imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.171 and 1.222

-version 1.171, 2014/12/23 13:26:59
+version 1.222, 2016/02/17 08:14:50
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.222  2016/02/17 08:14:50  brouard
+   Summary: Probably last 0.98 stable version 0.98r6
+   Revision 1.221  2016/02/15 23:35:36  brouard
+   Summary: minor bug
+   Revision 1.219  2016/02/15 00:48:12  brouard
+   *** empty log message ***
+   Revision 1.218  2016/02/12 11:29:23  brouard
+   Summary: 0.99 Back projections
+   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
- Line 471
+ Line 663
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
+ Back prevalence and projections:
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj)
+     Computes the back prevalence limit  for any combination     of covariate values k
+     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+  - hBijx Back Probability to be in state i at age x-h being in j at x
+    Computes for any combination of covariates k and any age between bage and fage
+    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);
+      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. Returns p3mat[i][j][h] after calling
+      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
             Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
- Line 528
+ Line 737
   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 537
+ Line 755
  #ifdef _WIN32
  #include <io.h>
+ #include <windows.h>
+ #include <tchar.h>
  #else
  #include <unistd.h>
  #endif
- Line 593  typedef struct {
+ Line 813  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 AGESUP 130 */
+ #define AGESUP 150
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
+ #define AGEOVERFLOW 1.e20
  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
  #ifdef _WIN32
  #define DIRSEPARATOR '\\'
- Line 611  typedef struct {
+ Line 836  typedef struct {
  /* $Id$ */
  /* $State$ */
+ #include "version.h"
- char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+ char 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 626  int cptcovage=0; /**< Number of covariat
+ Line 852  int cptcovage=0; /**< Number of covariat
  int cptcovprodnoage=0; /**< Number of covariate products without age */
  int cptcoveff=0; /* Total number of covariates to vary for printing results */
  int cptcov=0; /* Working variable */
+ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
- Line 648  double jmean=1; /* Mean space between 2
+ Line 875  double jmean=1; /* Mean space between 2
  double **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
  /*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 672  char fileresv[FILENAMELENGTH];
+ Line 901  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 728  static double maxarg1,maxarg2;
+ Line 957  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 747  int estepm;
+ Line 976  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 **pmmij, ***probs; /* Global pointer */
+ double ***mobaverage, ***mobaverages; /* New global variable */
  double *ageexmed,*agecens;
  double dateintmean=0;
- Line 758  int **s; /* Status */
+ Line 994  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;
+ int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
- Line 776  static int split( char *path, char *dirc
+ Line 1013  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 787  static int split( char *path, char *dirc
+ Line 1024  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 850  char *trimbb(char *out, char *in)
+ Line 1091  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 880  char *cutl(char *blocc, char *alocc, cha
+ Line 1164  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 1157  char *subdirf3(char fileres[], char *pre
+ Line 1441  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 1191  double f1dim(double x)
+ Line 1498  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 1244  double brent(double ax, double bx, doubl
+ Line 1557  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 1267  double brent(double ax, double bx, doubl
+ Line 1580  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 1294  void mnbrak(double *ax, double *bx, doub
+ Line 1626  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 1333  void linmin(double p[], double xi[], int
+ Line 1727  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 1375  void powell(double p[], double **xi, int
+ Line 1839  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 1385  void powell(double p[], double **xi, int
+ Line 1850  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 1397  void powell(double p[], double **xi, int
+ Line 1862  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 1425  void powell(double p[], double **xi, int
+ Line 1890  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 1454  void powell(double p[], double **xi, int
+ Line 1924  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 1485  void powell(double p[], double **xi, int
+ Line 1970  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 1517  void powell(double p[], double **xi, int
+ Line 2006  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 %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
- Line 1536  void powell(double p[], double **xi, int
+ Line 2056  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
+   /* Computes the prevalence limit in each live state at age x and for covariate ij 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 **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
    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);
+         /* Starting with matrix unity */
    for (ii=1;ii<=nlstate+ndeath;ii++)
      for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 1563  double **prevalim(double **prlim, int nl
+ Line 2109  double **prevalim(double **prlim, int nl
    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+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]]);*/
+                         /* Here comes the value of the covariate 'ij' */
-     }
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+       /* 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<=cptcovprod;k++) /\* Useless *\/ */
+     }
-     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
+     /*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 *\/ */
+                 /* age and covariate values of ij are in 'cov' */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
      oldm=newm;
-     maxmax=0.;
-     for(j=1;j<=nlstate;j++){
+     for(j=1; j<=nlstate; j++){
-       min=1.;
+       max[j]=0.;
-       max=0.;
+       min[j]=1.;
-       for(i=1; i<=nlstate; i++) {
+     }
-         sumnew=0;
+     for(i=1;i<=nlstate;i++){
-         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       sumnew=0;
+       for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+       for(j=1; j<=nlstate; j++){
          prlim[i][j]= newm[i][j]/(1-sumnew);
-         /*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 */
  }
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
+  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
+  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
+ {
+   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
+      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, *meandiff, maxmax,sumnew=0.;
+   /* double **matprod2(); */ /* test */
+   double **out, cov[NCOVMAX+1], **bmij();
+   double **newm;
+   double         **dnewm, **doldm, **dsavm;  /* for use */
+   double         **oldm, **savm;  /* for use */
+   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);
+         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+         oldm=oldms; savm=savms;
+         /* Starting with matrix unity */
+         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.;
+   /* 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){ /\* A changer en age *\/ */
+   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+     ncvloop++;
+     newm=savm; /* oldm should be kept from previous iteration or unity at start */
+                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
+     /* 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 *\/ */
+                 /* ij should be linked to the correct index of cov */
+                 /* age and covariate values ij are in 'cov', but we need to pass
+                  * ij for the observed prevalence at age and status and covariate
+                  * number:  prevacurrent[(int)agefin][ii][ij]
+                  */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
+     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     savm=oldm;
+     oldm=newm;
+     for(j=1; j<=nlstate; j++){
+       max[j]=0.;
+       min[j]=1.;
+     }
+     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]); /* Max in line */
+                                 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 )
- Line 1628  double **pmij(double **ps, double *cov,
+ Line 2334  double **pmij(double **ps, double *cov,
    /*double t34;*/
    int i,j, nc, ii, jj;
-     for(i=1; i<= nlstate; i++){
+         for(i=1; i<= nlstate; i++){
-       for(j=1; j<i;j++){
+                 for(j=1; j<i;j++){
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
-           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*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); */
+                                 /*       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) */
+                 }
          }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
- /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+         for(i=1; i<= nlstate; i++){
-       }
+                 s1=0;
-       for(j=i+1; j<=nlstate+ndeath;j++){
+                 for(j=1; j<i; j++){
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-           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); */
+                 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;
+                 }
          }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       }
-     }
+         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-     for(i=1; i<= nlstate; i++){
+         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-       s1=0;
+         /*   } */
-       for(j=1; j<i; j++){
+         /*   printf("\n "); */
-         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); */
+         /* printf("\n ");printf("%lf ",cov[2]);*/
-       }
+         /*
-       for(j=i+1; j<=nlstate+ndeath; j++){
+                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+                 goto end;*/
-         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+         return ps;
-       }
+ }
-       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-       ps[i][i]=1./(s1+1.);
+ /*************** backward transition probabilities ***************/
-       /* Computing other pijs */
-       for(j=1; j<i; j++)
+  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
-       for(j=i+1; j<=nlstate+ndeath; j++)
+  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
+ {
-       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+   /* Computes the backward probability at age agefin and covariate ij
-     } /* end i */
+    * and returns in **ps as well as **bmij.
+    */
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+   int i, ii, j,k;
-       for(jj=1; jj<= nlstate+ndeath; jj++){
-         ps[ii][jj]=0;
+   double **out, **pmij();
-         ps[ii][ii]=1;
+   double sumnew=0.;
+   double agefin;
+   double **dnewm, **dsavm, **doldm;
+   double **bbmij;
+   doldm=ddoldms; /* global pointers */
+   dnewm=ddnewms;
+   dsavm=ddsavms;
+   agefin=cov[2];
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
+      the observed prevalence (with this covariate ij) */
+   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+   /* We do have the matrix Px in savm  and we need pij */
+   for (j=1;j<=nlstate+ndeath;j++){
+     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
+     for (ii=1;ii<=nlstate;ii++){
+       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
+     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       if(sumnew >= 1.e-10){
+         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else */
+         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
+       }else{
+         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
        }
-     }
+     } /*End ii */
+   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
+   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
-     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
-     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
-     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-     /*   } */
+   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-     /*   printf("\n "); */
+   /* left Product of this matrix by diag matrix of prevalences (savm) */
-     /* } */
+   for (j=1;j<=nlstate+ndeath;j++){
-     /* printf("\n ");printf("%lf ",cov[2]);*/
+     for (ii=1;ii<=nlstate+ndeath;ii++){
-     /*
+       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     }
-       goto end;*/
+   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
-     return ps;
+   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
+   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
+   /* end bmij */
+   return ps;
+ }
+ /*************** transition probabilities ***************/
+ double **bpmij(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 */ /* Transposed matrix too */
+         for(jj=1; jj<= nlstate+ndeath; jj++){
+                 s1=0.;
+                 for(ii=1; ii<= nlstate+ndeath; ii++){
+                         s1+=ps[ii][jj];
+                 }
+                 for(ii=1; ii<= nlstate; ii++){
+                         ps[ii][jj]=ps[ii][jj]/s1;
+                 }
+         }
+         /* Transposition */
+         for(jj=1; jj<= nlstate+ndeath; jj++){
+                 for(ii=jj; ii<= nlstate+ndeath; ii++){
+                         s1=ps[ii][jj];
+                         ps[ii][jj]=ps[jj][ii];
+                         ps[jj][ii]=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 1713  double **matprod2(double **out, double *
+ Line 2579  double **matprod2(double **out, double *
  double ***hpxij(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
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 1728  double ***hpxij(double ***po, int nhstep
+ Line 2594  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 1741  double ***hpxij(double ***po, int nhstep
+ Line 2609  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]);*/
+                         /* right multiplication of oldm by the current matrix */
        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, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, 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;
+   double **oldm, **savm;
+   oldm=oldms;savm=savms;
+   /* 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]);*/
+       /* Careful transposed matrix */
+       /* age is in cov[2] */
+       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
+       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
+       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
+,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 1764  double ***hpxij(double ***po, int nhstep
+ Line 2743  double ***hpxij(double ***po, int nhstep
        }
      /*printf("h=%d ",h);*/
    } /* end h */
- /*     printf("\n H=%d \n",h); */
+   /*     printf("\n H=%d \n",h); */
    return po;
  }
  #ifdef NLOPT
    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    double fret;
- Line 1799  double func( double *x)
+ Line 2779  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 1820  double func( double *x)
+ Line 2801  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 1833  double func( double *x)
+ Line 2814  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 1887  double func( double *x)
+ Line 2871  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 1919  double func( double *x)
+ Line 2919  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 1932  double func( double *x)
+ Line 2936  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 1953  double func( double *x)
+ Line 2960  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 1962  double func( double *x)
+ Line 2969  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 1983  double func( double *x)
+ Line 2993  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 1992  double func( double *x)
+ Line 3002  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 2007  double func( double *x)
+ Line 3020  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 2018  double func( double *x)
+ Line 3035  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 2027  double func( double *x)
+ Line 3044  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 2065  double funcone( double *x)
+ Line 3085  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 2076  double funcone( double *x)
+ Line 3098  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 2100  double funcone( double *x)
+ Line 3131  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 2127  double funcone( double *x)
+ Line 3162  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 2161  void likelione(FILE *ficres,double p[],
+ Line 3196  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 2178  void likelione(FILE *ficres,double p[],
+ Line 3213  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 2211  void mlikeli(FILE *ficres,double p[], in
+ Line 3260  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 2256  void mlikeli(FILE *ficres,double p[], in
+ Line 3305  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 2290  void hesscov(double **matcov, double p[]
+ Line 3339  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 2326  void hesscov(double **matcov, double p[]
+ Line 3375  void hesscov(double **matcov, double p[]
    fprintf(ficlog,"\n#Hessian matrix#\n");
    for (i=1;i<=npar;i++) {
      for (j=1;j<=npar;j++) {
-       printf("%.3e ",hess[i][j]);
+       printf("%.6e ",hess[i][j]);
-       fprintf(ficlog,"%.3e ",hess[i][j]);
+       fprintf(ficlog,"%.6e ",hess[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
+   /* printf("\n#Covariance matrix#\n"); */
+   /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
+   /* for (i=1;i<=npar;i++) {  */
+   /*   for (j=1;j<=npar;j++) {  */
+   /*     printf("%.6e ",matcov[i][j]); */
+   /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
    /* Recompute Inverse */
-   for (i=1;i<=npar;i++)
+   /* for (i=1;i<=npar;i++) */
-     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+   /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
-   ludcmp(a,npar,indx,&pd);
+   /* ludcmp(a,npar,indx,&pd); */
+   /*  printf("\n#Hessian matrix recomputed#\n"); */
+   /* for (j=1;j<=npar;j++) { */
+   /*   for (i=1;i<=npar;i++) x[i]=0; */
+   /*   x[j]=1; */
+   /*   lubksb(a,npar,indx,x); */
+   /*   for (i=1;i<=npar;i++){  */
+   /*     y[i][j]=x[i]; */
+   /*     printf("%.3e ",y[i][j]); */
+   /*     fprintf(ficlog,"%.3e ",y[i][j]); */
+   /*   } */
+   /*   printf("\n"); */
+   /*   fprintf(ficlog,"\n"); */
+   /* } */
+   /* Verifying the inverse matrix */
+ #ifdef DEBUGHESS
+   y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
-   /*  printf("\n#Hessian matrix recomputed#\n");
+    printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
+    fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
    for (j=1;j<=npar;j++) {
-     for (i=1;i<=npar;i++) x[i]=0;
-     x[j]=1;
-     lubksb(a,npar,indx,x);
      for (i=1;i<=npar;i++){
-       y[i][j]=x[i];
+       printf("%.2f ",y[i][j]);
-       printf("%.3e ",y[i][j]);
+       fprintf(ficlog,"%.2f ",y[i][j]);
-       fprintf(ficlog,"%.3e ",y[i][j]);
      }
      printf("\n");
      fprintf(ficlog,"\n");
    }
-   */
+ #endif
    free_matrix(a,1,npar,1,npar);
    free_matrix(y,1,npar,1,npar);
    free_vector(x,1,npar);
    free_ivector(indx,1,npar);
-   free_matrix(hess,1,npar,1,npar);
+   /* free_matrix(hess,1,npar,1,npar); */
  }
  /*************** hessian matrix ****************/
  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
- {
+ { /* Around values of x, computes the function func and returns the scales delti and hessian */
    int i;
    int l=1, lmax=20;
-   double k1,k2;
+   double k1,k2, res, fx;
    double p2[MAXPARM+1]; /* identical to x */
-   double res;
    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
-   double fx;
    int k=0,kmax=10;
    double l1;
- Line 2388  double hessii(double x[], double delta,
+ Line 3462  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 2404  double hessii(double x[], double delta,
+ Line 3478  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; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may 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 2522  void lubksb(double **a, int n, int *indx
+ Line 3673  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, \
- {  /* Some frequencies */
+                                                                          int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],  \
+                                                                          int firstpass,  int lastpass, int stepm, int weightopt, char model[])
-   int i, m, jk, j1, bool, z1,j;
+  {  /* Some frequencies */
-   int first;
-   double ***freq; /* Frequencies */
+          int i, m, jk, j1, bool, z1,j;
-   double *pp, **prop;
+          int iind=0, iage=0;
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+          int mi; /* Effective wave */
-   char fileresp[FILENAMELENGTH];
+          int first;
+          double ***freq; /* Frequencies */
-   pp=vector(1,nlstate);
+          double *pp, **prop, *posprop, *pospropt;
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+          double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
-   strcpy(fileresp,"p");
+          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
-   strcat(fileresp,fileres);
+          double agebegin, ageend;
-   if((ficresp=fopen(fileresp,"w"))==NULL) {
-     printf("Problem with prevalence resultfile: %s\n", fileresp);
+          pp=vector(1,nlstate);
-     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+          prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-     exit(0);
+          posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
-   }
+          pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+          /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
-   j1=0;
+          strcpy(fileresp,"P_");
+          strcat(fileresp,fileresu);
-   j=cptcoveff;
+          /*strcat(fileresphtm,fileresu);*/
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+          if((ficresp=fopen(fileresp,"w"))==NULL) {
+                  printf("Problem with prevalence resultfile: %s\n", fileresp);
-   first=1;
+                  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-AGEMARGE,iagemax+3+AGEMARGE);
+          j1=0;
+          j=cptcoveff;
+          if (cptcovn<1) {j=1;ncodemax[1]=1;}
+          first=1;
+          /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
+                         reference=low_education V1=0,V2=0
+                         med_educ                V1=1 V2=0,
+                         high_educ               V1=0 V2=1
+                         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
+          */
-   /* 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 */
+                  posproptt=0.;
-   /*    j1++; */
+                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
+                          scanf("%d", i);*/
-       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+                  for (i=-5; i<=nlstate+ndeath; i++)
-         scanf("%d", i);*/
+                          for (jk=-5; jk<=nlstate+ndeath; jk++)
-       for (i=-5; i<=nlstate+ndeath; i++)
+                                  for(m=iagemin; m <= iagemax+3; m++)
-         for (jk=-5; jk<=nlstate+ndeath; jk++)
+                                          freq[i][jk][m]=0;
-           for(m=iagemin; m <= iagemax+3; m++)
-             freq[i][jk][m]=0;
+                  for (i=1; i<=nlstate; i++)  {
+                          for(m=iagemin; m <= iagemax+3; m++)
-       for (i=1; i<=nlstate; i++)
+                                  prop[i][m]=0;
-         for(m=iagemin; m <= iagemax+3; m++)
+                          posprop[i]=0;
-           prop[i][m]=0;
+                          pospropt[i]=0;
+                  }
-       dateintsum=0;
-       k2cpt=0;
+                  dateintsum=0;
-       for (i=1; i<=imx; i++) {
+                  k2cpt=0;
-         bool=1;
-         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]]){
-                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
-               bool=0;
-               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
-                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
-             }
-         }
-         if (bool==1){
-           for(m=firstpass; m<=lastpass; m++){
-             k2=anint[m][i]+(mint[m][i]/12.);
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
-               if (m<lastpass) {
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
-               }
-               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
-                 dateintsum=dateintsum+k2;
-                 k2cpt++;
-               }
-               /*}*/
-           }
-         }
-       } /* end i */
-       /*      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(ficresp, "**********\n#");
-         fprintf(ficlog, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-         fprintf(ficlog, "**********\n#");
-       }
-       for(i=1; i<=nlstate;i++)
-         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresp, "\n");
-       for(i=iagemin; i <= iagemax+3; i++){
-         if(i==iagemax+3){
-           fprintf(ficlog,"Total");
-         }else{
-           if(first==1){
-             first=0;
-             printf("See log file for details...\n");
-           }
-           fprintf(ficlog,"Age %d", i);
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-             pp[jk] += freq[jk][m][i];
-         }
-         for(jk=1; jk <=nlstate ; jk++){
-           for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
-           if(pp[jk]>=1.e-10){
-             if(first==1){
-               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-             }
-             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-           }else{
-             if(first==1)
-               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-           }
-         }
-         for(jk=1; jk <=nlstate ; jk++){
+                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+                          bool=1;
-             pp[jk] += freq[jk][m][i];
+                          if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-         }
+                                  for (z1=1; z1<=cptcoveff; z1++) {
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-           pos += pp[jk];
+                                                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
-           posprop += prop[jk][i];
+                                                  bool=0;
-         }
+                                                  /* 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",
-         for(jk=1; jk <=nlstate ; jk++){
+                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-           if(pos>=1.e-5){
+                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-             if(first==1)
+                                                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                          }
-             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                  } /* end z1 */
-           }else{
+                          } /* cptcovn > 0 */
-             if(first==1)
-               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                          if (bool==1){
-             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                  /* for(m=firstpass; m<=lastpass; m++){ */
-           }
+                                  for(mi=1; mi<wav[iind];mi++){
-           if( i <= iagemax){
+                                          m=mw[mi][iind];
-             if(pos>=1.e-5){
+                                          /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+                                                         and mw[mi+1][iind]. dh depends on stepm. */
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+                                          agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+                                          ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
-             }
+                                          if(m >=firstpass && m <=lastpass){
-             else
+                                                  k2=anint[m][iind]+(mint[m][iind]/12.);
-               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
+                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-           }
+                                                  if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-         }
+                                                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                                                  if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
-         for(jk=-1; jk <=nlstate+ndeath; jk++)
+                                                          prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
-           for(m=-1; m <=nlstate+ndeath; m++)
+                                                  if (m<lastpass) {
-             if(freq[jk][m][i] !=0 ) {
+                                                          /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-             if(first==1)
+                                                          /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
-               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+                                                          if(s[m][iind]==-1)
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+                                                                  printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
-             }
+                                                          freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-         if(i <= iagemax)
+                                                          /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-           fprintf(ficresp,"\n");
+                                                          freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
-         if(first==1)
+                                                  }
-           printf("Others in log...\n");
+                                          }
-         fprintf(ficlog,"\n");
+                                          if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
-       }
+                                                  dateintsum=dateintsum+k2;
-       /*}*/
+                                                  k2cpt++;
-   }
+                                                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-   dateintmean=dateintsum/k2cpt;
+                                          }
+                                          /*}*/
-   fclose(ficresp);
+                                  } /* end m */
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+                          } /* end bool */
-   free_vector(pp,1,nlstate);
+                  } /* end iind = 1 to imx */
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+        /* prop[s][age] is feeded for any initial and valid live state as well as
-   /* End of Freq */
+                                         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
- }
+                  /*      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 ");
+                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+                          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]][codtabm(j1,z1)]);
+                          fprintf(ficlog, "**********\n");
+                  }
+                  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(iage=iagemin; iage <= iagemax+3; iage++){
+                          fprintf(ficresphtm,"<tr>");
+                          if(iage==iagemax+1){
+                                  fprintf(ficlog,"1");
+                                  fprintf(ficresphtmfr,"<tr><th>0</th> ");
+                          }else if(iage==iagemax+2){
+                                  fprintf(ficlog,"0");
+                                  fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+                          }else if(iage==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> ",iage);
+                                  fprintf(ficlog,"Age %d", iage);
+                          }
+                          for(jk=1; jk <=nlstate ; jk++){
+                                  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+                                          pp[jk] += freq[jk][m][iage];
+                          }
+                          for(jk=1; jk <=nlstate ; jk++){
+                                  for(m=-1, pos=0; m <=0 ; m++)
+                                          pos += freq[jk][m][iage];
+                                  if(pp[jk]>=1.e-10){
+                                          if(first==1){
+                                                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                                          }
+                                          fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                                  }else{
+                                          if(first==1)
+                                                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                                          fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                                  }
+                          }
+                          for(jk=1; jk <=nlstate ; jk++){
+                                  /* posprop[jk]=0; */
+                                  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+                                          pp[jk] += freq[jk][m][iage];
+                          }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+                          for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+                                  pos += pp[jk]; /* pos is the total number of transitions until this age */
+                                  posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
+                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+                                  pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
+                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+                          }
+                          for(jk=1; jk <=nlstate ; jk++){
+                                  if(pos>=1.e-5){
+                                          if(first==1)
+                                                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                          fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                                  }else{
+                                          if(first==1)
+                                                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                          fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                                  }
+                                  if( iage <= iagemax){
+                                          if(pos>=1.e-5){
+                                                  fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                                  fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+                                                  /*probs[iage][jk][j1]= pp[jk]/pos;*/
+                                                  /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
+                                          }
+                                          else{
+                                                  fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+                                                  fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+                                          }
+                                  }
+                                  pospropt[jk] +=posprop[jk];
+                          } /* end loop jk */
+                          /* pospropt=0.; */
+                          for(jk=-1; jk <=nlstate+ndeath; jk++){
+                                  for(m=-1; m <=nlstate+ndeath; m++){
+                                          if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                                                  if(first==1){
+                                                          printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                                  }
+                                                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                                          }
+                                          if(jk!=0 && m!=0)
+                                                  fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+                                  }
+                          } /* end loop jk */
+                          posproptt=0.;
+                          for(jk=1; jk <=nlstate; jk++){
+                                  posproptt += pospropt[jk];
+                          }
+                          fprintf(ficresphtmfr,"</tr>\n ");
+                          if(iage <= iagemax){
+                                  fprintf(ficresp,"\n");
+                                  fprintf(ficresphtm,"</tr>\n");
+                          }
+                          if(first==1)
+                                  printf("Others in log...\n");
+                          fprintf(ficlog,"\n");
+                  } /* end loop age iage */
+                  fprintf(ficresphtm,"<tr><th>Tot</th>");
+                  for(jk=1; jk <=nlstate ; jk++){
+                          if(posproptt < 1.e-5){
+                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+                          }else{
+                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+                          }
+                  }
+                  fprintf(ficresphtm,"</tr>\n");
+                  fprintf(ficresphtm,"</table>\n");
+                  fprintf(ficresphtmfr,"</table>\n");
+                  if(posproptt < 1.e-5){
+                          fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+                          fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+                          fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+                          invalidvarcomb[j1]=1;
+                  }else{
+                          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+                          invalidvarcomb[j1]=0;
+                  }
+                  fprintf(ficresphtmfr,"</table>\n");
+          } /* end selected combination of covariate j1 */
+          dateintmean=dateintsum/k2cpt;
+          fclose(ficresp);
+          fclose(ficresphtm);
+          fclose(ficresphtmfr);
+          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+          free_vector(pospropt,1,nlstate);
+          free_vector(posprop,1,nlstate);
+          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+          free_vector(pp,1,nlstate);
+          /* End of Freq */
+  }
  /************ Prevalence ********************/
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
- {
+  {
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+    /* 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).
+       in each health status at the date of interview (if between dateprev1 and dateprev2).
-      We still use firstpass and lastpass as another selection.
+       We still use firstpass and lastpass as another selection.
-   */
+    */
-   int i, m, jk, j1, bool, z1,j;
+    int i, m, jk, j1, bool, z1,j;
+    int mi; /* Effective wave */
-   double **prop;
+    int iage;
-   double posprop;
+    double agebegin, ageend;
-   double  y2; /* in fractional years */
-   int iagemin, iagemax;
+    double **prop;
-   int first; /** to stop verbosity which is redirected to log file */
+    double posprop;
+    double  y2; /* in fractional years */
-   iagemin= (int) agemin;
+    int iagemin, iagemax;
-   iagemax= (int) agemax;
+    int first; /** to stop verbosity which is redirected to log file */
-   /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+    iagemin= (int) agemin;
-   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+    iagemax= (int) agemax;
-   j1=0;
+    /*pp=vector(1,nlstate);*/
+    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-   /*j=cptcoveff;*/
+    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-   if (cptcovn<1) {j=1;ncodemax[1]=1;}
+    j1=0;
-   first=1;
+    /*j=cptcoveff;*/
-   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-     /*for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;*/
+    first=1;
+    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-       for (i=1; i<=nlstate; i++)
+      for (i=1; i<=nlstate; i++)
-         for(m=iagemin; m <= iagemax+3; m++)
+        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-           prop[i][m]=0.0;
+          prop[i][iage]=0.0;
-       for (i=1; i<=imx; i++) { /* Each individual */
+      for (i=1; i<=imx; i++) { /* Each individual */
-         bool=1;
+        bool=1;
-         if  (cptcovn>0) {
+        if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-           for (z1=1; z1<=cptcoveff; z1++)
+          for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
-               bool=0;
+              bool=0;
-         }
+        }
-         if (bool==1) {
+        if (bool==1) { /* For this combination of covariates values, this individual fits */
-           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
+          /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+          for(mi=1; mi<wav[i];mi++){
-             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+            m=mw[mi][i];
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;
+            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;
+            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-               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(m >=firstpass && m <=lastpass){
-               if (s[m][i]>0 && s[m][i]<=nlstate) {
+              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-                 /*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]]);*/
+              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];
+                if(agev[m][i]==0) agev[m][i]=iagemax+1;
-                 prop[s[m][i]][iagemax+3] += weight[i];
+                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               }
+                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
-             }
+                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
-           } /* end selection of waves */
+                  exit(1);
-         }
+                }
-       }
+                if (s[m][i]>0 && s[m][i]<=nlstate) {
-       for(i=iagemin; i <= iagemax+3; i++){
+                  /*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]]);*/
-         for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
-           posprop += prop[jk][i];
+                  prop[s[m][i]][iagemax+3] += weight[i];
-         }
+                } /* end valid statuses */
+              } /* end selection of dates */
-         for(jk=1; jk <=nlstate ; jk++){
+            } /* end selection of waves */
-           if( i <=  iagemax){
+          } /* end effective waves */
-             if(posprop>=1.e-5){
+        } /* end bool */
-               probs[i][jk][j1]= prop[jk][i]/posprop;
+      }
-             } else{
+      for(i=iagemin; i <= iagemax+3; i++){
-               if(first==1){
+        for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-                 first=0;
+          posprop += prop[jk][i];
-                 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]);
+        }
-               }
-             }
+        for(jk=1; jk <=nlstate ; jk++){
-           }
+          if( i <=  iagemax){
-         }/* end jk */
+            if(posprop>=1.e-5){
-       }/* end i */
+              probs[i][jk][j1]= prop[jk][i]/posprop;
-     /*} *//* end i1 */
+            } else{
-   } /* end j1 */
+              if(first==1){
+                first=0;
-   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+                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]);
-   /*free_vector(pp,1,nlstate);*/
+              }
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+            }
- }  /* End of prevalence */
+          }
+        }/* end jk */
+      }/* end i */
+      /*} *//* end i1 */
+    } /* end j1 */
+    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+    /*free_vector(pp,1,nlstate);*/
+    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 2799  void  concatwav(int wav[], int **dh, int
+ Line 4104  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, firstfour;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
+   firstwo=0;
+   firsthree=0;
+   firstfour=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);
+             firsthree=1;
+           }
+           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.\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 ((int)anint[m][i]!= 9999) { /* date of last interview is known */
+         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 );
+           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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+       }else{ /* end date of interview is known */
+         /* death is known but not confirmed by death status at any wave */
+         if(firstfour==0){
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %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 );
+           firstfour=1;
+         }
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %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.\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 2836  void  concatwav(int wav[], int **dh, int
+ Line 4183  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 2928  void  concatwav(int wav[], int **dh, int
+ Line 4277  void  concatwav(int wav[], int **dh, int
   }
  /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
+  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
  {
    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
     * Boring subroutine which should only output nbcode[Tvar[j]][k]
     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
-    * nbcode[Tvar[j]][1]=
+    * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
    */
    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
- Line 2943  void tricode(int *Tvar, int **nbcode, in
+ Line 4292  void tricode(int *Tvar, int **nbcode, in
    int modmincovj=0; /* Modality min of covariates j */
-   cptcoveff=0;
+   /* cptcoveff=0;  */
+         *cptcov=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;
-                                modality of this covariate Vj*/
+     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 *:
+                                                                                                                                                 * If product of Vn*Vm, still boolean *:
-                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+                                                                                                                                                 * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+                                                                                                                                                 * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                        modality of the nth covariate of individual i. */
        if (ij > modmaxcovj)
          modmaxcovj=ij;
        else if (ij < modmincovj)
-         modmincovj=ij;
+                                 modmincovj=ij;
        if ((ij < -1) && (ij > NCOVMAX)){
-         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-         exit(1);
+                                 exit(1);
        }else
        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
- Line 2972  void tricode(int *Tvar, int **nbcode, in
+ Line 4322  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 */
+                                  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 (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.*/
+                 /* 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 */
+                 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) */
+         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]);*/
+                 /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+                 if((Ndum[i]!=0) && (i<=ncovcol)){
-      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+                         ij++;
-      Tvaraff[ij]=i; /*For printing (unclear) */
+                         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-      ij++;
+                         Tvaraff[ij]=i; /*For printing (unclear) */
-    }else
+                 }else{
-        Tvaraff[ij]=0;
+                         /* Tvaraff[ij]=0; */
-  }
+                 }
-  ij--;
+         }
-  cptcoveff=ij; /*Number of total covariates*/
+         /* ij--; */
+         /* cptcoveff=ij; /\*Number of total covariates*\/ */
+         *cptcov=ij; /*Number of total covariates*/
  }
- Line 3151  void cvevsij(double ***eij, double x[],
+ Line 4523  void cvevsij(double ***eij, double x[],
  {
    /* Covariances of health expectancies eij and of total life expectancies according
-    to initial status i, ei. .
+      to initial status i, ei. .
    */
    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    int nhstepma, nstepma; /* Decreasing with age */
- Line 3245  void cvevsij(double ***eij, double x[],
+ Line 4617  void cvevsij(double ***eij, double x[],
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      /* If stepm=6 months */
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* Computing  Variances of health expectancies */
      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         decrease memory allocation */
- Line 3262  void cvevsij(double ***eij, double x[],
+ Line 4634  void cvevsij(double ***eij, double x[],
        }
        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
            for(h=0; h<=nhstepm-1; h++){
- Line 3271  void cvevsij(double ***eij, double x[],
+ Line 4643  void cvevsij(double ***eij, double x[],
            }
          }
        }
        for(ij=1; ij<= nlstate*nlstate; ij++)
          for(h=0; h<=nhstepm-1; h++){
            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- Line 3284  void cvevsij(double ***eij, double x[],
+ Line 4656  void cvevsij(double ***eij, double x[],
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+     for(ij=1;ij<=nlstate*nlstate;ij++)
        for(ji=1;ji<=nlstate*nlstate;ji++)
          varhe[ij][ji][(int)age] =0.;
-      printf("%d|",(int)age);fflush(stdout);
+     printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
+     for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- Line 3300  void cvevsij(double ***eij, double x[],
+ Line 4672  void cvevsij(double ***eij, double x[],
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* Computing expectancies */
      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 3325  void cvevsij(double ***eij, double x[],
+ Line 4697  void cvevsij(double ***eij, double x[],
        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      }
      fprintf(ficresstdeij,"\n");
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 3338  void cvevsij(double ***eij, double x[],
+ Line 4710  void cvevsij(double ***eij, double x[],
            }
        }
      fprintf(ficrescveij,"\n");
    }
    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- Line 3348  void cvevsij(double ***eij, double x[],
+ Line 4720  void cvevsij(double ***eij, double x[],
    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
    free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
  /************ 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 */
+    /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   /* double **newm;*/
+    /* double **newm;*/
-   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-   int movingaverage();
+    /* int movingaverage(); */
-   double **dnewm,**doldm;
+    double **dnewm,**doldm;
-   double **dnewmp,**doldmp;
+    double **dnewmp,**doldmp;
-   int i, j, nhstepm, hstepm, h, nstepm ;
+    int i, j, nhstepm, hstepm, h, nstepm ;
-   int k;
+    int k;
-   double *xp;
+    double *xp;
-   double **gp, **gm;  /* for var eij */
+    double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg; /*for var eij */
+    double ***gradg, ***trgradg; /*for var eij */
-   double **gradgp, **trgradgp; /* for var p point j */
+    double **gradgp, **trgradgp; /* for var p point j */
-   double *gpp, *gmp; /* for var p point j */
+    double *gpp, *gmp; /* for var p point j */
-   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-   double ***p3mat;
+    double ***p3mat;
-   double age,agelim, hf;
+    double age,agelim, hf;
-   double ***mobaverage;
+    /* double ***mobaverage; */
-   int theta;
+    int theta;
-   char digit[4];
+    char digit[4];
-   char digitp[25];
+    char digitp[25];
-   char fileresprobmorprev[FILENAMELENGTH];
+    char fileresprobmorprev[FILENAMELENGTH];
-   if(popbased==1){
+    if(popbased==1){
-     if(mobilav!=0)
+      if(mobilav!=0)
-       strcpy(digitp,"-populbased-mobilav-");
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-     else strcpy(digitp,"-populbased-nomobil-");
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-   }
+    }
-   else
+    else
-     strcpy(digitp,"-stablbased-");
+      strcpy(digitp,"-STABLBASED_");
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   strcpy(fileresprobmorprev,"prmorprev");
+    /* if (mobilav!=0) { */
-   sprintf(digit,"%-d",ij);
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-   strcat(fileresprobmorprev,fileres);
+    /*   } */
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+    /* } */
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    strcpy(fileresprobmorprev,"PRMORPREV-");
-   }
+    sprintf(digit,"%-d",ij);
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   pstamp(ficresprobmorprev);
+    strcat(fileresprobmorprev,fileresu);
-   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);
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-     fprintf(ficresprobmorprev," p.%-d SE",j);
+    }
-     for(i=1; i<=nlstate;i++)
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   }
+    pstamp(ficresprobmorprev);
-   fprintf(ficresprobmorprev,"\n");
+    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
-   fprintf(ficgp,"\n# Routine varevsij");
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
-   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-   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(ficresprobmorprev," p.%-d SE",j);
-   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
+      for(i=1; i<=nlstate;i++)
- /*   } */
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    }
-   pstamp(ficresvij);
+    fprintf(ficresprobmorprev,"\n");
-   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
-   if(popbased==1)
+    fprintf(ficgp,"\n# Routine varevsij");
-     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
+    fprintf(ficgp,"\nunset title \n");
-   else
+    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
-     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
-   fprintf(ficresvij,"# Age");
+    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-   for(i=1; i<=nlstate;i++)
+    /*   } */
-     for(j=1; j<=nlstate;j++)
+    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    pstamp(ficresvij);
-   fprintf(ficresvij,"\n");
+    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
+    if(popbased==1)
-   xp=vector(1,npar);
+      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
-   dnewm=matrix(1,nlstate,1,npar);
+    else
-   doldm=matrix(1,nlstate,1,nlstate);
+      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    fprintf(ficresvij,"# Age");
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    for(i=1; i<=nlstate;i++)
+      for(j=1; j<=nlstate;j++)
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   gpp=vector(nlstate+1,nlstate+ndeath);
+    fprintf(ficresvij,"\n");
-   gmp=vector(nlstate+1,nlstate+ndeath);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    xp=vector(1,npar);
+    dnewm=matrix(1,nlstate,1,npar);
-   if(estepm < stepm){
+    doldm=matrix(1,nlstate,1,nlstate);
-     printf ("Problem %d lower than %d\n",estepm, stepm);
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   }
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   else  hstepm=estepm;
-   /* For example we decided to compute the life expectancy with the smallest unit */
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
+    gpp=vector(nlstate+1,nlstate+ndeath);
-      nhstepm is the number of hstepm from age to agelim
+    gmp=vector(nlstate+1,nlstate+ndeath);
-      nstepm is the number of stepm from age to agelin.
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-      Look at function hpijx to understand why (it is linked to memory size questions) */
-   /* 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
-      results. So we changed our mind and took the option of the best precision.
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
-     gm=matrix(0,nhstepm,1,nlstate);
-     for(theta=1; theta <=npar; theta++){
-       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);
-       if (popbased==1) {
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
-       }
-       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
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
-         for(i=1,gpp[j]=0.; i<= nlstate; i++)
-           gpp[j] += prlim[i][i]*p3mat[i][j][1];
-       }
-       /* end probability of death */
-       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);
-       if (popbased==1) {
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][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++)
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
-         }
-       }
-       /* This for computing probability of death (h=1 means
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       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];
-       }
-       /* end probability of death */
-       for(j=1; j<= nlstate; j++) /* vareij */
-         for(h=0; h<=nhstepm; h++){
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
-         }
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
-       }
-     } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       for(theta=1; theta <=npar; theta++)
-         trgradgp[j][theta]=gradgp[theta][j];
-     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
-     for(i=1;i<=nlstate;i++)
-       for(j=1;j<=nlstate;j++)
-         vareij[i][j][(int)age] =0.;
-     for(h=0;h<=nhstepm;h++){
-       for(k=0;k<=nhstepm;k++){
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
-         for(i=1;i<=nlstate;i++)
-           for(j=1;j<=nlstate;j++)
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
-       }
-     }
-     /* pptj */
+    if(estepm < stepm){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      printf ("Problem %d lower than %d\n",estepm, stepm);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+    }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+    else  hstepm=estepm;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+    /* For example we decided to compute the life expectancy with the smallest unit */
-         varppt[j][i]=doldmp[j][i];
+    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     /* end ppptj */
+       nhstepm is the number of hstepm from age to agelim
-     /*  x centered again */
+       nstepm is the number of stepm from age to agelim.
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+       Look at function hpijx to understand why because of memory size limitations,
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+       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
-     if (popbased==1) {
+       means that if the survival funtion is printed every two years of age and if
-       if(mobilav ==0){
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         for(i=1; i<=nlstate;i++)
+       results. So we changed our mind and took the option of the best precision.
-           prlim[i][i]=probs[(int)age][i][ij];
+    */
-       }else{ /* mobilav */
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(i=1; i<=nlstate;i++)
+    agelim = AGESUP;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       }
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     }
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* This for computing probability of death (h=1 means
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+      gp=matrix(0,nhstepm,1,nlstate);
-        as a weighted average of prlim.
+      gm=matrix(0,nhstepm,1,nlstate);
+      for(theta=1; theta <=npar; theta++){
+        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
+          xp[i] = x[i] + (i==theta ?delti[theta]:0);
+        }
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        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];
+          }
+        }
+        /* Next for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        for(j=nlstate+1;j<=nlstate+ndeath;j++){
+          for(i=1,gpp[j]=0.; i<= nlstate; i++)
+            gpp[j] += prlim[i][i]*p3mat[i][j][1];
+        }
+        /* end probability of death */
+        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
+          xp[i] = x[i] - (i==theta ?delti[theta]:0);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        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++)
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+          }
+        }
+        /* This for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        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];
+        }
+        /* end probability of death */
+        for(j=1; j<= nlstate; j++) /* vareij */
+          for(h=0; h<=nhstepm; h++){
+            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+          }
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+        }
+      } /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+      for(h=0; h<=nhstepm; h++) /* veij */
+        for(j=1; j<=nlstate;j++)
+          for(theta=1; theta <=npar; theta++)
+            trgradg[h][j][theta]=gradg[h][theta][j];
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+        for(theta=1; theta <=npar; theta++)
+          trgradgp[j][theta]=gradgp[theta][j];
+      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
+      for(i=1;i<=nlstate;i++)
+        for(j=1;j<=nlstate;j++)
+          vareij[i][j][(int)age] =0.;
+      for(h=0;h<=nhstepm;h++){
+        for(k=0;k<=nhstepm;k++){
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+          for(i=1;i<=nlstate;i++)
+            for(j=1;j<=nlstate;j++)
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+        }
+      }
+      /* pptj */
+      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+      for(j=nlstate+1;j<=nlstate+ndeath;j++)
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
+          varppt[j][i]=doldmp[j][i];
+      /* end ppptj */
+      /*  x centered again */
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
+      if (popbased==1) {
+        if(mobilav ==0){
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
+        }else{ /* mobilav */
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=mobaverage[(int)age][i][ij];
+        }
+      }
+      /* This for computing probability of death (h=1 means
+         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];
+      }
+      /* end probability of death */
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+        }
+      }
+      fprintf(ficresprobmorprev,"\n");
+      fprintf(ficresvij,"%.0f ",age );
+      for(i=1; i<=nlstate;i++)
+        for(j=1; j<=nlstate;j++){
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+        }
+      fprintf(ficresvij,"\n");
+      free_matrix(gp,0,nhstepm,1,nlstate);
+      free_matrix(gm,0,nhstepm,1,nlstate);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    } /* End age */
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
+    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 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)) 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.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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
      */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     }
-     /* end probability of death */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       }
-     }
-     fprintf(ficresprobmorprev,"\n");
-     fprintf(ficresvij,"%.0f ",age );
+    free_vector(xp,1,npar);
-     for(i=1; i<=nlstate;i++)
+    free_matrix(doldm,1,nlstate,1,nlstate);
-       for(j=1; j<=nlstate;j++){
+    free_matrix(dnewm,1,nlstate,1,npar);
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-       }
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-     fprintf(ficresvij,"\n");
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-     free_matrix(gp,0,nhstepm,1,nlstate);
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-     free_matrix(gm,0,nhstepm,1,nlstate);
+    fclose(ficresprobmorprev);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+    fflush(ficgp);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+    fflush(fichtm);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+  }  /* end varevsij */
-   } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   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");
-   /* 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,"\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)) not w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
- */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-   free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficresprobmorprev);
-   fflush(ficgp);
-   fflush(fichtm);
- }  /* 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 3674  void varprevlim(char fileres[], double *
+ Line 5053  void varprevlim(char fileres[], double *
    double *xp;
    double *gp, *gm;
    double **gradg, **trgradg;
+   double **mgm, **mgp;
    double age,agelim;
    int theta;
- Line 3696  void varprevlim(char fileres[], double *
+ Line 5076  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 3703  void varprevlim(char fileres[], double *
+ Line 5085  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 3722  void varprevlim(char fileres[], double *
+ Line 5113  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 3736  void varprevlim(char fileres[], double *
+ Line 5150  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 3748  void varprevlim(char fileres[], double *
+ Line 5164  void varprevlim(char fileres[], double *
  /************ Variance of one-step probabilities  ******************/
  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
- {
+  {
-   int i, j=0,  k1, l1, tj;
+    int i, j=0,  k1, l1, tj;
-   int k2, l2, j1,  z1;
+    int k2, l2, j1,  z1;
-   int k=0, l;
+    int k=0, l;
-   int first=1, first1, first2;
+    int first=1, first1, first2;
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+    double **dnewm,**doldm;
-   double *xp;
+    double *xp;
-   double *gp, *gm;
+    double *gp, *gm;
-   double **gradg, **trgradg;
+    double **gradg, **trgradg;
-   double **mu;
+    double **mu;
-   double age, cov[NCOVMAX+1];
+    double age, cov[NCOVMAX+1];
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+    int theta;
-   char fileresprob[FILENAMELENGTH];
+    char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+    char fileresprobcov[FILENAMELENGTH];
-   char fileresprobcor[FILENAMELENGTH];
+    char fileresprobcor[FILENAMELENGTH];
-   double ***varpij;
+    double ***varpij;
-   strcpy(fileresprob,"prob");
+    strcpy(fileresprob,"PROB_");
-   strcat(fileresprob,fileres);
+    strcat(fileresprob,fileres);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprob);
+      printf("Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"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) {
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-     fprintf(ficlog,"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) {
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+    }
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
+    pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   fprintf(ficresprob,"# Age");
+    fprintf(ficresprob,"# Age");
-   pstamp(ficresprobcov);
+    pstamp(ficresprobcov);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+    fprintf(ficresprobcov,"# Age");
-   pstamp(ficresprobcor);
+    pstamp(ficresprobcor);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"# Age");
+    fprintf(ficresprobcor,"# Age");
-   for(i=1; i<=nlstate;i++)
+    for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+      for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+      }
-  /* fprintf(ficresprob,"\n");
+    /* fprintf(ficresprob,"\n");
-   fprintf(ficresprobcov,"\n");
+       fprintf(ficresprobcov,"\n");
-   fprintf(ficresprobcor,"\n");
+       fprintf(ficresprobcor,"\n");
-  */
+    */
-   xp=vector(1,npar);
+    xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   first=1;
+    first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+    fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   fprintf(fichtm,"\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. \
+    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. \
  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
  standard deviations wide on each axis. <br>\
- Line 3836  standard deviations wide on each axis. <
+ Line 5251  standard deviations wide on each axis. <
   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   cov[1]=1;
+    cov[1]=1;
-   /* tj=cptcoveff; */
+    /* tj=cptcoveff; */
-   tj = (int) pow(2,cptcoveff);
+    tj = (int) pow(2,cptcoveff);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   j1=0;
+    j1=0;
-   for(j1=1; j1<=tj;j1++){
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */
-     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+      if  (cptcovn>0) {
-     /*j1++;*/
+        fprintf(ficresprob, "\n#********** Variable ");
-       if  (cptcovn>0) {
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         fprintf(ficresprob, "\n#********** Variable ");
+        fprintf(ficresprob, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        fprintf(ficresprobcov, "\n#********** Variable ");
-         fprintf(ficresprob, "**********\n#\n");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+        fprintf(ficresprobcov, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[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]][codtabm(j1,z1)]);
-         fprintf(ficgp, "\n#********** Variable ");
+        fprintf(ficgp, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[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]][codtabm(j1,z1)]);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[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]][codtabm(j1,z1)]);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+        fprintf(ficresprobcor, "**********\n#");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+        if(invalidvarcomb[j1]){
-         fprintf(ficresprobcor, "**********\n#");
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-       }
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
+          continue;
-       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+        }
-       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      }
-       gp=vector(1,(nlstate)*(nlstate+ndeath));
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       gm=vector(1,(nlstate)*(nlstate+ndeath));
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       for (age=bage; age<=fage; age ++){
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
-         cov[2]=age;
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-         for (k=1; k<=cptcovn;k++) {
+      for (age=bage; age<=fage; age ++){
-           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+        cov[2]=age;
-                                                          * 1  1 1 1 1
+        if(nagesqr==1)
-                                                          * 2  2 1 1 1
+          cov[3]= age*age;
-                                                          * 3  1 2 1 1
+        for (k=1; k<=cptcovn;k++) {
-                                                          */
+          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-         }
+                                                                     * 1  1 1 1 1
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+                                                                     * 2  2 1 1 1
-         for (k=1; k<=cptcovprod;k++)
+                                                                     * 3  1 2 1 1
-           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+                                                                     */
+          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+        }
-         for(theta=1; theta <=npar; theta++){
+        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-           for(i=1; i<=npar; i++)
+        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+        for (k=1; k<=cptcovprod;k++)
+          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           k=0;
+        for(theta=1; theta <=npar; theta++){
-           for(i=1; i<= (nlstate); i++){
+          for(i=1; i<=npar; i++)
-             for(j=1; j<=(nlstate+ndeath);j++){
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-               k=k+1;
-               gp[k]=pmmij[i][j];
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-             }
-           }
+          k=0;
+          for(i=1; i<= (nlstate); i++){
-           for(i=1; i<=npar; i++)
+            for(j=1; j<=(nlstate+ndeath);j++){
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+              k=k+1;
+              gp[k]=pmmij[i][j];
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+            }
-           k=0;
+          }
-           for(i=1; i<=(nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+          for(i=1; i<=npar; i++)
-               k=k+1;
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-               gm[k]=pmmij[i][j];
-             }
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           }
+          k=0;
+          for(i=1; i<=(nlstate); i++){
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+            for(j=1; j<=(nlstate+ndeath);j++){
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
+              k=k+1;
-         }
+              gm[k]=pmmij[i][j];
+            }
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+          }
-           for(theta=1; theta <=npar; theta++)
-             trgradg[j][theta]=gradg[theta][j];
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+        }
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
-         k=0;
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
-           }
-         }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-             varpij[i][j][(int)age] = doldm[i][j];
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
-         fprintf(ficresprob,"\n%d ",(int)age);
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
-         i=0;
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i++;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-             for (j=1; j<=i;j++){
-               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
-           }
-         }/* end of loop for state */
-       } /* end of loop for age */
-       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       /* Confidence intervalle of pij  */
-       /*
-         fprintf(ficgp,"\nunset parametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;first2=2;
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
-               if(i<=j) continue;
-               for (age=bage; age<=fage; age ++){
-                 if ((int)age %5==0){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
-                   c12=cv12/sqrt(v1*v2);
-                   /* Computing eigen value of matrix of covariance */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   if ((lc2 <0) || (lc1 <0) ){
-                     if(first2==1){
-                       first1=0;
-                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-                     }
-                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-                     /* lc2=fabs(lc2); */
-                   }
-                   /* Eigen vectors */
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+          for(theta=1; theta <=npar; theta++)
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+            trgradg[j][theta]=gradg[theta][j];
-                   v21=(lc1-v1)/cv12*v11;
-                   v12=-v21;
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                   v22=v11;
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                   tnalp=v21/v11;
-                   if(first1==1){
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     first1=0;
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+        k=0;
-                   }
+        for(i=1; i<=(nlstate); i++){
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+          for(j=1; j<=(nlstate+ndeath);j++){
-                   /*printf(fignu*/
+            k=k+1;
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+            mu[k][(int) age]=pmmij[i][j];
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+          }
-                   if(first==1){
+        }
-                     first=0;
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                     fprintf(ficgp,"\nset parametric;unset label");
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                     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);
+            varpij[i][j][(int)age] = doldm[i][j];
-                     fprintf(ficgp,"\nset ter png small size 320, 240");
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+        /*printf("\n%d ",(int)age);
-  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
+          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
+          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-                             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> Correlation at age %d (%.3f),",(int) age, c12);
+        fprintf(ficresprob,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
-                     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",\
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-                   }else{
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-                     first=0;
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+        }
-                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+        i=0;
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+        for (k=1; k<=(nlstate);k++){
-                     fprintf(ficgp,"\nreplot %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",\
+          for (l=1; l<=(nlstate+ndeath);l++){
-                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
+            i++;
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-                   }/* if first */
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-                 } /* age mod 5 */
+            for (j=1; j<=i;j++){
-               } /* end loop age */
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               first=1;
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             } /*l12 */
+            }
-           } /* k12 */
+          }
-         } /*l1 */
+        }/* end of loop for state */
-       }/* k1 */
+      } /* end of loop for age */
-       /* } */ /* loop covariates */
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-   }
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+      /* Confidence intervalle of pij  */
-   free_vector(xp,1,npar);
+      /*
-   fclose(ficresprob);
+        fprintf(ficgp,"\nunset parametric;unset label");
-   fclose(ficresprobcov);
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-   fclose(ficresprobcor);
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-   fflush(ficgp);
+        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-   fflush(fichtmcov);
+        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
- }
+        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      */
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+      first1=1;first2=2;
+      for (k2=1; k2<=(nlstate);k2++){
+        for (l2=1; l2<=(nlstate+ndeath);l2++){
+          if(l2==k2) continue;
+          j=(k2-1)*(nlstate+ndeath)+l2;
+          for (k1=1; k1<=(nlstate);k1++){
+            for (l1=1; l1<=(nlstate+ndeath);l1++){
+              if(l1==k1) continue;
+              i=(k1-1)*(nlstate+ndeath)+l1;
+              if(i<=j) continue;
+              for (age=bage; age<=fage; age ++){
+                if ((int)age %5==0){
+                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  mu1=mu[i][(int) age]/stepm*YEARM ;
+                  mu2=mu[j][(int) age]/stepm*YEARM;
+                  c12=cv12/sqrt(v1*v2);
+                  /* Computing eigen value of matrix of covariance */
+                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  if ((lc2 <0) || (lc1 <0) ){
+                    if(first2==1){
+                      first1=0;
+                      printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                    }
+                    fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                    /* lc2=fabs(lc2); */
+                  }
+                  /* Eigen vectors */
+                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  /*v21=sqrt(1.-v11*v11); *//* error */
+                  v21=(lc1-v1)/cv12*v11;
+                  v12=-v21;
+                  v22=v11;
+                  tnalp=v21/v11;
+                  if(first1==1){
+                    first1=0;
+                    printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  }
+                  fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  /*printf(fignu*/
+                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                  /* 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 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.svg\">                                                                                                                                           \
+ %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);
+                    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.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",      \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                  }else{
+                    first=0;
+                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    fprintf(ficgp,"\nreplot %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", \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                  }/* if first */
+                } /* age mod 5 */
+              } /* end loop age */
+              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 on combination of covariates j1 */
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+    free_vector(xp,1,npar);
+    fclose(ficresprob);
+    fclose(ficresprobcov);
+    fclose(ficresprobcor);
+    fflush(ficgp);
+    fflush(fichtmcov);
+  }
  /******************* 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>");
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-  m=pow(2,cptcoveff);
+    m=pow(2,cptcoveff);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    jj1=0;
-  for(k1=1; k1<=m;k1++){
+    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\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
+          printf("\nCombination (%d) ignored because no cases \n",k1);
+          continue;
+        }
       }
+      /* 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> \
+ <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+      /* Survival functions (period) in state j */
+      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>- 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> \
+          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.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ <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 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\
+    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,"\
+    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,"\
+    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,"\
+    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,"\
+    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,"\
+    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,"\
+    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,"\
+    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 4180  fprintf(fichtm," \n<ul><li><b>Graphs</b>
+ Line 5658  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
-  fflush(fichtm);
+    fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=pow(2,cptcoveff);
+    m=pow(2,cptcoveff);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    jj1=0;
-  for(k1=1; k1<=m;k1++){
+    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\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
+        }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<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</a>\n <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</a>\n<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 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
-  fflush(fichtm);
+    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, int backcast, char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
+         char gplotcondition[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;
+         int ioffset; /* variable offset for columns */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 4229  void printinggnuplot(char fileres[], cha
+ Line 5717  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 valid 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 k get corresponding value lv for combination k1 */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
- set ylabel \"Probability\" \n\
+                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- set ter png small size 320, 240\n\
+                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+                                 vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-      for (i=1; i<= nlstate ; i ++) {
+                         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-        else        fprintf(ficgp," %%*lf (%%*lf)");
+       }
-      }
+       fprintf(ficgp,"\n#\n");
-      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);
+                         if(invalidvarcomb[k1]){
-      for (i=1; i<= nlstate ; i ++) {
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+                                                 continue;
-        else fprintf(ficgp," %%*lf (%%*lf)");
+                         }
-      }
-      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+                         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
-      for (i=1; i<= nlstate ; i ++) {
+                         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
-        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+                         fprintf(ficgp,"set xlabel \"Age\" \n\
-        else fprintf(ficgp," %%*lf (%%*lf)");
+ set ylabel \"Probability\" \n   \
-      }
+ set ter svg size 640, 480\n     \
-      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+ 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)");
+                                 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(fileresu,"VPL_"),k1-1,k1-1);
+                         for (i=1; i<= nlstate ; i ++) {
+                                 if (i==cpt) 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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+                         for (i=1; i<= nlstate ; i ++) {
+                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+                                 else fprintf(ficgp," %%*lf (%%*lf)");
+                         }
+                         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+                         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+                                 /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+                                 fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+                                 kl=0;
+                                 for (k=1; k<=cptcoveff; k++){    /* For each combination of 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[k]][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):($5==2000? 3:2) t 'p.1' with line lc variable*/
+                                         if(k==cptcoveff){
+                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++(cpt-1),  cpt );
+                                         }else{
+                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+                                                 kl++;
+                                         }
+                                 } /* end covariate */
+                         }
+                         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,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-     for (i=1; i<= nlstate+1 ; i ++) {
+                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-       k=2*i;
+                                 /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         if (j==i) fprintf(ficgp," %%lf (%%lf)");
+                                 vlv= nbcode[Tvaraff[k]][lv];
-         else fprintf(ficgp," %%*lf (%%*lf)");
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        }
-       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+       fprintf(ficgp,"\n#\n");
-       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+                         if(invalidvarcomb[k1]){
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                                 continue;
-         if (j==i) fprintf(ficgp," %%lf (%%lf)");
+                         }
-         else fprintf(ficgp," %%*lf (%%*lf)");
-       }
+                         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-       fprintf(ficgp,"\" t\"\" w l lt 0,");
+                         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
+                                 if(vpopbased==0)
-       for (j=1; j<= nlstate+1 ; j ++) {
+                                         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-         if (j==i) fprintf(ficgp," %%lf (%%lf)");
+                                 else
-         else fprintf(ficgp," %%*lf (%%*lf)");
+                                         fprintf(ficgp,"\nreplot ");
-       }
+                                 for (i=1; i<= nlstate+1 ; i ++) {
-       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+                                         k=2*i;
-       else fprintf(ficgp,"\" t\"\" w l lt 0,");
+                                         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);
-     }
+                                         for (j=1; j<= nlstate+1 ; j ++) {
-   }
+                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");
+                                                 else fprintf(ficgp," %%*lf (%%*lf)");
+                                         }
+                                         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[k]][lv];
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+                         if(invalidvarcomb[k1]){
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                 continue;
+                         }
        /*       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*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+                                 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        */
        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%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) */
+         /* 4eme */
+   /* 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[k]][lv];
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+                         if(invalidvarcomb[k1]){
+                                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                         continue;
+                         }
+       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 */
+ /* 5eme */
+   /* 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[k]][lv];
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+                         if(invalidvarcomb[k1]){
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                 continue;
+                         }
+       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 */
+ /* 6eme */
+   /* 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[k]][lv];
+                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       }
+       fprintf(ficgp,"\n#\n");
+                         if(invalidvarcomb[k1]){
+                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                 continue;
+                         }
+       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)
+                                 if(i==1)
-           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         else
+                                 else
-           fprintf(ficgp,", '' ");
+                                         fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+                                 l=(nlstate+ndeath)*(i-1)+1;
-         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+                                 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);
+                                 fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\n");
+       fprintf(ficgp,"\nset out\n");
      } /* end cpt state*/
    } /* end covariate */
-   /* proba elementaires */
+ /* 7eme */
+   if(backcast == 1){
+     /* 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[k]][lv];
+                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+                                 }
+                                 fprintf(ficgp,"\n#\n");
+                                 if(invalidvarcomb[k1]){
+                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                                 continue;
+                                 }
+                                 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; */
+                                         l=(nlstate+ndeath)*(cpt-1)+1;
+                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
+                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
+                                         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+                                         /* for (j=2; j<= nlstate ; j ++) */
+                                         /*      fprintf(ficgp,"+$%d",k+l+j-1); */
+                                         /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+                                         fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+                                 } /* nlstate */
+                                 fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
+         /* 8eme */
+   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[k]][lv];
+                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+                                 }
+                                 fprintf(ficgp,"\n#\n");
+                                 if(invalidvarcomb[k1]){
+                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+                                                                 continue;
+                                 }
+                                 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 */
+                                                 ioffset=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 */
+                                                 /*# V1  = 1 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 */
+                                                 fprintf(ficgp," u %d:(", ioffset);
+                                                 if(i==nlstate+1)
+                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \
+                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                                                 else
+                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
+                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+                                         }else{ /* more than 2 covariates */
+                                                 if(cptcoveff ==1){
+                                                         ioffset=4; /* Age is in 4 */
+                                                 }else{
+                                                         ioffset=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 */
+                                                 }
+                                                 fprintf(ficgp," u %d:(",ioffset);
+                                                 kl=0;
+                                                 strcpy(gplotcondition,"(");
+                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+                                                         /* 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[k]][lv]; /* Value of the modality of Tvaraff[k] */
+                                                         kl++;
+                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+                                                         kl++;
+                                                         if(k <cptcoveff && cptcoveff>1)
+                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+                                                 }
+                                                 strcpy(gplotcondition+strlen(gplotcondition),")");
+                                                 /* 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(i==nlstate+1){
+                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                                                 }else{
+                                                                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+                                                 }
+                                         } /* 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 4409  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6326  plot [%.f:%.f]  ", ageminpar, agemaxpar)
  /*************** Moving average **************/
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+ /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
+  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
-   int i, cpt, cptcod;
-   int modcovmax =1;
+    int i, cpt, cptcod;
-   int mobilavrange, mob;
+    int modcovmax =1;
-   double age;
+    int mobilavrange, mob;
+    int iage=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-                            a covariate has 2 modalities */
+    double sum=0.;
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+    double age;
+    double *sumnewp, *sumnewm;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
-     if(mobilav==1) mobilavrange=5; /* default */
-     else mobilavrange=mobilav;
-     for (age=bage; age<=fage; age++)
+    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
-       for (i=1; i<=nlstate;i++)
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+    sumnewp = vector(1,ncovcombmax);
-     /* We keep the original values on the extreme ages bage, fage and for
+    sumnewm = vector(1,ncovcombmax);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+    agemingood = vector(1,ncovcombmax);
-        we use a 5 terms etc. until the borders are no more concerned.
+    agemaxgood = vector(1,ncovcombmax);
-     */
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+      sumnewm[cptcod]=0.;
-         for (i=1; i<=nlstate;i++){
+      sumnewp[cptcod]=0.;
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+      agemingood[cptcod]=0;
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+      agemaxgood[cptcod]=0;
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+    }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               }
+    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+      if(mobilav==1) mobilavrange=5; /* default */
-           }
+      else mobilavrange=mobilav;
-         }
+      for (age=bage; age<=fage; age++)
-       }/* end age */
+        for (i=1; i<=nlstate;i++)
-     }/* end mob */
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
-   }else return -1;
+            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   return 0;
+      /* We keep the original values on the extreme ages bage, fage and for
- }/* End movingaverage */
+         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         we use a 5 terms etc. until the borders are no more concerned.
+      */
+      for (mob=3;mob <=mobilavrange;mob=mob+2){
+        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+          for (i=1; i<=nlstate;i++){
+            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+              for (cpt=1;cpt<=(mob-1)/2;cpt++){
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
+              }
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+            }
+          }
+        }/* end age */
+      }/* end mob */
+    }else
+      return -1;
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
+      if(invalidvarcomb[cptcod]){
+        printf("\nCombination (%d) ignored because no cases \n",cptcod);
+        continue;
+      }
+      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemingood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+      /* From youngest, finding the oldest wrong */
+      agemaxgood[cptcod]=bage+(mob-1)/2;
+      for (age=bage+(mob-1)/2; age<=fage; age++){
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemaxgood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      }
+      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      for (age=bage; age<=fage; age++){
+        printf("%d %d ", cptcod, (int)age);
+        sumnewp[cptcod]=0.;
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewp[cptcod]+=probs[(int)age][i][cptcod];
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
+        }
+        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
+      }
+      /* printf("\n"); */
+      /* } */
+      /* brutal averaging */
+      for (i=1; i<=nlstate;i++){
+        for (age=1; age<=bage; age++){
+          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+        }
+        for (age=fage; age<=AGESUP; age++){
+          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+        }
+      } /* end i status */
+      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+        for (age=1; age<=AGESUP; age++){
+          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+          mobaverage[(int)age][i][cptcod]=0.;
+        }
+      }
+    }/* end cptcod */
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
+    free_vector(agemaxgood,1, ncovcombmax);
+    free_vector(agemingood,1, ncovcombmax);
+    return 0;
+  }/* End movingaverage */
  /************** Forecasting ******************/
  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){
- Line 4462  void prevforecast(char fileres[], double
+ Line 6492  void prevforecast(char fileres[], double
    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    double *popeffectif,*popcount;
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+   /* 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); */
-   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;
-   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;
- Line 4516  void prevforecast(char fileres[], double
+ Line 6544  void prevforecast(char fileres[], double
    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++)
+                                 for(i=1; i<=nlstate;i++)
            fprintf(ficresf," p%d%d",i,j);
-         fprintf(ficresf," p.%d",j);
+                                 fprintf(ficresf," wp.%d",j);
        }
        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-         fprintf(ficresf,"\n");
+                                 fprintf(ficresf,"\n");
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+                                 for (agec=fage; agec>=(ageminpar-1); agec--){
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+                                         nhstepm = nhstepm/hstepm;
-           nhstepm = nhstepm/hstepm;
+                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                         oldm=oldms;savm=savms;
-           oldm=oldms;savm=savms;
+                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+                                         for (h=0; h<=nhstepm; h++){
-           for (h=0; h<=nhstepm; h++){
+                                                 if (h*hstepm/YEARM*stepm ==yearp) {
-             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);
+                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-             }
+                                                 }
-             for(j=1; j<=nlstate+ndeath;j++) {
+                                                 for(j=1; j<=nlstate+ndeath;j++) {
-               ppij=0.;
+                                                         ppij=0.;
-               for(i=1; i<=nlstate;i++) {
+                                                         for(i=1; i<=nlstate;i++) {
-                 if (mobilav==1)
+                                                                 if (mobilav==1)
-                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
-                 else {
+                                                                 else {
-                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
-                 }
+                                                                 }
-                 if (h*hstepm/YEARM*stepm== yearp) {
+                                                                 if (h*hstepm/YEARM*stepm== yearp) {
-                   fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                 }
+                                                                 }
-               } /* end i */
+                                                         } /* end i */
-               if (h*hstepm/YEARM*stepm==yearp) {
+                                                         if (h*hstepm/YEARM*stepm==yearp) {
-                 fprintf(ficresf," %.3f", ppij);
+                                                                 fprintf(ficresf," %.3f", ppij);
-               }
+                                                         }
-             }/* end j */
+                                                 }/* end j */
-           } /* end h */
+                                         } /* end h */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         } /* end agec */
+                                 } /* end agec */
        } /* end yearp */
      } /* end cptcod */
    } /* end  cptcov */
-   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,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, 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*************/
  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){
- Line 4581  void populforecast(char fileres[], doubl
+ Line 6738  void populforecast(char fileres[], doubl
    double calagedatem, agelim, kk1, kk2;
    double *popeffectif,*popcount;
    double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char filerespop[FILENAMELENGTH];
    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- Line 4592  void populforecast(char fileres[], doubl
+ Line 6749  void populforecast(char fileres[], doubl
    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 4603  void populforecast(char fileres[], doubl
+ Line 6760  void populforecast(char fileres[], doubl
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
-   if (mobilav!=0) {
+   /* if (mobilav!=0) { */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+   /*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+   /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-       printf(" 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;
- Line 4618  void populforecast(char fileres[], doubl
+ Line 6775  void populforecast(char fileres[], doubl
    hstepm=1;
    hstepm=hstepm/stepm;
    if (popforecast==1) {
      if((ficpop=fopen(popfile,"r"))==NULL) {
        printf("Problem with population file : %s\n",popfile);exit(0);
- Line 4630  void populforecast(char fileres[], doubl
+ Line 6787  void populforecast(char fileres[], doubl
      i=1;
      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      imx=i;
      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
    }
    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        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 4650  void populforecast(char fileres[], doubl
+ Line 6807  void populforecast(char fileres[], doubl
        for (cpt=0; cpt<=0;cpt++) {
          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
            nhstepm = nhstepm/hstepm;
            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);
            for (h=0; h<=nhstepm; h++){
              if (h==(int) (calagedatem+YEARM*cpt)) {
                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- Line 4673  void populforecast(char fileres[], doubl
+ Line 6830  void populforecast(char fileres[], doubl
                }
                if (h==(int)(calagedatem+12*cpt)){
                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
-                   /*fprintf(ficrespop," %.3f", kk1);
+                 /*fprintf(ficrespop," %.3f", kk1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+                   if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                }
              }
              for(i=1; i<=nlstate;i++){
                kk1=0.;
-                 for(j=1; j<=nlstate;j++){
+               for(j=1; j<=nlstate;j++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+                 kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
+               }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+               tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
              }
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
+             if (h==(int)(calagedatem+12*cpt))
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+               for(j=1; j<=nlstate;j++)
+                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
            }
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          }
        }
-   /******/
+       /******/
        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- Line 4718  void populforecast(char fileres[], doubl
+ Line 6876  void populforecast(char fileres[], doubl
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          }
        }
-    }
+     }
    }
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
    if (popforecast==1) {
      free_ivector(popage,0,AGESUP);
      free_vector(popeffectif,0,AGESUP);
- Line 4732  void populforecast(char fileres[], doubl
+ Line 6890  void populforecast(char fileres[], doubl
    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fclose(ficrespop);
  } /* End of popforecast */
  int fileappend(FILE *fichier, char *optionfich)
  {
    if((fichier=fopen(optionfich,"a"))==NULL) {
- Line 4873  double gompertz(double x[])
+ Line 7031  double gompertz(double x[])
    double A,B,L=0.0,sump=0.,num=0.;
    int i,n=0; /* n is the size of the sample */
-   for (i=0;i<=imx-1 ; i++) {
+   for (i=1;i<=imx ; i++) {
      sump=sump+weight[i];
      /*    sump=sump+1;*/
      num=num+1;
- Line 4946  double gompertz_f(const gsl_vector *v, v
+ Line 7104  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 4955  void printinghtmlmort(char fileres[], ch
+ Line 7113  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 4970  fprintf(fichtm,"<ul><li><h4>Life table</
+ Line 7128  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 4984  void printinggnuplotmort(char fileres[],
+ Line 7142  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 5007  int readdata(char datafile[], int firsto
+ Line 7165  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 with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
    }
    i=1;
- Line 5185  void removespace(char *str) {
+ Line 7343  void removespace(char *str) {
  }
  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 5202  int decodemodel ( char model[], int last
+ Line 7361  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 5225  int decodemodel ( char model[], int last
+ Line 7376  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 5356  int decodemodel ( char model[], int last
+ Line 7543  int decodemodel ( char model[], int last
  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
  {
    int i, m;
+   int firstone=0;
    for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++) {
        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;
-         s[m][i]=-1;
+         if (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 + 1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+         if(firstone == 0){
-         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);
+           firstone=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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         }
+         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 can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
          s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
- Line 5381  int calandcheckages(int imx, int maxwav,
+ Line 7573  int calandcheckages(int imx, int maxwav,
    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((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 {
                if ((int)andc[i]!=9999){
                  nbwarn++;
- Line 5396  int calandcheckages(int imx, int maxwav,
+ Line 7588  int calandcheckages(int imx, int maxwav,
                }
              }
            } /* 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 5412  int calandcheckages(int imx, int maxwav,
+ Line 7604  int calandcheckages(int imx, int maxwav,
            }
            /*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)) {
- Line 5451  int calandcheckages(int imx, int maxwav,
+ Line 7649  int calandcheckages(int imx, int maxwav,
      return (1);
  }
- void 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> */ /* Only on gnu */
+    /* command line Intel compiler 32bit windows, XP compatible:*/
+    /* /GS /W3 /Gy
+       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
+       "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
+       "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
+       /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
+    */
+    /* 64 bits */
+    /*
+      /GS /W3 /Gy
+      /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
+      /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
+      /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
+      "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
+    /* Optimization are useless and O3 is slower than O2 */
+    /*
+      /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
+      /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
+      /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
+      /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
+    */
+    /* Link is */ /* /OUT:"visual studio
+\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
+       /PDB:"visual studio
+\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
+       "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
+       "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
+       "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
+       /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
+       /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
+       uiAccess='false'"
+       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
+       /NOLOGO /TLBID:1
+    */
+ #if defined __INTEL_COMPILER
+ #if defined(__GNUC__)
+         struct utsname sysInfo;  /* For Intel on Linux and OS/X */
+ #endif
+ #elif defined(__GNUC__)
+ #ifndef  __APPLE__
+ #include <gnu/libc-version.h>  /* Only on gnu */
+ #endif
+    struct utsname sysInfo;
+    int cross = CROSS;
+    if (cross){
+            printf("Cross-");
+            if(logged) fprintf(ficlog, "Cross-");
+    }
+ #endif
  #include <stdint.h>
-    printf("Compiled with:");fprintf(ficlog,"Compiled with:");
+    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
  #if defined(__clang__)
-    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
+    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
  #endif
  #if defined(__ICC) || defined(__INTEL_COMPILER)
-    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
+    printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
  #endif
  #if defined(__GNUC__) || defined(__GNUG__)
-    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
+    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++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
+    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++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
+    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");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
+    printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
  #endif
  #if defined(__PGI)
-    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
+    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");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
+    printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
  #endif
-    printf(". ");fprintf(ficlog,". ");
+    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 5505  void syscompilerinfo()
+ Line 7794  void syscompilerinfo()
  /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
  #if UINTPTR_MAX == 0xffffffff
-    printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
+    printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
  #elif UINTPTR_MAX == 0xffffffffffffffff
-    printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
+    printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
  #else
-    printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
+    printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
  #endif
- /* struct utsname sysInfo;
-    if (uname(&sysInfo) != -1) {
-      printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-      fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
-    }
-    else
-       perror("uname() error");
-           */
  #if defined(__GNUC__)
  # if defined(__GNUC_PATCHLEVEL__)
  #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
- Line 5530  void syscompilerinfo()
+ Line 7810  void syscompilerinfo()
  #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                              + __GNUC_MINOR__ * 100)
  # endif
-    printf("GNU C version %d.\n", __GNUC_VERSION__);
+    printf(" using GNU C version %d.\n", __GNUC_VERSION__);
-    fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
+    if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
+    if (uname(&sysInfo) != -1) {
+      printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+          if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
+    }
+    else
+       perror("uname() error");
+    //#ifndef __INTEL_COMPILER
+ #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
+    printf("GNU libc version: %s\n", gnu_get_libc_version());
+    if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
  #endif
+ #endif
+    //   void main()
+    //   {
  #if defined(_MSC_VER)
-    /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+    if (IsWow64()){
-    /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
+            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
-   /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
-  }
+ }
+ 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(k=1; k<=i1;k++){
+   /* 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");
+                 if(invalidvarcomb[k]){
+                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+                                                 continue;
+                 }
+     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, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
+         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+         /* Computes the back prevalence limit  for any combination      of covariate values
+    * at any age between ageminpar and agemaxpar
+          */
+   int i, j, k, i1 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   /* double ***mobaverage; */
+   /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
+   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(k=1; k<=i1;k++){
+   /* 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");
+                 if(invalidvarcomb[k]){
+                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+                                                 continue;
+                 }
+     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++){ */
+       if(mobilavproj > 0){
+         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+                                 bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
+       }else if (mobilavproj == 0){
+                                 printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+                                 fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+                                 exit(1);
+       }else{
+                                 /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+                                 bprevalim(bprlim, probs, nlstate, p, age, 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 */
+   /* hBijx(p, bage, fage); */
+   /* fclose(ficrespijb); */
+   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, double ***prevacurrent){
+     /*------------- h Bij x at various ages ------------*/
+   int stepsize;
+   /* int agelim; */
+         int ageminl;
+   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; */
+   ageminl=30;
+   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");
+     if(invalidvarcomb[k]){
+       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+       continue;
+     }
+     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       /*          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);   */
+       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
+       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, 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;
+  } /*  hBijx */
  /***********************************************/
  /**************** Main Program *****************/
- Line 5557  int main(int argc, char *argv[])
+ Line 8195  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 5568  int main(int argc, char *argv[])
+ Line 8207  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 ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
    double fret;
-   double dum; /* Dummy variable */
+   double dum=0.; /* Dummy variable */
    double ***p3mat;
-   double ***mobaverage;
+   /* 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 5606  int main(int argc, char *argv[])
+ Line 8254  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 5649  int main(int argc, char *argv[])
+ Line 8299  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 5685  int main(int argc, char *argv[])
+ Line 8348  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){
- Line 5702  int main(int argc, char *argv[])
+ Line 8370  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 5710  int main(int argc, char *argv[])
+ Line 8378  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 5718  int main(int argc, char *argv[])
+ Line 8386  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 5729  int main(int argc, char *argv[])
+ Line 8397  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 5744  int main(int argc, char *argv[])
+ Line 8414  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 5754  int main(int argc, char *argv[])
+ Line 8424  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 5788  int main(int argc, char *argv[])
+ Line 8536  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 5806  int main(int argc, char *argv[])
+ Line 8553  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==-5) { /* Main Wizard */
-   else if(mle==-3) {
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
+     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{
+   }  else{ /* Begin of mle != -1 or -5 */
      /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 5836  int main(int argc, char *argv[])
+ Line 8582  int main(int argc, char *argv[])
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      for(i=1; i <=nlstate; i++){
-       j=0;
+                         j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
-         if(jj==i) continue;
+                                 if(jj==i) continue;
-         j++;
+                                 j++;
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+                                 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 \
+                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
  It might be a problem of design; if ncovcol and the model are correct\n \
  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-           exit(1);
+                                         exit(1);
-         }
+                                 }
-         fprintf(ficparo,"%1d%1d",i1,j1);
+                                 fprintf(ficparo,"%1d%1d",i1,j1);
-         if(mle==1)
+                                 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++){
+                                 for(k=1; k<=ncovmodel;k++){
-           fscanf(ficpar," %lf",&param[i][j][k]);
+                                         fscanf(ficpar," %lf",&param[i][j][k]);
-           if(mle==1){
+                                         if(mle==1){
-             printf(" %lf",param[i][j][k]);
+                                                 printf(" %lf",param[i][j][k]);
-             fprintf(ficlog," %lf",param[i][j][k]);
+                                                 fprintf(ficlog," %lf",param[i][j][k]);
-           }
+                                         }
-           else
+                                         else
-             fprintf(ficlog," %lf",param[i][j][k]);
+                                                 fprintf(ficlog," %lf",param[i][j][k]);
-           fprintf(ficparo," %lf",param[i][j][k]);
+                                         fprintf(ficparo," %lf",param[i][j][k]);
-         }
+                                 }
-         fscanf(ficpar,"\n");
+                                 fscanf(ficpar,"\n");
-         numlinepar++;
+                                 numlinepar++;
-         if(mle==1)
+                                 if(mle==1)
-           printf("\n");
+                                         printf("\n");
-         fprintf(ficlog,"\n");
+                                 fprintf(ficlog,"\n");
-         fprintf(ficparo,"\n");
+                                 fprintf(ficparo,"\n");
        }
      }
      fflush(ficlog);
- Line 5887  run imach with mle=-1 to get a correct t
+ Line 8633  run imach with mle=-1 to get a correct t
      for(i=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath-1; j++){
-         fscanf(ficpar,"%1d%1d",&i1,&j1);
+                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
-         if ( (i1-i) * (j1-j) != 0){
+                                 if ( (i1-i) * (j1-j) != 0){
-           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-           exit(1);
+                                         exit(1);
-         }
+                                 }
-         printf("%1d%1d",i,j);
+                                 printf("%1d%1d",i,j);
-         fprintf(ficparo,"%1d%1d",i1,j1);
+                                 fprintf(ficparo,"%1d%1d",i1,j1);
-         fprintf(ficlog,"%1d%1d",i1,j1);
+                                 fprintf(ficlog,"%1d%1d",i1,j1);
-         for(k=1; k<=ncovmodel;k++){
+                                 for(k=1; k<=ncovmodel;k++){
-           fscanf(ficpar,"%le",&delti3[i][j][k]);
+                                         fscanf(ficpar,"%le",&delti3[i][j][k]);
-           printf(" %le",delti3[i][j][k]);
+                                         printf(" %le",delti3[i][j][k]);
-           fprintf(ficparo," %le",delti3[i][j][k]);
+                                         fprintf(ficparo," %le",delti3[i][j][k]);
-           fprintf(ficlog," %le",delti3[i][j][k]);
+                                         fprintf(ficlog," %le",delti3[i][j][k]);
-         }
+                                 }
-         fscanf(ficpar,"\n");
+                                 fscanf(ficpar,"\n");
-         numlinepar++;
+                                 numlinepar++;
-         printf("\n");
+                                 printf("\n");
-         fprintf(ficparo,"\n");
+                                 fprintf(ficparo,"\n");
-         fprintf(ficlog,"\n");
+                                 fprintf(ficlog,"\n");
        }
      }
      fflush(ficlog);
      /* Reads covariance matrix */
      delti=delti3[1][1];
      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
- Line 5926  run imach with mle=-1 to get a correct t
+ Line 8672  run imach with mle=-1 to get a correct t
        fputs(line,ficlog);
      }
      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(mle==1)
+       if(count != 3){
-         printf("%s",str);
+                                 printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
-       fprintf(ficlog,"%s",str);
+ This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
-       fprintf(ficparo,"%s",str);
+ 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("%1d%1d%1d",i1,j1,jk);
+                         }
+       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
        for(j=1; j <=i; j++){
-         fscanf(ficpar," %le",&matcov[i][j]);
+                                 fscanf(ficpar," %le",&matcov[i][j]);
-         if(mle==1){
+                                 if(mle==1){
-           printf(" %.5le",matcov[i][j]);
+                                         printf(" %.5le",matcov[i][j]);
-         }
+                                 }
-         fprintf(ficlog," %.5le",matcov[i][j]);
+                                 fprintf(ficlog," %.5le",matcov[i][j]);
-         fprintf(ficparo," %.5le",matcov[i][j]);
+                                 fprintf(ficparo," %.5le",matcov[i][j]);
        }
        fscanf(ficpar,"\n");
        numlinepar++;
        if(mle==1)
-         printf("\n");
+                                 printf("\n");
        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];
+                                 matcov[i][j]=matcov[j][i];
      if(mle==1)
        printf("\n");
- Line 5968  run imach with mle=-1 to get a correct t
+ Line 8727  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);
    annais=vector(1,n);
    moisdc=vector(1,n);
    andc=vector(1,n);
+   weight=vector(1,n);
    agedc=vector(1,n);
    cod=ivector(1,n);
-   weight=vector(1,n);
+   for(i=1;i<=n;i++){
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+                 num[i]=0;
+                 moisnais[i]=0;
+                 annais[i]=0;
+                 moisdc[i]=0;
+                 andc[i]=0;
+                 agedc[i]=0;
+                 cod[i]=0;
+                 weight[i]=1.0; /* Equal weights, 1 by default */
+         }
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
    s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
    tab=ivector(1,NCOVMAX);
    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
+   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 6025  run imach with mle=-1 to get a correct t
+ Line 8795  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 6050  run imach with mle=-1 to get a correct t
+ Line 8823  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);
    /* */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   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)
+         cptcoveff=0;
-     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
+     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+         }
+         ncovcombmax=pow(2,cptcoveff);
+         invalidvarcomb=ivector(1, ncovcombmax);
+         for(i=1;i<ncovcombmax;i++)
+                 invalidvarcomb[i]=0;
+   /* 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;
    /*if (cptcovn > 0) */
    m=pow(2,cptcoveff);
-   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
-       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
-         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
-           h++;
-           if (h>m)
-             h=1;
            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
-            *     h     1     2     3     4
+            * For k=4 covariates, h goes from 1 to m=2**k
+            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
+            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
+            *     h\k   1     2     3     4
             *______________________________
             *     1 i=1 1 i=1 1 i=1 1 i=1 1
             *     2     2     1     1     1
- Line 6099  run imach with mle=-1 to get a correct t
+ Line 8895  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
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+      * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
-      codtab[1][2]=1;codtab[2][2]=2; */
+      * We are keeping this crazy system in order to be able (in the future?)
-   /* for(i=1; i <=m ;i++){
+      * to have more than 2 values (0 or 1) for a covariate.
-      for(k=1; k <=cptcovn; k++){
+      * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
-        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+      * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
-      }
+      *              bbbbbbbb
-      printf("\n");
+      *              76543210
-      }
+      *   h-1        00000101 (6-1=5)
-      scanf("%d",i);*/
+      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
+      *           &
+      *     1        00000001 (1)
+      *              00000000        = 1 & ((h-1) >> (k-1))
+      *          +1= 00000001 =1
+      *
+      * 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
+                  * codtabm and decodtabm are identical
+      */
   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 6164  run imach with mle=-1 to get a correct t
+ Line 8990  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 6187  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 9015  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 for any valid combination of covariates
       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, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 6199  Youngest age at first (selected) pass %.
+ Line 9034  Youngest age at first (selected) pass %.
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
            imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    /* For Powell, parameters are in a vector p[] starting at p[1]
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
    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); */
+                 for(i=1;i<=NDIM;i++)
+                         for(j=1;j<=NDIM;j++)
+                                 ximort[i][j]=0.;
+     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
- Line 6222  Interval (in months) between two waves:
+ Line 9059  Interval (in months) between two waves:
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
        for (m=firstpass; m<=lastpass; m++)
-         if (s[m][i]>nlstate) {
+                                 if (s[m][i]>nlstate) {
-           dcwave[i]=m;
+                                         dcwave[i]=m;
-           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
+                                         /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
-           break;
+                                         break;
-         }
+                                 }
      }
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
-         ageexmed[i]=agev[mw[1][i]][i];
+                                 ageexmed[i]=agev[mw[1][i]][i];
-         j=wav[i];
+                                 j=wav[i];
-         agecens[i]=1.;
+                                 agecens[i]=1.;
-         if (ageexmed[i]> 1 && wav[i] > 0){
+                                 if (ageexmed[i]> 1 && wav[i] > 0){
-           agecens[i]=agev[mw[j][i]][i];
+                                         agecens[i]=agev[mw[j][i]][i];
-           cens[i]= 1;
+                                         cens[i]= 1;
-         }else if (ageexmed[i]< 1)
+                                 }else if (ageexmed[i]< 1)
-           cens[i]= -1;
+                                         cens[i]= -1;
-         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+                                 if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
-           cens[i]=0 ;
+                                         cens[i]=0 ;
        }
        else cens[i]=-1;
      }
      for (i=1;i<=NDIM;i++) {
        for (j=1;j<=NDIM;j++)
-         ximort[i][j]=(i == j ? 1.0 : 0.0);
+                                 ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
      /*p[1]=0.0268; p[NDIM]=0.083;*/
- Line 6260  Interval (in months) between two waves:
+ Line 9097  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 6303  Interval (in months) between two waves:
+ Line 9140  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 6357  Interval (in months) between two waves:
+ Line 9194  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];
+                                 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]);
+                                 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 6406  Interval (in months) between two waves:
+ Line 9246  Interval (in months) between two waves:
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
-     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 ageminpar=50;
+                 agemaxpar=100;
-     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
+     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{
+                         printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+                         fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 }
+     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
      free_vector(lsurv,1,AGESUP);
      free_vector(lpop,1,AGESUP);
      free_vector(tpop,1,AGESUP);
- #ifdef GSL
+     free_matrix(ximort,1,NDIM,1,NDIM);
      free_ivector(cens,1,n);
      free_vector(agecens,1,n);
      free_ivector(dcwave,1,n);
-     free_matrix(ximort,1,NDIM,1,NDIM);
+ #ifdef GSL
  #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 6449  Interval (in months) between two waves:
+ Line 9308  Interval (in months) between two waves:
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
-         if (k != i) {
+                                 if (k != i) {
-           printf("%d%d ",i,k);
+                                         printf("%d%d ",i,k);
-           fprintf(ficlog,"%d%d ",i,k);
+                                         fprintf(ficlog,"%d%d ",i,k);
-           fprintf(ficres,"%1d%1d ",i,k);
+                                         fprintf(ficres,"%1d%1d ",i,k);
-           for(j=1; j <=ncovmodel; j++){
+                                         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++;
+                                                 jk++;
-           }
+                                         }
-           printf("\n");
+                                         printf("\n");
-           fprintf(ficlog,"\n");
+                                         fprintf(ficlog,"\n");
-           fprintf(ficres,"\n");
+                                         fprintf(ficres,"\n");
-         }
+                                 }
        }
      }
-     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");
      for(i=1,jk=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath; j++){
-         if (j!=i) {
+                                 if (j!=i) {
-           fprintf(ficres,"%1d%1d",i,j);
+                                         fprintf(ficres,"%1d%1d",i,j);
-           printf("%1d%1d",i,j);
+                                         printf("%1d%1d",i,j);
-           fprintf(ficlog,"%1d%1d",i,j);
+                                         fprintf(ficlog,"%1d%1d",i,j);
-           for(k=1; k<=ncovmodel;k++){
+                                         for(k=1; k<=ncovmodel;k++){
-             printf(" %.5e",delti[jk]);
+                                                 printf(" %.5e",delti[jk]);
-             fprintf(ficlog," %.5e",delti[jk]);
+                                                 fprintf(ficlog," %.5e",delti[jk]);
-             fprintf(ficres," %.5e",delti[jk]);
+                                                 fprintf(ficres," %.5e",delti[jk]);
-             jk++;
+                                                 jk++;
-           }
+                                         }
-           printf("\n");
+                                         printf("\n");
-           fprintf(ficlog,"\n");
+                                         fprintf(ficlog,"\n");
-           fprintf(ficres,"\n");
+                                         fprintf(ficres,"\n");
-         }
+                                 }
        }
      }
      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 6512  Interval (in months) between two waves:
+ Line 9390  Interval (in months) between two waves:
      for(itimes=1;itimes<=2;itimes++){
        jj=0;
        for(i=1; i <=nlstate; i++){
-         for(j=1; j <=nlstate+ndeath; j++){
+                                 for(j=1; j <=nlstate+ndeath; j++){
-           if(j==i) continue;
+                                         if(j==i) continue;
-           for(k=1; k<=ncovmodel;k++){
+                                         for(k=1; k<=ncovmodel;k++){
-             jj++;
+                                                 jj++;
-             ca[0]= k+'a'-1;ca[1]='\0';
+                                                 ca[0]= k+'a'-1;ca[1]='\0';
-             if(itimes==1){
+                                                 if(itimes==1){
-               if(mle>=1)
+                                                         if(mle>=1)
-                 printf("#%1d%1d%d",i,j,k);
+                                                                 printf("#%1d%1d%d",i,j,k);
-               fprintf(ficlog,"#%1d%1d%d",i,j,k);
+                                                         fprintf(ficlog,"#%1d%1d%d",i,j,k);
-               fprintf(ficres,"#%1d%1d%d",i,j,k);
+                                                         fprintf(ficres,"#%1d%1d%d",i,j,k);
-             }else{
+                                                 }else{
-               if(mle>=1)
+                                                         if(mle>=1)
-                 printf("%1d%1d%d",i,j,k);
+                                                                 printf("%1d%1d%d",i,j,k);
-               fprintf(ficlog,"%1d%1d%d",i,j,k);
+                                                         fprintf(ficlog,"%1d%1d%d",i,j,k);
-               fprintf(ficres,"%1d%1d%d",i,j,k);
+                                                         fprintf(ficres,"%1d%1d%d",i,j,k);
-             }
+                                                 }
-             ll=0;
+                                                 ll=0;
-             for(li=1;li <=nlstate; li++){
+                                                 for(li=1;li <=nlstate; li++){
-               for(lj=1;lj <=nlstate+ndeath; lj++){
+                                                         for(lj=1;lj <=nlstate+ndeath; lj++){
-                 if(lj==li) continue;
+                                                                 if(lj==li) continue;
-                 for(lk=1;lk<=ncovmodel;lk++){
+                                                                 for(lk=1;lk<=ncovmodel;lk++){
-                   ll++;
+                                                                         ll++;
-                   if(ll<=jj){
+                                                                         if(ll<=jj){
-                     cb[0]= lk +'a'-1;cb[1]='\0';
+                                                                                 cb[0]= lk +'a'-1;cb[1]='\0';
-                     if(ll<jj){
+                                                                                 if(ll<jj){
-                       if(itimes==1){
+                                                                                         if(itimes==1){
-                         if(mle>=1)
+                                                                                                 if(mle>=1)
-                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                                                                                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                                                                                 fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
+                                                                                                 fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
-                       }else{
+                                                                                         }else{
-                         if(mle>=1)
+                                                                                                 if(mle>=1)
-                           printf(" %.5e",matcov[jj][ll]);
+                                                                                                         printf(" %.5e",matcov[jj][ll]);
-                         fprintf(ficlog," %.5e",matcov[jj][ll]);
+                                                                                                 fprintf(ficlog," %.5e",matcov[jj][ll]);
-                         fprintf(ficres," %.5e",matcov[jj][ll]);
+                                                                                                 fprintf(ficres," %.5e",matcov[jj][ll]);
-                       }
+                                                                                         }
-                     }else{
+                                                                                 }else{
-                       if(itimes==1){
+                                                                                         if(itimes==1){
-                         if(mle>=1)
+                                                                                                 if(mle>=1)
-                           printf(" Var(%s%1d%1d)",ca,i,j);
+                                                                                                         printf(" Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
+                                                                                                 fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
-                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
+                                                                                                 fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
-                       }else{
+                                                                                         }else{
-                         if(mle>=1)
+                                                                                                 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]);
-                       }
+                                                                                         }
-                     }
+                                                                                 }
-                   }
+                                                                         }
-                 } /* end lk */
+                                                                 } /* end lk */
-               } /* end lj */
+                                                         } /* end lj */
-             } /* end li */
+                                                 } /* end li */
-             if(mle>=1)
+                                                 if(mle>=1)
-               printf("\n");
+                                                         printf("\n");
-             fprintf(ficlog,"\n");
+                                                 fprintf(ficlog,"\n");
-             fprintf(ficres,"\n");
+                                                 fprintf(ficres,"\n");
-             numlinepar++;
+                                                 numlinepar++;
-           } /* end k*/
+                                         } /* end k*/
-         } /*end j */
+                                 } /*end j */
        } /* end i */
      } /* end itimes */
      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,stdout);
-       fputs(line,ficparo);
+                                 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("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
+                                 fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\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 6595  Interval (in months) between two waves:
+ Line 9496  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 6625  Interval (in months) between two waves:
+ Line 9527  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 6643  Interval (in months) between two waves:
+ Line 9546  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);
+     fprintf(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);
+     fprintf(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);
+     fprintf(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); */
+                 /* 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\
-     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
+ This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+                         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\
-    /*------------ free_vector  -------------*/
+ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-    /*  chdir(path); */
+     }else{
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
-     free_ivector(wav,1,imx);
+     }
-     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
+                                                                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
-     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+                                                                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+                 /*------------ free_vector  -------------*/
+                 /*  chdir(path); */
+     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
+     /* 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);    */
      free_lvector(num,1,n);
      free_vector(agedc,1,n);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
      fclose(ficres);
+     /* 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);
- #ifdef FREEEXIT2
- #include "freeexit2.h"
- #endif
      /*------------- h Pij x at various ages ------------*/
- #include "hpijx.h"
+     /*#include "hpijx.h"*/
+     hPijx(p, bage, fage);
      fclose(ficrespij);
-   /*-------------- Variance of one-step probabilities---*/
+     /* ncovcombmax=  pow(2,cptcoveff); */
+     /*-------------- Variance of one-step probabilities---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     /* Prevalence for each covariates in probs[age][status][cov] */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      for(i=1;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
-         for(k=1;k<=NCOVMAX;k++)
+                                 for(k=1;k<=ncovcombmax;k++)
-           probs[i][j][k]=0.;
+                                         probs[i][j][k]=0.;
+     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     if (mobilav!=0 ||mobilavproj !=0 ) {
+       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+                         for(i=1;i<=AGESUP;i++)
+                                 for(j=1;j<=nlstate;j++)
+                                         for(k=1;k<=ncovcombmax;k++)
+                                                 mobaverages[i][j][k]=0.;
+       mobaverage=mobaverages;
+       if (mobilav!=0) {
+                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+                                         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+                                         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+                                 }
+       }
+       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+       else if (mobilavproj !=0) {
+                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+                                         fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+                                         printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+                                 }
+       }
+     }/* end if moving average */
      /*---------- Forecasting ------------------*/
      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
        /*    if(stepm ==1){*/
-       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       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){
+       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
+       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-     /*  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",\
+       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
+       bprlim=matrix(1,nlstate,1,nlstate);
+       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
-     if (mobilav!=0) {
+       fclose(ficresplb);
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
+       hBijx(p, bage, fage, mobaverage);
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+       fclose(ficrespijb);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
-       }
+       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
+       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
      }
+     /* ------ Other prevalence ratios------------ */
+     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);
      /*---------- 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#****** ");
+       fprintf(ficreseij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                                 fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         }
+       }
-         fprintf(ficreseij,"******\n");
+       fprintf(ficreseij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
-         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
-       /*}*/
+       oldm=oldms;savm=savms;
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
      fclose(ficreseij);
+     printf("done evsij\n");fflush(stdout);
+     fprintf(ficlog,"done evsij\n");fflush(ficlog);
      /*---------- Health expectancies and variances ------------*/
-     strcpy(filerest,"t");
+     strcpy(filerest,"T_");
-     strcat(filerest,fileres);
+     strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
      }
-     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
-     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
+     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
+     strcpy(fileresstde,"STDE_");
-     strcpy(fileresstde,"stde");
+     strcat(fileresstde,fileresu);
-     strcat(fileresstde,fileres);
      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++)
+                                         fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-               for(j=1;j <=nlstate;j++)
+                                         /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-                 vepp += vareij[i][j][(int)age];
+                                         /* printf(" age %4.0f ",age); */
-             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+                                         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-             for(j=1;j <=nlstate;j++){
+                                                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
-               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+                                                         epj[j] += prlim[i][i]*eij[i][j][(int)age];
-             }
+                                                         /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-             fprintf(ficrest,"\n");
+                                                         /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
-           }
+                                                 }
-         }
+                                                 epj[nlstate+1] +=epj[j];
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+                                         }
-         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+                                         /* printf(" age %4.0f \n",age); */
-         free_vector(epj,1,nlstate+1);
+                                         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");
+                                 }
+       } /* End vpopbased */
+       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       free_vector(epj,1,nlstate+1);
+       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 6889  Interval (in months) between two waves:
+ Line 9859  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++){*/
      for (k=1; k <= (int) pow(2,cptcoveff); k++){
          fprintf(ficresvpl,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++)
+                         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficresvpl,"******\n");
+                         fprintf(ficresvpl,"******\n");
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+                         varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+                         oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,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);
+                         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);
+     if (mobilav!=0 ||mobilavproj !=0)
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-   }  /* mle==-3 arrives here for freeing */
+     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-  /* endfree:*/
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
+  /* endfree:*/
      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
      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(invalidvarcomb,1,ncovcombmax);
      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 6981  Interval (in months) between two waves:
+ Line 9960  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 7038  Interval (in months) between two waves:
+ Line 10023  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);
    }
  }

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