Diff for /imach/src/imach.c between versions 1.169 and 1.197

version 1.169, 2014/12/22 23:08:31 version 1.197, 2015/09/01 18:24:39
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
     Revision 1.194  2015/08/18 13:32:00  brouard
     Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
     Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
     Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   
     Revision 1.190  2015/05/05 08:51:13  brouard
     Summary: Adding digits in output parameters (7 digits instead of 6)
   
     Fix 1+age+.
   
     Revision 1.189  2015/04/30 14:45:16  brouard
     Summary: 0.98q2
   
     Revision 1.188  2015/04/30 08:27:53  brouard
     *** empty log message ***
   
     Revision 1.187  2015/04/29 09:11:15  brouard
     *** empty log message ***
   
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
     Revision 1.183  2015/03/10 20:34:32  brouard
     Summary: 0.98q0, trying with directest, mnbrak fixed
   
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
     Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
     Author: Nicolas Brouard
   
     Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
     Author:
   
     Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
     Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   
     Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
   Revision 1.169  2014/12/22 23:08:31  brouard    Revision 1.169  2014/12/22 23:08:31  brouard
   Summary: 0.98p    Summary: 0.98p
   
   Outputs some informations on compiler used, OS etc. Testing on different platforms.    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
   Revision 1.168  2014/12/22 15:17:42  brouard    Revision 1.168  2014/12/22 15:17:42  brouard
   Summary: udate    Summary: update
   
   Revision 1.167  2014/12/22 13:50:56  brouard    Revision 1.167  2014/12/22 13:50:56  brouard
   Summary: Testing uname and compiler version and if compiled 32 or 64    Summary: Testing uname and compiler version and if compiled 32 or 64
Line 518 Line 625
  end   end
 */  */
   
   /* #define DEBUG */
   /* #define DEBUGBRENT */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
   #define POWELLF1F3 /* Skip test */
   /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
   /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 527 Line 639
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
   #include <windows.h>
   #include <tchar.h>
 #else  #else
 #include <unistd.h>  #include <unistd.h>
 #endif  #endif
   
 #include <limits.h>  #include <limits.h>
 #include <sys/types.h>  #include <sys/types.h>
 #include <sys/utsname.h>  
   #if defined(__GNUC__)
   #include <sys/utsname.h> /* Doesn't work on Windows */
   #endif
   
 #include <sys/stat.h>  #include <sys/stat.h>
 #include <errno.h>  #include <errno.h>
 /* extern int errno; */  /* extern int errno; */
Line 579  typedef struct { Line 697  typedef struct {
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  1 & (h-1) >> (k-1) ;  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
   #define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32  #ifdef _WIN32
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
Line 597  typedef struct { Line 716  typedef struct {
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   #include "version.h"
 char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char version[]=__IMACH_VERSION__;
   char copyright[]="September 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 714  static double maxarg1,maxarg2; Line 834  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 733  int estepm; Line 853  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;  int firstpass=0, lastpass=4,*cod, *cens;
   int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                      covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
Line 744  int **s; /* Status */ Line 870  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 *Tage;
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 int **codtab; /**< codtab=imatrix(1,100,1,10); */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
Line 762  static int split( char *path, char *dirc Line 889  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 773  static int split( char *path, char *dirc Line 900  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 784  static int split( char *path, char *dirc Line 915  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 836  char *trimbb(char *out, char *in) Line 967  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 866  char *cutl(char *blocc, char *alocc, cha Line 1040  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 1177  double f1dim(double x) Line 1351  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 1230  double brent(double ax, double bx, doubl Line 1410  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 1253  double brent(double ax, double bx, doubl Line 1433  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 1280  void mnbrak(double *ax, double *bx, doub Line 1479  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; */
   /*       } */
   #ifdef DEBUG
         printf("mnbrak34  fu < or >= fc \n");
         fprintf(ficlog, "mnbrak34 fu < fc\n");
   #endif
         dum=u; /* Shifting c and u */
         u = *cx;
         *cx = dum;
         dum = fu;
         fu = *fc;
         *fc =dum;
   #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } 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 1319  void linmin(double p[], double xi[], int Line 1580  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 1328  void linmin(double p[], double xi[], int Line 1591  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); */
   
   #ifdef DEBUGLINMIN
     printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   #endif
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
     /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
     /* fmin = f(p[j] + xmin * xi[j]) */
     /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
     /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
 #ifdef DEBUG  #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
   #ifdef DEBUGLINMIN
     printf("linmin end ");
   #endif
   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"); */
   #ifdef DEBUGLINMIN
     printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     for (j=1;j<=n;j++) { 
       printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0)
         printf("\n");
     }
   #endif
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
Line 1361  void powell(double p[], double **xi, int Line 1663  void powell(double p[], double **xi, int
               double (*func)(double []));                 double (*func)(double [])); 
   int i,ibig,j;     int i,ibig,j; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
     double directest;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
Line 1373  void powell(double p[], double **xi, int Line 1676  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 1383  void powell(double p[], double **xi, int Line 1686  void powell(double p[], double **xi, int
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 1411  void powell(double p[], double **xi, int Line 1714  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) {                                       /* Outputs are fret(new point p) p is updated and xit rescaled */
         if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
           /* because that direction will be replaced unless the gain del is small */
           /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
           /* Unless the n directions are conjugate some gain in the determinant may be obtained */
           /* with the new direction. */
         del=fabs(fptt-(*fret));           del=fabs(fptt-(*fret)); 
         ibig=i;           ibig=i; 
       }         } 
Line 1440  void powell(double p[], double **xi, int Line 1748  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 */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
       /* New value of last point Pn is not computed, P(n-1) */
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
         /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
         /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
         /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
         /* decreased of more than 3.84  */
         /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
         /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
         /* By adding 10 parameters more the gain should be 18.31 */
   
         /* Starting the program with initial values given by a former maximization will simply change */
         /* the scales of the directions and the directions, because the are reset to canonical directions */
         /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
         /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
       k[0]=1;        k[0]=1;
Line 1471  void powell(double p[], double **xi, int Line 1794  void powell(double p[], double **xi, int
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     }       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes an extrapolated point */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt);       fptt=(*func)(ptt); /* f_3 */
   #ifdef POWELLF1F3
   #else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   #endif
       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       /* From x1 (P0) distance of x2 is at h and x3 is 2h */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       /* Let f"(x2) be the 2nd derivative equal everywhere.  */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       /* Thus we compare delta(2h) with observed f1-f3 */  
       /* or best gain on one ancient line 'del' with total  */  
       /* gain f1-f2 = f1 - f2 - 'del' with del  */  
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   #ifdef NRCORIGINAL
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       t= t- del*SQR(fp-fptt);        t= t- del*SQR(fp-fptt);
       printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);  #endif
       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If 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);
         fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
       printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
              (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
Line 1503  void powell(double p[], double **xi, int Line 1830  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
       if (t < 0.0) { /* Then we use it for last direction */  #ifdef POWELLORIGINAL
         linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/        if (t < 0.0) { /* Then we use it for new direction */
   #else
         if (directest*t < 0.0) { /* Contradiction between both tests */
           printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
           printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
           fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
           fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         } 
         if (directest < 0.0) { /* Then we use it for new direction */
   #endif
   #ifdef DEBUGLINMIN
           printf("Before linmin in direction P%d-P0\n",n);
           for (j=1;j<=n;j++) { 
             printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
               printf("\n");
           }
   #endif
           linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
   #ifdef DEBUGLINMIN
           for (j=1;j<=n;j++) { 
             printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0)
               printf("\n");
           }
   #endif
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
         }          }
         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 1522  void powell(double p[], double **xi, int Line 1874  void powell(double p[], double **xi, int
         printf("\n");          printf("\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t negative */        } /* end of t or directest negative */
   #ifdef POWELLF1F3
   #else
     } /* end if (fptt < fp)  */      } /* end if (fptt < fp)  */
   }   #endif
     } /* loop iteration */ 
 }   } 
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
Line 1553  double **prevalim(double **prlim, int nl Line 1908  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 1714  double ***hpxij(double ***po, int nhstep Line 2071  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 1727  double ***hpxij(double ***po, int nhstep Line 2085  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 1785  double func( double *x) Line 2147  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 1806  double func( double *x) Line 2169  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 1819  double func( double *x) Line 2182  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 1873  double func( double *x) Line 2239  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 1905  double func( double *x) Line 2290  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 1918  double func( double *x) Line 2307  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 1939  double func( double *x) Line 2331  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 1948  double func( double *x) Line 2340  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 1969  double func( double *x) Line 2364  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 1978  double func( double *x) Line 2373  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 2004  double func( double *x) Line 2402  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 2013  double func( double *x) Line 2411  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 2051  double funcone( double *x) Line 2452  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 2062  double funcone( double *x) Line 2464  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 2071  double funcone( double *x) Line 2473  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 2240  void mlikeli(FILE *ficres,double p[], in Line 2646  void mlikeli(FILE *ficres,double p[], in
 #endif  #endif
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
Line 2508  void lubksb(double **a, int n, int *indx Line 2914  void lubksb(double **a, int n, int *indx
   
 void pstamp(FILE *fichier)  void pstamp(FILE *fichier)
 {  {
   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
Line 2931  void tricode(int *Tvar, int **nbcode, in Line 3337  void tricode(int *Tvar, int **nbcode, in
   
   cptcoveff=0;     cptcoveff=0; 
     
   for (k=-1; k < maxncov; k++) Ndum[k]=0;  
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    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 (k=-1; k < maxncov; k++) Ndum[k]=0;
       for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                modality of this covariate Vj*/                                  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 2958  void tricode(int *Tvar, int **nbcode, in Line 3364  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 i */
     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);
       fprintf(ficlog," 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 (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
       printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
           if( k != -1){
             ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered excluding 
                                undefined. Usually 2: 0 and 1. */
           }
           ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
       }        }
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     } /* Ndum[-1] number of undefined modalities */      } /* 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;
        nbcode[Tvar[j]][3]=2;         nbcode[Tvar[j]][3]=2;
          To be continued (not working yet).
     */      */
     ij=1; /* ij is similar to i but can jumps over null modalities */      ij=0; /* ij is similar to i but can jump over null modalities */
     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */          if (Ndum[i] == 0) { /* If nobody responded to this modality k */
         /*recode from 0 */            break;
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          }
           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.           ij++;
                                      k is a modality. If we have model=V1+V1*sex           nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */          cptcode = ij; /* New max modality for covar j */
           ij++;      } /* end of loop on modality i=-1 to 1 or more */
         }        
         if (ij > ncodemax[j]) break;       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
       }  /* end of loop on */      /*  /\*recode from 0 *\/ */
     } /* end of loop on modality */       /*                               k is a modality. If we have model=V1+V1*sex  */
       /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
       /*  } */
       /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
       /*  if (ij > ncodemax[j]) { */
       /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
       /*    break; */
       /*  } */
       /*   }  /\* end of loop on modality k *\/ */
   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       
  for (k=-1; k< maxncov; k++) Ndum[k]=0;    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       
   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
    Ndum[ij]++;      Ndum[ij]++; /* Might be supersed V1 + V1*age */
  }    } 
   
  ij=1;   ij=0;
  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){     if((Ndum[i]!=0) && (i<=ncovcol)){
        ij++;
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */       Tvaraff[ij]=i; /*For printing (unclear) */
      ij++;     }else{
    }else         /* Tvaraff[ij]=0; */
        Tvaraff[ij]=0;     }
  }   }
  ij--;   /* ij--; */
  cptcoveff=ij; /*Number of total covariates*/   cptcoveff=ij; /*Number of total covariates*/
   
 }  }
Line 3628  void varevsij(char optionfilefiname[], d Line 4055  void varevsij(char optionfilefiname[], d
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
Line 3808  void varprob(char optionfilefiname[], do Line 4235  void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
   file %s<br>\n",optionfilehtmcov);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\  
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
Line 3858  To be simple, these graphs help to under Line 4284  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 4100  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4529  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
  jj1=0;   jj1=0;
  for(k1=1; k1<=m;k1++){   for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
Line 4124  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4555  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
   
   
  fprintf(fichtm,"\   fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
    - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
   But because parameters are usually highly correlated (a higher incidence of disability \
   and a higher incidence of recovery can give very close observed transition) it might \
   be very useful to look not only at linear confidence intervals estimated from the \
   variances but at the covariance matrix. And instead of looking at the estimated coefficients \
   (parameters) of the logistic regression, it might be more meaningful to visualize the \
   covariance matrix of the one-step probabilities. \
   See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 4174  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4612  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
  jj1=0;   jj1=0;
  for(k1=1; k1<=m;k1++){   for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
Line 4193  true period expectancies (those weighted Line 4631  true period expectancies (those weighted
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences: %s%d.png<br>\   observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
  fflush(fichtm);   fflush(fichtm);
Line 4226  void printinggnuplot(char fileres[], cha Line 4664  void printinggnuplot(char fileres[], cha
      fprintf(ficgp,"set xlabel \"Age\" \n\       fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n\  set ylabel \"Probability\" \n\
 set ter png small size 320, 240\n\  set ter png small size 320, 240\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else        fprintf(ficgp," \%%*lf (\%%*lf)");         else        fprintf(ficgp," %%*lf (%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }     }
Line 4253  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4691  plot [%.f:%.f] \"%s\" every :::%d::%d u
           
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       fprintf(ficgp,"\" t\"\" w l lt 0,");        fprintf(ficgp,"\" t\"\" w l lt 0,");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
       else fprintf(ficgp,"\" t\"\" w l lt 0,");        else fprintf(ficgp,"\" t\"\" w l lt 0,");
Line 4328  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4766  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 4354  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4814  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 *\/ */                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */                 if(ij <=cptcovage) { /* Bug valgrind */
                /*        ij++; */                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                /* } */                     fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                /* else */                     ij++;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   }
                  }
                  else
                    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(ij <=cptcovage) { /* Bug valgrind */
                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                  /*   ij++; */                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                  /* } */                       ij++;
                  /* else */                     }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
              }               }
Line 4993  int readdata(char datafile[], int firsto Line 5468  int readdata(char datafile[], int firsto
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s\n", datafile);return 1;      printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;      fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
   }    }
   
   i=1;    i=1;
Line 5171  void removespace(char *str) { Line 5646  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 5188  int decodemodel ( char model[], int last Line 5664  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 5211  int decodemodel ( char model[], int last Line 5679  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 5437  int calandcheckages(int imx, int maxwav, Line 5941  int calandcheckages(int imx, int maxwav,
     return (1);      return (1);
 }  }
   
 void syscompilerinfo()  #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
  {   {
    /* #include "syscompilerinfo.h"*/     /* #include "syscompilerinfo.h"*/
    /* #include <gnu/libc-version.h> */ /* Only on gnu */     /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         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(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
    printf("Compiled with:");fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
 #endif  #endif
 #if defined(__ICC) || defined(__INTEL_COMPILER)  #if defined(__ICC) || defined(__INTEL_COMPILER)
    printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */     printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
 #endif  #endif
 #if defined(__GNUC__) || defined(__GNUG__)  #if defined(__GNUC__) || defined(__GNUG__)
    printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */     printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
 #endif  #endif
 #if defined(__HP_cc) || defined(__HP_aCC)  #if defined(__HP_cc) || defined(__HP_aCC)
    printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */     printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
 #endif  #endif
 #if defined(__IBMC__) || defined(__IBMCPP__)  #if defined(__IBMC__) || defined(__IBMCPP__)
    printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */     printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
 #endif  #endif
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */     printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
 #endif  #endif
 #if defined(__PGI)  #if defined(__PGI)
    printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */     printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
 #endif  #endif
 #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)  #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
    printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */     printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
 #endif  #endif
    printf(". ");fprintf(ficlog,". ");     printf(" for "); if (logged) fprintf(ficlog, " for ");
         
 // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros  // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
 #ifdef _WIN32 // note the underscore: without it, it's not msdn official!  #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
     // Windows (x64 and x86)      // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
 #elif __unix__ // all unices, not all compilers  #elif __unix__ // all unices, not all compilers
     // Unix      // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
 #elif __linux__  #elif __linux__
     // linux      // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
 #elif __APPLE__  #elif __APPLE__
     // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...      // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
 #endif  #endif
   
 /*  __MINGW32__   */  /*  __MINGW32__   */
Line 5489  void syscompilerinfo() Line 6084  void syscompilerinfo()
 /* _WIN64  // Defined for applications for Win64. */  /* _WIN64  // Defined for applications for Win64. */
 /* _M_X64 // Defined for compilations that target x64 processors. */  /* _M_X64 // Defined for compilations that target x64 processors. */
 /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */  /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
 #include <stdint.h>  
 #if UINTPTR_MAX == 0xffffffff  #if UINTPTR_MAX == 0xffffffff
    printf(" 32-bit."); /* 32-bit */     printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
 #elif UINTPTR_MAX == 0xffffffffffffffff  #elif UINTPTR_MAX == 0xffffffffffffffff
   printf(" 64-bit.");/* 64-bit */     printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
 #else  #else
  printf(" wtf-bit."); /* wtf */     printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
 #endif  #endif
   
 struct utsname sysInfo;  
   
    if (uname(&sysInfo) != -1) {  
      printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);  
      fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);  
    }  
    else  
       perror("uname() error");  
 #if defined(__GNUC__)  #if defined(__GNUC__)
 # if defined(__GNUC_PATCHLEVEL__)  # if defined(__GNUC_PATCHLEVEL__)
 #  define __GNUC_VERSION__ (__GNUC__ * 10000 \  #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
Line 5515  struct utsname sysInfo; Line 6102  struct utsname sysInfo;
 #  define __GNUC_VERSION__ (__GNUC__ * 10000 \  #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                             + __GNUC_MINOR__ * 100)                              + __GNUC_MINOR__ * 100)
 # endif  # endif
    printf("GNU C version %d.\n", __GNUC_VERSION__);     printf(" using GNU C version %d.\n", __GNUC_VERSION__);
    fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);     if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
            if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
 #endif  #endif
   #endif
   
      //   void main()
      //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);     if (IsWow64()){
    fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);             printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
 #endif  #endif
         
   /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */  
   
  }   }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
 /***********************************************/  /***********************************************/
Line 5545  int main(int argc, char *argv[]) Line 6295  int main(int argc, char *argv[])
   
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
Line 5553  int main(int argc, char *argv[]) Line 6304  int main(int argc, char *argv[])
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb;    double agedeb=0.;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
   
   double fret;    double fret;
   double dum; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int c,  h , cpt;    int c,  h , cpt, c2;
   int jl;    int jl=0;
   int i1, j1, jk, stepsize;    int i1, j1, jk, stepsize=0;
     int count=0;
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
   float  sumlpop=0.;    float  sumlpop=0.;
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   double bage=0, fage=110, age, agelim, agebase;    double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
Line 5634  int main(int argc, char *argv[]) Line 6390  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);    syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     fgets(pathr,FILENAMELENGTH,stdin);      fgets(pathr,FILENAMELENGTH,stdin);
Line 5670  int main(int argc, char *argv[]) Line 6430  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 5687  int main(int argc, char *argv[]) Line 6452  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 5695  int main(int argc, char *argv[]) Line 6460  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);    fprintf(ficlog,"Version %s %s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: \n");    fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\   path=%s \n\
Line 5703  int main(int argc, char *argv[]) Line 6468  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   syscompilerinfo();    syscompilerinfo(1);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
Line 5716  int main(int argc, char *argv[]) Line 6481  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 5739  int main(int argc, char *argv[]) Line 6504  int main(int argc, char *argv[])
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* First parameter line */
     fgets(line, MAXLINE, ficpar);    while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
     numlinepar++;      numlinepar++;
     fputs(line,stdout);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     fputs(line,ficparo);    }
     fputs(line,ficlog);    /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 8) {
         printf("Not 8\n");
       }
       printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
   }    }
   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);    /* Third parameter line */
   numlinepar++;    while(fgets(line, MAXLINE, ficpar)) {
   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);      /* If line starts with a # it is a comment */
   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 (line[0] == '#') {
   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);        numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
       if (num_filled != 1) {
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
         }
         strcpy(model,modeltemp); 
       }
       printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
     }
     /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the 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);
     numlinepar++;      numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);      fputs(line, stdout);
     //puts(line);      //puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
Line 5773  int main(int argc, char *argv[]) Line 6613  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 5791  int main(int argc, char *argv[]) Line 6630  int main(int argc, char *argv[])
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);      fclose (ficparo);
     fclose (ficlog);      fclose (ficlog);
     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 chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   }    }
Line 5826  int main(int argc, char *argv[]) Line 6665  int main(int argc, char *argv[])
         if(jj==i) continue;          if(jj==i) continue;
         j++;          j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){          if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 It might be a problem of design; if ncovcol and the model are correct\n \  It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
Line 5834  run imach with mle=-1 to get a correct t Line 6673  run imach with mle=-1 to get a correct t
         }          }
         fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)          if(mle==1)
           printf("%1d%1d",i,j);            printf("%1d%1d",i,jj);
         fprintf(ficlog,"%1d%1d",i,j);          fprintf(ficlog,"%1d%1d",i,jj);
         for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);            fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){            if(mle==1){
Line 5916  run imach with mle=-1 to get a correct t Line 6755  run imach with mle=-1 to get a correct t
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;        for(j=1; j <=npar; j++) matcov[i][j]=0.;
               
       /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",str);        count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
         if(count != 3){
           printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           exit(1);
         }else
       if(mle==1)        if(mle==1)
         printf("%s",str);          printf("%1d%1d%1d",i1,j1,jk);
       fprintf(ficlog,"%s",str);        fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
       fprintf(ficparo,"%s",str);        fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){          if(mle==1){
Line 5937  run imach with mle=-1 to get a correct t Line 6786  run imach with mle=-1 to get a correct t
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
Line 5959  run imach with mle=-1 to get a correct t Line 6809  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 5975  run imach with mle=-1 to get a correct t Line 6826  run imach with mle=-1 to get a correct t
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
   /* Reads data from file datafile */    /* Reads data from file datafile */
   if (readdata(datafile, firstobs, lastobs, &imx)==1)    if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 6010  run imach with mle=-1 to get a correct t Line 6862  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 6053  run imach with mle=-1 to get a correct t Line 6908  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 6066  run imach with mle=-1 to get a correct t Line 6925  run imach with mle=-1 to get a correct t
     
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */  
     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */   
       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/  
         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */   
           h++;  
           if (h>m)   
             h=1;  
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1            /**< 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 6084  run imach with mle=-1 to get a correct t Line 6938  run imach with mle=-1 to get a correct t
            *     6     2     1     2     1             *     6     2     1     2     1
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1
            *     8     2     2     2     1             *     8     2     2     2     1
            *     9 i=5 1 i=3 1 i=2 1     1             *     9 i=5 1 i=3 1 i=2 1     2
            *    10     2     1     1     1             *    10     2     1     1     2
            *    11 i=6 1     2     1     1             *    11 i=6 1     2     1     2
            *    12     2     2     1     1             *    12     2     2     1     2
            *    13 i=7 1 i=4 1     2     1                 *    13 i=7 1 i=4 1     2     2    
            *    14     2     1     2     1             *    14     2     1     2     2
            *    15 i=8 1     2     2     1             *    15 i=8 1     2     2     2
            *    16     2     2     2     1             *    16     2     2     2     2
            */             */
           codtab[h][k]=j;    for(h=1; h <=100 ;h++){ 
           /*codtab[h][Tvar[k]]=j;*/      /* printf("h=%2d ", h); */
           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]]);       for(k=1; k <=10; k++){
         }          /* printf("k=%d %d ",k,codtabm(h,k)); */
       }         codtab[h][k]=codtabm(h,k);
     }       }
   }        /* printf("\n"); */
     }
     /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
     /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
     /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
     /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
     /*      h++; */
     /*      if (h>m)  */
     /*        h=1; */
     /*      codtab[h][k]=j; */
     /*      /\* codtab[12][3]=1; *\/ */
     /*      /\*codtab[h][Tvar[k]]=j;*\/ */
     /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
     /*    }  */
     /*     } */
     /*   } */
     /* }  */
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
      codtab[1][2]=1;codtab[2][2]=2; */       codtab[1][2]=1;codtab[2][2]=2; */
   /* for(i=1; i <=m ;i++){     /* for(i=1; i <=m ;i++){  */
      for(k=1; k <=cptcovn; k++){    /*    for(k=1; k <=cptcovn; k++){ */
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
      }    /*    } */
      printf("\n");    /*    printf("\n"); */
      }    /* } */
      scanf("%d",i);*/    /*   scanf("%d",i);*/
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
   
           
   /*------------ gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-mort");
Line 6130  run imach with mle=-1 to get a correct t Line 7000  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 6172  Title=%s <br>Datafile=%s Firstpass=%d La Line 7044  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 6195  Interval (in months) between two waves: Line 7072  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 6288  Interval (in months) between two waves: Line 7165  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 6357  Interval (in months) between two waves: Line 7234  Interval (in months) between two waves:
     }      }
           
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
     for (i=1;i<=NDIM;i++)       for (i=1;i<=NDIM;i++) {
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
         fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       }
     lsurv=vector(1,AGESUP);      lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(1,AGESUP);
Line 6391  Interval (in months) between two waves: Line 7269  Interval (in months) between two waves:
           
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
               printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else
         printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \      printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
Line 6406  Interval (in months) between two waves: Line 7291  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 6439  Interval (in months) between two waves: Line 7325  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 6455  Interval (in months) between two waves: Line 7341  Interval (in months) between two waves:
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);        hesscov(matcov, p, npar, delti, ftolhess, func);
     }      }
       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
   
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 6582  Interval (in months) between two waves: Line 7486  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 6610  Interval (in months) between two waves: Line 7515  Interval (in months) between two waves:
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);         fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);         fprintf(ficres,"pop_based=%d\n",popbased);   
           
Line 6634  Interval (in months) between two waves: Line 7540  Interval (in months) between two waves:
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else
         printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
           
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\                   model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
Line 6655  Interval (in months) between two waves: Line 7569  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);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  #ifdef FREEEXIT2
Line 6664  Interval (in months) between two waves: Line 7583  Interval (in months) between two waves:
 #endif  #endif
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
 #include "hpijx.h"      /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
   
   /*-------------- Variance of one-step probabilities---*/    /*-------------- Variance of one-step probabilities---*/
Line 6691  Interval (in months) between two waves: Line 7611  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 6922  Interval (in months) between two waves: Line 7843  Interval (in months) between two waves:
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
     free_ivector(ncodemax,1,NCOVMAX);      free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);      free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);      free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);      free_ivector(Tvaraff,1,NCOVMAX);
Line 6966  Interval (in months) between two waves: Line 7888  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");
Line 7023  Interval (in months) between two waves: Line 7951  Interval (in months) between two waves:
   }    }
   end:    end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: ");      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }

Removed from v.1.169  
changed lines
  Added in v.1.197


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