcovage++;
-           Tage[cptcovage]=k;
+             Tage[cptcovage]=k;
-         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-           /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             /* 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++;
-           cptcovprodnoage++;k1++;
+           Tvar[k]=atoi(strd);
-           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
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-                                   because this model-covariate is a construction we invent a new column
+         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-                                   ncovcol + k1
+           scanf("%d",i);*/
-                                   If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+       } /* end of loop + on total covariates */
-                                   Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+     } /* end if strlen(modelsave == 0) age*age might exist */
-           cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+   } /* end if strlen(model == 0) */
-           Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-           Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-           Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-           k2=k2+2;
-           Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
-           Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
-           for (i=1; i<=lastobs;i++){
-             /* Computes the new covariate which is a product of
-                covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-             covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-           }
-         } /* End age is not in the model */
-       } /* End if model includes a product */
-       else { /* no more sum */
-         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-        /*  scanf("%d",i);*/
-         cutl(strd,strc,strb,'V');
-         ks++; /**< Number of simple covariates */
-         cptcovn++;
-         Tvar[k]=atoi(strd);
-       }
-       strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-         scanf("%d",i);*/
-     } /* end of loop + */
-   } /* end model */
    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
- Line 5328  int decodemodel ( char model[], int last
+ Line 7150  int decodemodel ( char model[], int last
      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 5336  calandcheckages(int imx, int maxwav, dou
+ Line 7158  calandcheckages(int imx, int maxwav, dou
      for(m=2; (m<= maxwav); m++) {
        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;
-         s[m][i]=-1;
+         if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
+           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 5356  calandcheckages(int imx, int maxwav, dou
+ Line 7179  calandcheckages(int imx, int maxwav, dou
    for (i=1; i<=imx; i++)  {
      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
      for(m=firstpass; (m<= lastpass); m++){
-       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
+       if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
          if (s[m][i] >= nlstate+1) {
-           if(agedc[i]>0)
+           if(agedc[i]>0){
-             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
+             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                agev[m][i]=agedc[i];
-           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+               /*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 5370  calandcheckages(int imx, int maxwav, dou
+ Line 7193  calandcheckages(int imx, int maxwav, dou
                  agev[m][i]=-1;
                }
              }
-         }
+           } /* agedc > 0 */
+         } /* end if */
          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                   years but with the precision of a month */
            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
- Line 5386  calandcheckages(int imx, int maxwav, dou
+ Line 7210  calandcheckages(int imx, int maxwav, dou
            }
            /*agev[m][i]=anint[m][i]-annais[i];*/
            /*     agev[m][i] = age[i]+2*m;*/
-         }
+         } /* en if 9*/
          else { /* =9 */
+           /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
            agev[m][i]=1;
            s[m][i]=-1;
          }
        }
-       else /*= 0 Unknown */
+       else if(s[m][i]==0) /*= 0 Unknown */
          agev[m][i]=1;
-     }
+       else{
+         printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
+         agev[m][i]=0;
+       }
+     } /* End for lastpass */
    }
    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 5425  calandcheckages(int imx, int maxwav, dou
+ Line 7255  calandcheckages(int imx, int maxwav, dou
      return (1);
  }
- syscompilerinfo()
+ #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"*/
- #include <gnu/libc-version.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__)
- # if defined(__GNUC_PATCHLEVEL__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
- #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ #endif
-                             + __GNUC_MINOR__ * 100 \
+ #elif defined(__GNUC__)
-                             + __GNUC_PATCHLEVEL__)
+ #ifndef  __APPLE__
- # else
+ #include <gnu/libc-version.h>  /* Only on gnu */
- #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
+ #endif
-                             + __GNUC_MINOR__ * 100)
+    struct utsname sysInfo;
- # endif
+    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...
+     // 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__   */
- Line 5460  syscompilerinfo()
+ Line 7398  syscompilerinfo()
  /* _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. */
- #include <stdint.h>
  #if UINTPTR_MAX == 0xffffffff
-    printf("32-bit \n"); /* 32-bit */
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
  #elif UINTPTR_MAX == 0xffffffffffffffff
-   printf("64-bit \n");/* 64-bit */
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
  #else
-  printf("wtf-bit \n"); /* wtf */
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
  #endif
- struct utsname sysInfo;
+ #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) {
-       puts(sysInfo.sysname);
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       puts(sysInfo.nodename);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-       puts(sysInfo.release);
-       puts(sysInfo.version);
-       puts(sysInfo.machine);
     }
     else
        perror("uname() error");
-    printf("GNU C version %d\n", __GNUC_VERSION__);
+    //#ifndef __INTEL_COMPILER
-   printf("GNU libc version: %s\n", gnu_get_libc_version());
+ #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 back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+   /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+   int i, j, k, i1 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   strcpy(fileresplb,"PLB_");
+   strcat(fileresplb,fileresu);
+   if((ficresplb=fopen(fileresplb,"w"))==NULL) {
+     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+   }
+   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   pstamp(ficresplb);
+   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficresplb,"#Age ");
+   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
+   fprintf(ficresplb,"\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(ficresplb,"#******");
+         printf("#******");
+         fprintf(ficlog,"#******");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresplb," 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(ficresplb,"******\n");
+         printf("******\n");
+         fprintf(ficlog,"******\n");
+         fprintf(ficresplb,"#Age ");
+         for(j=1;j<=cptcoveff;j++) {
+           fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
+         for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+         fprintf(ficresplb,"Total Years_to_converge\n");
+         for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+           bprevalim(bprlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+           fprintf(ficresplb,"%.0f ",age );
+           for(j=1;j<=cptcoveff;j++)
+             fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           tot=0.;
+           for(i=1; i<=nlstate;i++){
+             tot +=  bprlim[i][i];
+             fprintf(ficresplb," %.5f", bprlim[i][i]);
+           }
+           fprintf(ficresplb," %.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;
+ }
+  int hBijx(double *p, int bage, int fage){
+     /*------------- h Bij x at various ages ------------*/
+   int stepsize;
+   int agelim;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k;
+   double agedeb;
+   double ***p3mat;
+     strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
+     if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
+       printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+       fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+     }
+     printf("Computing pij back: result on file '%s' \n", filerespijb);
+     fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
+     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(ficrespijb);
+     fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j 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(ficrespijb,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficrespijb,"******\n");
+       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       for (agedeb=bage; agedeb<=fage; 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;
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
+         for(i=1; i<=nlstate;i++)
+           for(j=1; j<=nlstate+ndeath;j++)
+             fprintf(ficrespijb," %1d-%1d",i,j);
+         fprintf(ficrespijb,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+           /* fprintf(ficrespijb,"%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(ficrespijb," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespijb,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespijb,"\n");
+       }
+       /*}*/
+     }
+         return 0;
+ }
  /***********************************************/
  /**************** Main Program *****************/
  /***********************************************/
- Line 5500  int main(int argc, char *argv[])
+ Line 7754  int main(int argc, char *argv[])
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int ncvyear=0; /* Number of years needed for the period prevalence to converge */
    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;
- Line 5511  int main(int argc, char *argv[])
+ Line 7766  int main(int argc, char *argv[])
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
    struct stat info;
-   double agedeb;
+   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 dum; /* Dummy variable */
+   double dum=0.; /* Dummy variable */
    double ***p3mat;
    double ***mobaverage;
    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 *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
-   int c,  h , cpt;
+   int c,  h , cpt, c2;
-   int jl;
+   int jl=0;
-   int i1, j1, jk, stepsize;
+   int i1, j1, jk, stepsize=0;
+   int count=0;
    int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
+   int backcast=0;
    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=0, fage=110, age, agelim, agebase;
+   double bage=0, fage=110., age, agelim=0., agebase=0.;
    double ftolpl=FTOL;
    double **prlim;
+   double **bprlim;
    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;
- Line 5549  int main(int argc, char *argv[])
+ Line 7812  int main(int argc, char *argv[])
    double *epj, vepp;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
    double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    int *dcwave;
- Line 5592  int main(int argc, char *argv[])
+ Line 7857  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';
      i=strlen(pathr);
-     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
+     if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
        pathr[i-1]='\0';
-    for (tok = pathr; tok != NULL; ){
+     }
+     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 5628  int main(int argc, char *argv[])
+ Line 7906  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 5645  int main(int argc, char *argv[])
+ Line 7928  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 5653  int main(int argc, char *argv[])
+ Line 7936  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\
- Line 5661  int main(int argc, char *argv[])
+ Line 7944  int main(int argc, char *argv[])
   optionfilext=%s\n\
   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-   syscompilerinfo();
+   syscompilerinfo(1);
    printf("Local time (at start):%s",strstart);
    fprintf(ficlog,"Local time (at start): %s",strstart);
- Line 5672  int main(int argc, char *argv[])
+ Line 7955  int main(int argc, char *argv[])
    /* */
    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' with errno='%s'\n",optionfile,strerror(errno));
- Line 5687  int main(int argc, char *argv[])
+ Line 7972  int main(int argc, char *argv[])
    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 5697  int main(int argc, char *argv[])
+ Line 7982  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 5731  int main(int argc, char *argv[])
+ Line 8094  int main(int argc, char *argv[])
       v1+v2*age+v2*v3 makes cptcovn = 3
    */
    if (strlen(model)>1)
-     ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+     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*/
    else
-     ncovmodel=2;
+     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 5749  int main(int argc, char *argv[])
+ Line 8111  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 guessed parameters */
- Line 5784  int main(int argc, char *argv[])
+ Line 8147  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 5792  run imach with mle=-1 to get a correct t
+ Line 8155  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 5871  run imach with mle=-1 to get a correct t
+ Line 8234  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 5895  run imach with mle=-1 to get a correct t
+ Line 8269  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 5911  run imach with mle=-1 to get a correct t
+ Line 8286  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 5933  run imach with mle=-1 to get a correct t
+ Line 8309  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 5968  run imach with mle=-1 to get a correct t
+ Line 8345  run imach with mle=-1 to get a correct t
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                        */
+ /* Main decodemodel */
    if(decodemodel(model, lastobs) == 1)
      goto end;
- Line 5993  run imach with mle=-1 to get a correct t
+ Line 8373  run imach with mle=-1 to get a correct t
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
+   /* free_vector(moisdc,1,n); */
-   free_vector(andc,1,n);
+   /* free_vector(andc,1,n); */
    /* */
    wav=ivector(1,imx);
-   dh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   bh=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
-   mw=imatrix(1,lastpass-firstpass+1,1,imx);
+   /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
+   dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
+   bh=imatrix(1,lastpass-firstpass+2,1,imx);
+   mw=imatrix(1,lastpass-firstpass+2,1,imx);
    /* Concatenates waves */
+   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+      Death is a valid wave (if date is known).
+      mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
+      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+      and mw[mi+1][i]. dh depends on stepm.
+   */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
    /* */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
    /* 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;
    Ndum =ivector(-1,NCOVMAX);
-   if (ncovmodel > 2)
+   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
      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).
+    */
-   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
    h=0;
- Line 6024  run imach with mle=-1 to get a correct t
+ Line 8428  run imach with mle=-1 to get a correct t
    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 6042  run imach with mle=-1 to get a correct t
+ Line 8442  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 6107  run imach with mle=-1 to get a correct t
+ Line 8568  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\
+ <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=%s<br>\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 6130  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 8593  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'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 6153  Interval (in months) between two waves:
+ Line 8622  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 6203  Interval (in months) between two waves:
+ Line 8672  Interval (in months) between two waves:
  #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);
- Line 6246  Interval (in months) between two waves:
+ Line 8715  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 6300  Interval (in months) between two waves:
+ Line 8769  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 6349  Interval (in months) between two waves:
+ Line 8821  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 6364  Interval (in months) between two waves:
+ Line 8843  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 6397  Interval (in months) between two waves:
+ Line 8883  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 6408  Interval (in months) between two waves:
+ Line 8894  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 6436  Interval (in months) between two waves:
+ Line 8941  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 6499  Interval (in months) between two waves:
+ Line 9004  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 6520  Interval (in months) between two waves:
+ Line 9025  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 6538  Interval (in months) between two waves:
+ Line 9066  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 6568  Interval (in months) between two waves:
+ Line 9097  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 6586  Interval (in months) between two waves:
+ Line 9116  Interval (in months) between two waves:
      fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
      /* day and month of proj2 are not used but only year anproj2.*/
+     while((c=getc(ficpar))=='#' && c!= EOF){
+       ungetc(c,ficpar);
+       fgets(line, MAXLINE, ficpar);
+       fputs(line,stdout);
+       fputs(line,ficparo);
+     }
+     ungetc(c,ficpar);
+     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
+     fscanf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
+     fscanf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
+     fscanf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
+     /* day and month of proj2 are not used but only year anproj2.*/
       /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+     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,backcast, estepm, \
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
-     free_ivector(wav,1,imx);
+     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
      free_lvector(num,1,n);
      free_vector(agedc,1,n);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
- Line 6613  Interval (in months) between two waves:
+ Line 9164  Interval (in months) between two waves:
      fclose(ficres);
+     /* Other results (useful)*/
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
- #include "prevlim.h"  /* Use ficrespl, ficlog */
+     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
+     prlim=matrix(1,nlstate,1,nlstate);
+     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
      fclose(ficrespl);
+     /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+     /*#include "prevlim.h"*/  /* Use ficresplb, ficlog */
+     bprlim=matrix(1,nlstate,1,nlstate);
+     back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
+     fclose(ficresplb);
  #ifdef FREEEXIT2
  #include "freeexit2.h"
  #endif
      /*------------- h Pij x at various ages ------------*/
- #include "hpijx.h"
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
      fclose(ficrespij);
+     hBijx(p, bage, fage);
+     fclose(ficrespijb);
    /*-------------- Variance of one-step probabilities---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
- Line 6640  Interval (in months) between two waves:
+ Line 9207  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{ */
-       /*        erreur=108; */
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*      } */
      }
+     if(backcast==1){
+       prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
+     }
+     /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
+     /*      }  */
+     /*      else{ */
+     /*        erreur=108; */
+     /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
+     /*      } */
+     /* ------ Other prevalence ratios------------ */
      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- Line 6657  Interval (in months) between two waves:
+ Line 9229  Interval (in months) between two waves:
      /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
          ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
      */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
+     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
      if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- Line 6669  Interval (in months) between two waves:
+ Line 9246  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(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
      for (k=1; k <= (int) pow(2,cptcoveff); k++){
          fprintf(ficreseij,"\n#****** ");
          for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          fprintf(ficreseij,"******\n");
- Line 6695  Interval (in months) between two waves:
+ Line 9272  Interval (in months) between two waves:
        /*}*/
      }
      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++){*/
      for (k=1; k <= (int) pow(2,cptcoveff); k++){
-         fprintf(ficrest,"\n#****** ");
+       fprintf(ficrest,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+       for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficrest,"******\n");
+       fprintf(ficrest,"******\n");
-         fprintf(ficresstdeij,"\n#****** ");
+       fprintf(ficresstdeij,"\n#****** ");
-         fprintf(ficrescveij,"\n#****** ");
+       fprintf(ficrescveij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         }
+       }
-         fprintf(ficresstdeij,"******\n");
+       fprintf(ficresstdeij,"******\n");
-         fprintf(ficrescveij,"******\n");
+       fprintf(ficrescveij,"******\n");
-         fprintf(ficresvij,"\n#****** ");
+       fprintf(ficresvij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+       for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficresvij,"******\n");
+       fprintf(ficresvij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+       oldm=oldms;savm=savms;
-         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       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);
-         /* goto endfree; */
+       printf(" end cvevsij \n ");
+       fprintf(ficlog, " end cvevsij \n ");
-         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         pstamp(ficrest);
+       /*
+        */
+       /* goto endfree; */
-         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-           oldm=oldms;savm=savms; /* Segmentation fault */
+       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-           cptcod= 0; /* To be deleted */
+       pstamp(ficrest);
-           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
-           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
-           if(vpopbased==1)
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==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);
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
-           else
+         cptcod= 0; /* To be deleted */
-             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+         printf("varevsij %d \n",vpopbased);
-           fprintf(ficrest,"# Age e.. (std) ");
+         fprintf(ficlog, "varevsij %d \n",vpopbased);
-           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         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,"\n");
+         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)
-           epj=vector(1,nlstate+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);
-           for(age=bage; age <=fage ;age++){
+         else
-             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-             if (vpopbased==1) {
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
-               if(mobilav ==0){
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-                 for(i=1; i<=nlstate;i++)
+         fprintf(ficrest,"\n");
-                   prlim[i][i]=probs[(int)age][i][k];
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
-               }else{ /* mobilav */
+         epj=vector(1,nlstate+1);
-                 for(i=1; i<=nlstate;i++)
+         printf("Computing age specific period (stable) prevalences in each health state \n");
-                   prlim[i][i]=mobaverage[(int)age][i][k];
+         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) {
-             fprintf(ficrest," %4.0f",age);
+             if(mobilav ==0){
-             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+               for(i=1; i<=nlstate;i++)
-               for(i=1, epj[j]=0.;i <=nlstate;i++) {
+                 prlim[i][i]=probs[(int)age][i][k];
-                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
+             }else{ /* mobilav */
-                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               for(i=1; i<=nlstate;i++)
-               }
+                 prlim[i][i]=mobaverage[(int)age][i][k];
-               epj[nlstate+1] +=epj[j];
              }
+           }
-             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,NCOVMAX,1,2);
      free_imatrix(s,1,maxwav+1,1,n);
- Line 6832  Interval (in months) between two waves:
+ Line 9426  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(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
- Line 6850  Interval (in months) between two waves:
+ Line 9447  Interval (in months) between two waves:
      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);
- Line 6874  Interval (in months) between two waves:
+ Line 9473  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,NCOVMAX);
+     free_ivector(ncodemaxwundef,1,NCOVMAX);
      free_ivector(Tvar,1,NCOVMAX);
      free_ivector(Tprod,1,NCOVMAX);
      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);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
    }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
- Line 6924  Interval (in months) between two waves:
+ Line 9525  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");
- Line 6981  Interval (in months) between two waves:
+ Line 9588  Interval (in months) between two waves:
    }
    end:
    while (z[0] != 'q') {
-     printf("\nType  q for exiting: ");
+     printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
  }

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