Diff for /imach/src/imach.c between versions 1.182 and 1.190

version 1.182, 2015/02/12 08:19:57 version 1.190, 2015/05/05 08:51:13
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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    Revision 1.182  2015/02/12 08:19:57  brouard
   Summary: Trying to keep directest which seems simpler and more general    Summary: Trying to keep directest which seems simpler and more general
   Author: Nicolas Brouard    Author: Nicolas Brouard
Line 564 Line 599
  end   end
 */  */
   
   /* #define DEBUG */
   /* #define DEBUGBRENT */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 #define POWELLDIRECT /* Directest to decide new direction instead of Powell 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 <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 651  typedef struct { Line 689  typedef struct {
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98p, Février 2015,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 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar=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 */  /* 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 cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
Line 767  static double maxarg1,maxarg2; Line 805  static double maxarg1,maxarg2;
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)  #define rint(a) floor(a+0.5)
 /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */  /* 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) */  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
 /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
 /* static double dsqrarg; */  /* static double dsqrarg; */
Line 797  int **s; /* Status */ Line 835  int **s; /* Status */
 double *agedc;  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * covar=matrix(0,NCOVMAX,1,n);                     * 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;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
Line 815  static int split( char *path, char *dirc Line 853  static int split( char *path, char *dirc
      the name of the file (name), its extension only (ext) and its first part of the name (finame)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   */     */ 
   char  *ss;                            /* pointer */    char  *ss;                            /* pointer */
   int   l1, l2;                         /* length counters */    int   l1=0, l2=0;                             /* length counters */
   
   l1 = strlen(path );                   /* length of path */    l1 = strlen(path );                   /* length of path */
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 826  static int split( char *path, char *dirc Line 864  static int split( char *path, char *dirc
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* get current working directory */      /* get current working directory */
     /*    extern  char* getcwd ( char *buf , int len);*/      /*    extern  char* getcwd ( char *buf , int len);*/
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   #else
           if (getcwd(dirc, FILENAME_MAX) == NULL) {
   #endif
       return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
     }      }
     /* got dirc from getcwd*/      /* got dirc from getcwd*/
Line 837  static int split( char *path, char *dirc Line 879  static int split( char *path, char *dirc
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     strcpy( name, ss );         /* save file name */      strcpy( name, ss );         /* save file name */
     strncpy( dirc, path, l1 - l2 );     /* now the directory */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     dirc[l1-l2] = 0;                    /* add zero */      dirc[l1-l2] = '\0';                 /* add zero */
     printf(" DIRC2 = %s \n",dirc);      printf(" DIRC2 = %s \n",dirc);
   }    }
   /* We add a separator at the end of dirc if not exists */    /* We add a separator at the end of dirc if not exists */
Line 889  char *trimbb(char *out, char *in) Line 931  char *trimbb(char *out, char *in)
   return s;    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)  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')       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       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
   char *s, *t;    char *s, *t;
Line 919  char *cutl(char *blocc, char *alocc, cha Line 1004  char *cutl(char *blocc, char *alocc, cha
 }  }
 char *cutv(char *blocc, char *alocc, char *in, char occ)  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')       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      gives blocc="abcdef2ghi" and alocc="j".       gives blocc="abcdef2ghi" and alocc="j".
      If occ is not found blocc is null and alocc is equal to in. Returns alocc       If occ is not found blocc is null and alocc is equal to in. Returns alocc
Line 1230  double f1dim(double x) Line 1315  double f1dim(double x)
   
 /*****************brent *************************/  /*****************brent *************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)   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;     int iter; 
   double a,b,d,etemp;    double a,b,d,etemp;
   double fu=0,fv,fw,fx;    double fu=0,fv,fw,fx;
Line 1283  double brent(double ax, double bx, doubl Line 1374  double brent(double ax, double bx, doubl
     if (fu <= fx) {       if (fu <= fx) { 
       if (u >= x) a=x; else b=x;         if (u >= x) a=x; else b=x; 
       SHFT(v,w,x,u)         SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu)         SHFT(fv,fw,fx,fu) 
         } else {       } else { 
           if (u < x) a=u; else b=u;         if (u < x) a=u; else b=u; 
           if (fu <= fw || w == x) {         if (fu <= fw || w == x) { 
             v=w;           v=w; 
             w=u;           w=u; 
             fv=fw;           fv=fw; 
             fw=fu;           fw=fu; 
           } else if (fu <= fv || v == x || v == w) {         } else if (fu <= fv || v == x || v == w) { 
             v=u;           v=u; 
             fv=fu;           fv=fu; 
           }         } 
         }       } 
   }     } 
   nrerror("Too many iterations in brent");     nrerror("Too many iterations in brent"); 
   *xmin=x;     *xmin=x; 
Line 1306  double brent(double ax, double bx, doubl Line 1397  double brent(double ax, double bx, doubl
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             double (*func)(double))               double (*func)(double)) 
 {   { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   the downhill direction (defined by the function as evaluated at the initial points) and returns
   new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
   values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
      */
   double ulim,u,r,q, dum;    double ulim,u,r,q, dum;
   double fu;     double fu; 
    
   *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) {     if (*fb > *fa) { 
     SHFT(dum,*ax,*bx,dum)       SHFT(dum,*ax,*bx,dum) 
       SHFT(dum,*fb,*fa,dum)       SHFT(dum,*fb,*fa,dum) 
       }     } 
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
   while (*fb > *fc) { /* 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);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* 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);         fu=(*func)(u); 
 #ifdef DEBUG  #ifdef DEBUG
       /* f(x)=A(x-u)**2+f(u) */        /* f(x)=A(x-u)**2+f(u) */
Line 1333  void mnbrak(double *ax, double *bx, doub Line 1443  void mnbrak(double *ax, double *bx, doub
       fparabu= *fa - A*(*ax-u)*(*ax-u);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);        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);        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   #endif 
   #ifdef MNBRAKORIGINAL
   #else
         if (fu > *fc) {
   #ifdef DEBUG
         printf("mnbrak4  fu > fc \n");
         fprintf(ficlog, "mnbrak4 fu > fc\n");
   #endif
           /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
           /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
           dum=u; /* Shifting c and u */
           u = *cx;
           *cx = dum;
           dum = fu;
           fu = *fc;
           *fc =dum;
         } else { /* end */
   #ifdef DEBUG
         printf("mnbrak3  fu < fc \n");
         fprintf(ficlog, "mnbrak3 fu < fc\n");
   #endif
           dum=u; /* Shifting c and u */
           u = *cx;
           *cx = dum;
           dum = fu;
           fu = *fc;
           *fc =dum;
         }
   #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
   #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim AND fu < fc\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
           SHFT(*fb,*fc,fu,(*func)(u))           SHFT(*fb,*fc,fu,(*func)(u)) 
           }         } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   #ifdef DEBUG
         printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
         fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else {       } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
         printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
         fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   #endif
       u=(*cx)+GOLD*(*cx-*bx);         u=(*cx)+GOLD*(*cx-*bx); 
       fu=(*func)(u);         fu=(*func)(u); 
     }       } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
       SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
       }   #ifdef DEBUG
         printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
         fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
   #endif
     } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
   
 /*************** linmin ************************/  /*************** linmin ************************/
Line 1372  void linmin(double p[], double xi[], int Line 1534  void linmin(double p[], double xi[], int
   int j;     int j; 
   double xx,xmin,bx,ax;     double xx,xmin,bx,ax; 
   double fx,fb,fa;    double fx,fb,fa;
   
     double scale=10., axs, xxs, xxss; /* Scale added for infinity */
     
   ncom=n;     ncom=n; 
   pcom=vector(1,n);     pcom=vector(1,n); 
Line 1381  void linmin(double p[], double xi[], int Line 1545  void linmin(double p[], double xi[], int
     pcom[j]=p[j];       pcom[j]=p[j]; 
     xicom[j]=xi[j];       xicom[j]=xi[j]; 
   }     } 
   ax=0.0;   
   xx=1.0;     axs=0.0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */    xxss=1; /* 1 and using scale */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */    xxs=1;
     do{
       ax=0.;
       xx= xxs;
       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]]*/
       if (fx != fx){
           xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
           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);
       }
     }while(fx != fx);
   
     *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  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #endif  #endif
     /* printf("linmin end "); */
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     xi[j] *= xmin;       /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
     p[j] += xi[j];       xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
       /* 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 ); */
       p[j] += xi[j]; /* Parameters values are updated accordingly */
   }     } 
     /* printf("\n"); */
     /* printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", *fret, (*func)(p)); */
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
Line 1427  void powell(double p[], double **xi, int Line 1618  void powell(double p[], double **xi, int
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
     rcurr_time = time(NULL);        rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret);       fp=(*fret); /* From former iteration or initial value */
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     rlast_time=rcurr_time;      rlast_time=rcurr_time;
Line 1465  void powell(double p[], double **xi, int Line 1656  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);          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);         fptt=(*fret); 
 #ifdef DEBUG  #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  #endif
       printf("%d",i);fflush(stdout);            printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        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) { /* We are keeping the max gain on each of the n directions                                       /* Outputs are fret(new point p) p is updated and xit rescaled */
                                        because that direction will be replaced unless the gain del is small        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
                                       in comparison with the 'probable' gain, mu^2, with the last average direction.          /* because that direction will be replaced unless the gain del is small */
                                       Unless the n directions are conjugate some gain in the determinant may be obtained          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
                                       with the new direction.          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
                                       */          /* with the new direction. */
         del=fabs(fptt-(*fret));           del=fabs(fptt-(*fret)); 
         ibig=i;           ibig=i; 
       }         } 
Line 1499  void powell(double p[], double **xi, int Line 1690  void powell(double p[], double **xi, int
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     } /* end i */      } /* end loop on each direction i */
       /* 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? */      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  #ifdef DEBUG
       int k[2],l;        int k[2],l;
       k[0]=1;        k[0]=1;
Line 1546  void powell(double p[], double **xi, int Line 1752  void powell(double p[], double **xi, int
       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* 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); /* Intel compiler doesn't work on one line */        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);        t= t- del*SQR(fp-fptt);
   #endif
       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
 #ifdef DEBUG  #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);        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);
Line 1560  void powell(double p[], double **xi, int Line 1769  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);        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);        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  #endif
 #ifdef POWELLDIRECT  #ifdef POWELLORIGINAL
         if (t < 0.0) { /* Then we use it for new direction */
   #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);        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 */        if (directest < 0.0) { /* Then we use it for new direction */
 #else  
       if (t < 0.0) { /* Then we use it for new direction */  
 #endif  #endif
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
Line 1620  double **prevalim(double **prlim, int nl Line 1829  double **prevalim(double **prlim, int nl
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
           if(nagesqr==1)
         cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
     }      }
     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */      for (k=1; k<=cptcovprod;k++) /* Useless */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 1781  double ***hpxij(double ***po, int nhstep Line 1992  double ***hpxij(double ***po, int nhstep
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
     double agexact;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
Line 1794  double ***hpxij(double ***po, int nhstep Line 2006  double ***hpxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         cov[2]=agexact;
         if(nagesqr==1)
           cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=cptcovn;k++) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
Line 1852  double func( double *x) Line 2068  double func( double *x)
   int s1, s2;    int s1, s2;
   double bbh, survp;    double bbh, survp;
   long ipmx;    long ipmx;
     double agexact;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 1873  double func( double *x) Line 2090  double func( double *x)
          to be observed in j being in i according to the model.           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 */        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]         /* 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]            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
Line 1886  double func( double *x) Line 2103  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            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++) {            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,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 1940  double func( double *x) Line 2160  double func( double *x)
         which slows down the processing. The difference can be up to 10%          which slows down the processing. The difference can be up to 10%
         lower mortality.          lower mortality.
           */            */
           lli=log(out[s1][s2] - savm[s1][s2]);          /* If, at the beginning of the maximization mostly, the
              cumulative probability or probability to be dead is
              constant (ie = 1) over time d, the difference is equal to
              0.  out[s1][3] = savm[s1][3]: probability, being at state
              s1 at precedent wave, to be dead a month before current
              wave is equal to probability, being at state s1 at
              precedent wave, to be dead at mont of the current
              wave. Then the observed probability (that this person died)
              is null according to current estimated parameter. In fact,
              it should be very low but not zero otherwise the log go to
              infinity.
           */
   /* #ifdef INFINITYORIGINAL */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
   /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   /*          lli=log(mytinydouble); */
   /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #endif */
               lli=log(out[s1][s2] - savm[s1][s2]);
   
         } else if  (s2==-2) {          } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
Line 1972  double func( double *x) Line 2211  double func( double *x)
         ipmx +=1;          ipmx +=1;
         sw += weight[i];          sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /* if (lli < log(mytinydouble)){ */
           /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
           /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
           /* } */
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   }  else if(mle==2){    }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 1985  double func( double *x) Line 2228  double func( double *x)
           }            }
         for(d=0; d<=dh[mi][i]; d++){          for(d=0; d<=dh[mi][i]; d++){
           newm=savm;            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++) {            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,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2006  double func( double *x) Line 2252  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }  else if(mle==3){  /* exponential inter-extrapolation */    }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 2015  double func( double *x) Line 2261  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            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++) {            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,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 2036  double func( double *x) Line 2285  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }else if (mle==4){  /* ml=4 no inter-extrapolation */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 2045  double func( double *x) Line 2294  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            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++) {            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,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2071  double func( double *x) Line 2323  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 2080  double func( double *x) Line 2332  double func( double *x)
           }            }
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            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++) {            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,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 2118  double funcone( double *x) Line 2373  double funcone( double *x)
   double llt;    double llt;
   int s1, s2;    int s1, s2;
   double bbh, survp;    double bbh, survp;
     double agexact;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2129  double funcone( double *x) Line 2385  double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
     for(mi=1; mi<= wav[i]-1; mi++){      for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=nlstate+ndeath;j++){
Line 2138  double funcone( double *x) Line 2394  double funcone( double *x)
         }          }
       for(d=0; d<dh[mi][i]; d++){        for(d=0; d<dh[mi][i]; d++){
         newm=savm;          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++) {          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); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 3002  void tricode(int *Tvar, int **nbcode, in Line 3262  void tricode(int *Tvar, int **nbcode, in
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* 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 (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                modality of this covariate Vj*/                                  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        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 *:
Line 3025  void tricode(int *Tvar, int **nbcode, in Line 3285  void tricode(int *Tvar, int **nbcode, in
       /* getting the maximum value of the modality of the covariate        /* 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           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
          female is 1, then modmaxcovj=1.*/           female is 1, then modmaxcovj=1.*/
     }      } /* end for loop on individuals */
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     cptcode=modmaxcovj;      cptcode=modmaxcovj;
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    /*for (i=0; i<=cptcode; i++) {*/     /*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 (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value 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], i, Ndum[i]);
       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
       }        }
Line 3040  void tricode(int *Tvar, int **nbcode, in Line 3300  void tricode(int *Tvar, int **nbcode, in
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
   
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */      /* 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;         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]][ij]=k;
        nbcode[Tvar[j]][1]=0;         nbcode[Tvar[j]][1]=0;
        nbcode[Tvar[j]][2]=1;         nbcode[Tvar[j]][2]=1;
Line 3056  void tricode(int *Tvar, int **nbcode, in Line 3316  void tricode(int *Tvar, int **nbcode, in
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
         /*recode from 0 */          /*recode from 0 */
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          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.             nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
                                      k is a modality. If we have model=V1+V1*sex                                        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; */                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           ij++;            ij++;
Line 3068  void tricode(int *Tvar, int **nbcode, in Line 3328  void tricode(int *Tvar, int **nbcode, in
       
  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=1;
Line 3925  To be simple, these graphs help to under Line 4185  To be simple, these graphs help to under
       gm=vector(1,(nlstate)*(nlstate+ndeath));        gm=vector(1,(nlstate)*(nlstate+ndeath));
       for (age=bage; age<=fage; age ++){         for (age=bage; age<=fage; age ++){ 
         cov[2]=age;          cov[2]=age;
           if(nagesqr==1)
             cov[3]= age*age;
         for (k=1; k<=cptcovn;k++) {          for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                          * 1  1 1 1 1                                                           * 1  1 1 1 1
                                                          * 2  2 1 1 1                                                           * 2  2 1 1 1
                                                          * 3  1 2 1 1                                                           * 3  1 2 1 1
                                                          */                                                           */
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
         for (k=1; k<=cptcovprod;k++)          for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
Line 4395  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4658  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   } /* end covariate */      } /* end covariate */  
       
   /* proba elementaires */    /* proba elementaires */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
         for(j=1; j <=ncovmodel; j++){          for(j=1; j <=ncovmodel; j++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
           jk++;             jk++; 
           fprintf(ficgp,"\n");  
         }          }
           fprintf(ficgp,"\n");
       }        }
     }      }
    }     }
     fprintf(ficgp,"##############\n#\n");
   
   /*goto avoid;*/    /*goto avoid;*/
     fprintf(ficgp,"\n##############\n#Graphics of 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<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"#    jk=%d\n",jk);
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)         if (ng==2)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
Line 4421  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4706  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          for(k=1; k<=(nlstate+ndeath); k++) {           for(k=1; k<=(nlstate+ndeath); k++) {
            if (k != k2){             if (k != k2){
              if(ng==2)               if(ng==2)
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                 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);
              else               else
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                 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);
              ij=1;/* To be checked else nbcode[0][0] wrong */               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 *\/ */                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                /*        ij++; */                   ij++;
                /* } */                 }
                /* else */                 else
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
              }               }
              fprintf(ficgp,")/(1");               fprintf(ficgp,")/(1");
                             
              for(k1=1; k1 <=nlstate; k1++){                  for(k1=1; k1 <=nlstate; k1++){ 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                 if(nagesqr==0)
                    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;                 ij=1;
                for(j=3; j <=ncovmodel; j++){                 for(j=3; j <=ncovmodel-nagesqr; j++){
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                  /*   ij++; */                     ij++;
                  /* } */                   }
                  /* else */                   else
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
              }               }
Line 5238  void removespace(char *str) { Line 5533  void removespace(char *str) {
 }  }
   
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:  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     * - cptcovage number of covariates with age*products =2
    * - cptcovs number of simple covariates     * - 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     * - 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 5255  int decodemodel ( char model[], int last Line 5551  int decodemodel ( char model[], int last
   int  j1, k1, k2;    int  j1, k1, k2;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
   /*removespace(model);*/    /*removespace(model);*/
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      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){      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;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
Line 5278  int decodemodel ( char model[], int last Line 5566  int decodemodel ( char model[], int last
       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
       return 1;        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]][codtab[ij][Tvar[k]]]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
         Tvar[k]=0;          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++;            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.    /*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*/      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
Line 5544  BOOL IsWow64() Line 5868  BOOL IsWow64()
 void syscompilerinfo()  void syscompilerinfo()
  {   {
    /* #include "syscompilerinfo.h"*/     /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 5733  int prevalence_limit(double *p, double * Line 6090  int prevalence_limit(double *p, double *
         } /* Age */          } /* Age */
         /* was end of cptcod */          /* was end of cptcod */
     } /* cptcov */      } /* cptcov */
           return 0;
 }  }
   
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
Line 5766  int hPijx(double *p, int bage, int fage) Line 6124  int hPijx(double *p, int bage, int fage)
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);      i1= pow(2,cptcoveff);
    for(cptcov=1,k=0;cptcov<=i1;cptcov++){     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
       /*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/     /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
         k=k+1;      /*   k=k+1;  */
     /* for (k=1; k <= (int) pow(2,cptcoveff); k++){*/      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");        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 */
                   
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          /*        nhstepm=nhstepm*YEARM; aff par mois*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;            for(j=1; j<=nlstate+ndeath;j++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with 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(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);                fprintf(ficrespij," %.5f", p3mat[i][j][h]);
           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");            fprintf(ficrespij,"\n");
         }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       /*}*/        /*}*/
     }      }
           return 0;
 }  }
   
   
Line 5912  int main(int argc, char *argv[]) Line 6271  int main(int argc, char *argv[])
   
   nberr=0; /* Number of errors and warnings */    nberr=0; /* Number of errors and warnings */
   nbwarn=0;    nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
   getcwd(pathcd, size);    getcwd(pathcd, size);
   #endif
   
   printf("\n%s\n%s",version,fullversion);    printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
Line 5948  int main(int argc, char *argv[]) Line 6311  int main(int argc, char *argv[])
   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
   chdir(path); /* Can be a relative path */    chdir(path); /* Can be a relative path */
   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */    if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
     printf("Current directory %s!\n",pathcd);  #endif
     printf("Current directory %s!\n",pathcd);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
Line 5965  int main(int argc, char *argv[]) Line 6333  int main(int argc, char *argv[])
   
   /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Main Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
   strcat(filelog,".log");    /* */    strcat(filelog,".log");    /* */
   if((ficlog=fopen(filelog,"w"))==NULL)    {    if((ficlog=fopen(filelog,"w"))==NULL)    {
Line 5994  int main(int argc, char *argv[]) Line 6362  int main(int argc, char *argv[])
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /* Main ---------arguments file --------*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
Line 6027  int main(int argc, char *argv[]) Line 6395  int main(int argc, char *argv[])
   }    }
   ungetc(c,ficpar);    ungetc(c,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);    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++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      model[strlen(model)-1]='\0';
     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);    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){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
Line 6051  int main(int argc, char *argv[]) Line 6431  int main(int argc, char *argv[])
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
   */    */
   if (strlen(model)>1)     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    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 */    nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
   npar= nforce*ncovmodel; /* Number of parameters like aij*/    npar= nforce*ncovmodel; /* Number of parameters like aij*/
   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){    if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
Line 6077  int main(int argc, char *argv[]) Line 6456  int main(int argc, char *argv[])
     goto end;      goto end;
     exit(0);      exit(0);
   }    }
   else if(mle==-3) {    else if(mle==-3) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 6237  run imach with mle=-1 to get a correct t Line 6616  run imach with mle=-1 to get a correct t
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
   
     /*  Main data
      */
   n= lastobs;    n= lastobs;
   num=lvector(1,n);    num=lvector(1,n);
   moisnais=vector(1,n);    moisnais=vector(1,n);
Line 6288  run imach with mle=-1 to get a correct t Line 6668  run imach with mle=-1 to get a correct t
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
   
   /* Main decodemodel */
   
   
   if(decodemodel(model, lastobs) == 1)    if(decodemodel(model, lastobs) == 1)
     goto end;      goto end;
   
Line 6331  run imach with mle=-1 to get a correct t Line 6714  run imach with mle=-1 to get a correct t
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   if (ncovmodel > 2)    if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */      tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */    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]);*/    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    h=0;
   
   
Line 6352  run imach with mle=-1 to get a correct t Line 6739  run imach with mle=-1 to get a correct t
           if (h>m)             if (h>m) 
             h=1;              h=1;
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 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 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
            *______________________________               *______________________________  
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1
            *     2     2     1     1     1             *     2     2     1     1     1
Line 6372  run imach with mle=-1 to get a correct t Line 6761  run imach with mle=-1 to get a correct t
            *    16     2     2     2     1             *    16     2     2     2     1
            */             */
           codtab[h][k]=j;            codtab[h][k]=j;
             /* codtab[12][3]=1; */
           /*codtab[h][Tvar[k]]=j;*/            /*codtab[h][Tvar[k]]=j;*/
           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);            printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
         }           } 
Line 6392  run imach with mle=-1 to get a correct t Line 6782  run imach with mle=-1 to get a correct t
   
   
           
   /*------------ gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-mort");
Line 6408  run imach with mle=-1 to get a correct t Line 6798  run imach with mle=-1 to get a correct t
     fprintf(ficgp,"set datafile missing 'NaNq'\n");      fprintf(ficgp,"set datafile missing 'NaNq'\n");
   }    }
   /*  fclose(ficgp);*/    /*  fclose(ficgp);*/
   /*--------- index.htm --------*/  
   
     /* Initialisation of --------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
Line 6450  Title=%s <br>Datafile=%s Firstpass=%d La Line 6842  Title=%s <br>Datafile=%s Firstpass=%d La
   
   strcpy(pathr,path);    strcpy(pathr,path);
   strcat(pathr,optionfilefiname);    strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
   chdir(optionfilefiname); /* Move to directory named optionfile */    chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
Line 6473  Interval (in months) between two waves: Line 6870  Interval (in months) between two waves:
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
 /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
Line 6566  Interval (in months) between two waves: Line 6963  Interval (in months) between two waves:
       
     /* Initialize method and iterate */      /* Initialize method and iterate */
     /*     p[1]=0.0268; p[NDIM]=0.083; */      /*     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, 0, p[1]);
     gsl_vector_set(x, 1, p[2]);      gsl_vector_set(x, 1, p[2]);
   
Line 6684  Interval (in months) between two waves: Line 7081  Interval (in months) between two waves:
     free_ivector(dcwave,1,n);      free_ivector(dcwave,1,n);
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
 #endif  #endif
   } /* Endof if mle==-3 */    } /* Endof if mle==-3 mortality only */
       /* Standard maximisation */
   else{ /* For mle >=1 */    else{ /* For mle >=1 */
     globpr=0;/* debug */      globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     globpr=1; /* to print the contributions */      globpr=1; /* again, to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */      if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
           
     /*--------- results files --------------*/      /*--------- 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");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 6717  Interval (in months) between two waves: Line 7115  Interval (in months) between two waves:
           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");
Line 6860  Interval (in months) between two waves: Line 7258  Interval (in months) between two waves:
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
Line 6933  Interval (in months) between two waves: Line 7332  Interval (in months) between two waves:
     fclose(ficres);      fclose(ficres);
   
   
       /* Other results (useful)*/
   
   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
Line 6972  Interval (in months) between two waves: Line 7374  Interval (in months) between two waves:
       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */        /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
       /*      } */        /*      } */
     }      }
      
       /* ------ Other prevalence ratios------------ */
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
Line 7247  Interval (in months) between two waves: Line 7650  Interval (in months) between two waves:
   
   
    printf("Before Current directory %s!\n",pathcd);     printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
    if(chdir(pathcd) != 0)     if(chdir(pathcd) != 0)
     printf("Can't move to directory %s!\n",path);             printf("Can't move to directory %s!\n", path);
   if(getcwd(pathcd,MAXLINE) > 0)     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");

Removed from v.1.182  
changed lines
  Added in v.1.190


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