Diff for /imach/src/imach.c between versions 1.147 and 1.201

version 1.147, 2014/06/16 10:33:11 version 1.201, 2015/09/15 17:34:58
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.201  2015/09/15 17:34:58  brouard
     Summary: 0.98r0
   
     - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
   
     Revision 1.200  2015/09/09 16:53:55  brouard
     Summary: Big bug thanks to Flavia
   
     Even model=1+age+V2. did not work anymore
   
     Revision 1.199  2015/09/07 14:09:23  brouard
     Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   
     Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
   
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
     Revision 1.194  2015/08/18 13:32:00  brouard
     Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
     Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
     Revision 1.191  2015/07/14 10:00:33  brouard
     Summary: Some fixes
   
     Revision 1.190  2015/05/05 08:51:13  brouard
     Summary: Adding digits in output parameters (7 digits instead of 6)
   
     Fix 1+age+.
   
     Revision 1.189  2015/04/30 14:45:16  brouard
     Summary: 0.98q2
   
     Revision 1.188  2015/04/30 08:27:53  brouard
     *** empty log message ***
   
     Revision 1.187  2015/04/29 09:11:15  brouard
     *** empty log message ***
   
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
     Revision 1.183  2015/03/10 20:34:32  brouard
     Summary: 0.98q0, trying with directest, mnbrak fixed
   
     We use directest instead of original Powell test; probably no
     incidence on the results, but better justifications;
     We fixed Numerical Recipes mnbrak routine which was wrong and gave
     wrong results.
   
     Revision 1.182  2015/02/12 08:19:57  brouard
     Summary: Trying to keep directest which seems simpler and more general
     Author: Nicolas Brouard
   
     Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
     Author:
   
     Revision 1.180  2015/02/11 17:33:45  brouard
     Summary: Finishing move from main to function (hpijx and prevalence_limit)
   
     Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   
     Revision 1.178  2015/01/04 09:35:48  brouard
     *** empty log message ***
   
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
     Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
   
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
     Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
   
     Testing on Linux 64
   
     Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
   
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
   
     Revision 1.1  2014/09/16 11:06:58  brouard
     Summary: With some code (wrong) for nlopt
   
     Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
   
     Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
   
     Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
     Author: Brouard
   
     Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   
     Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
     Author: Brouard
   
     In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
   
     Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
   
     Revision 1.155  2014/08/25 18:32:34  brouard
     Summary: New compile, minor changes
     Author: Brouard
   
     Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
   
     Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
   
     Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
     Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
   
     Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
   
     Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
   
     Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
     Author: Brouard
   
     Just a new packaging for OS/X version 0.98nS
   
   Revision 1.147  2014/06/16 10:33:11  brouard    Revision 1.147  2014/06/16 10:33:11  brouard
   *** empty log message ***    *** empty log message ***
   
Line 424 Line 642
  end   end
 */  */
   
   /* #define DEBUG */
   /* #define DEBUGBRENT */
   #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>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   
   #ifdef _WIN32
   #include <io.h>
   #include <windows.h>
   #include <tchar.h>
   #else
 #include <unistd.h>  #include <unistd.h>
   #endif
   
 #include <limits.h>  #include <limits.h>
 #include <sys/types.h>  #include <sys/types.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; */
   
   /* #ifdef LINUX */
   /* #include <time.h> */
   /* #include "timeval.h" */
   /* #else */
   /* #include <sys/time.h> */
   /* #endif */
   
 #ifdef LINUX  
 #include <time.h>  #include <time.h>
 #include "timeval.h"  
 #else  
 #include <sys/time.h>  
 #endif  
   
 #ifdef GSL  #ifdef GSL
 #include <gsl/gsl_errno.h>  #include <gsl/gsl_errno.h>
 #include <gsl/gsl_multimin.h>  #include <gsl/gsl_multimin.h>
 #endif  #endif
   
   
   #ifdef NLOPT
   #include <nlopt.h>
   typedef struct {
     double (* function)(double [] );
   } myfunc_data ;
   #endif
   
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
Line 470  extern int errno; Line 714  extern int errno;
 #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 AGEGOMP 10. /**< Minimal age for Gompertz adjustment */  #define AGEOVERFLOW 1.e20
 #ifdef UNIX  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #define DIRSEPARATOR '/'  #ifdef _WIN32
 #define CHARSEPARATOR "/"  
 #define ODIRSEPARATOR '\\'  
 #else  
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #define CHARSEPARATOR "\\"  #define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'  #define ODIRSEPARATOR '/'
   #else
   #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   #include "version.h"
 char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";  char version[]=__IMACH_VERSION__;
   char copyright[]="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 520  int **mw; /* mw[mi][i] is number of the Line 766  int **mw; /* mw[mi][i] is number of the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int countcallfunc=0;  /* Count the number of calls to func */
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
Line 555  char command[FILENAMELENGTH]; Line 802  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char fileresu[FILENAMELENGTH]; /* Without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
Line 563  char popfile[FILENAMELENGTH]; Line 810  char popfile[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 struct timeval start_time, end_time, curr_time, last_time, forecast_time;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
 struct timezone tzp;  /* struct timezone tzp; */
 extern int gettimeofday();  /* extern int gettimeofday(); */
 struct tm tmg, tm, tmf, *gmtime(), *localtime();  struct tm tml, *gmtime(), *localtime();
 long time_value;  
 extern long time();  extern time_t time();
   
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
   
 char strcurr[80], strfor[80];  char strcurr[80], strfor[80];
   
 char *endptr;  char *endptr;
Line 598  static double maxarg1,maxarg2; Line 850  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 */
   #define mytinydouble 1.0e-16
   /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
 static double sqrarg;  static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
Line 613  int estepm; Line 870  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 624  int **s; /* Status */ Line 887  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;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
Line 642  static int split( char *path, char *dirc Line 906  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 653  static int split( char *path, char *dirc Line 917  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 664  static int split( char *path, char *dirc Line 932  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 716  char *trimbb(char *out, char *in) Line 984  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, *bl;    char *s, *t;
   t=in;s=in;    t=in;s=in;
   while ((*in != occ) && (*in != '\0')){    while ((*in != occ) && (*in != '\0')){
     *alocc++ = *in++;      *alocc++ = *in++;
Line 746  char *cutl(char *blocc, char *alocc, cha Line 1057  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 807  int nbocc(char *s, char occ) Line 1118  int nbocc(char *s, char occ)
 /*   } */  /*   } */
 /* } */  /* } */
   
   #ifdef _WIN32
   char * strsep(char **pp, const char *delim)
   {
     char *p, *q;
            
     if ((p = *pp) == NULL)
       return 0;
     if ((q = strpbrk (p, delim)) != NULL)
     {
       *pp = q + 1;
       *q = '\0';
     }
     else
       *pp = 0;
     return p;
   }
   #endif
   
 /********************** nrerror ********************/  /********************** nrerror ********************/
   
 void nrerror(char error_text[])  void nrerror(char error_text[])
Line 1006  char *subdirf3(char fileres[], char *pre Line 1335  char *subdirf3(char fileres[], char *pre
   return tmpout;    return tmpout;
 }  }
   
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
   
 /***************** f1dim *************************/  /***************** f1dim *************************/
 extern int ncom;   extern int ncom; 
 extern double *pcom,*xicom;  extern double *pcom,*xicom;
Line 1026  double f1dim(double x) Line 1368  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,fv,fw,fx;    double fu=0,fv,fw,fx;
   double ftemp;    double ftemp=0.;
   double p,q,r,tol1,tol2,u,v,w,x,xm;     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double e=0.0;     double e=0.0; 
     
Line 1044  double brent(double ax, double bx, doubl Line 1392  double brent(double ax, double bx, doubl
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     printf(".");fflush(stdout);      printf(".");fflush(stdout);
     fprintf(ficlog,".");fflush(ficlog);      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUGBRENT
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
Line 1079  double brent(double ax, double bx, doubl Line 1427  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 1102  double brent(double ax, double bx, doubl Line 1450  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) {   #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));         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx);       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
     if ((*bx-u)*(u-*cx) > 0.0) {       if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
       fu=(*func)(u);         fu=(*func)(u); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {   #ifdef DEBUG
         /* f(x)=A(x-u)**2+f(u) */
         double A, fparabu; 
         A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
         printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         /* And thus,it can be that fu > *fc even if fparabu < *fc */
         /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
           (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
         /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
   #endif 
   #ifdef MNBRAKORIGINAL
   #else
   /*       if (fu > *fc) { */
   /* #ifdef DEBUG */
   /*       printf("mnbrak4  fu > fc \n"); */
   /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
   /* #endif */
   /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
   /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
   /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
   /*      dum = fu; */
   /*      fu = *fc; */
   /*      *fc =dum; */
   /*       } else { /\* end *\/ */
   /* #ifdef DEBUG */
   /*       printf("mnbrak3  fu < fc \n"); */
   /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
   /* #endif */
   /*      dum=u; /\* Shifting c and u *\/ */
   /*      u = *cx; */
   /*      *cx = dum; */
   /*      dum = fu; */
   /*      fu = *fc; */
   /*      *fc =dum; */
   /*       } */
   #ifdef DEBUG
         printf("mnbrak34  fu < or >= fc \n");
         fprintf(ficlog, "mnbrak34 fu < fc\n");
   #endif
         dum=u; /* Shifting c and u */
         u = *cx;
         *cx = dum;
         dum = fu;
         fu = *fc;
         *fc =dum;
   #endif
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim\n");
         fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   #endif
       fu=(*func)(u);         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) {       } 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 ************************/
   /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   the value of func at the returned location p . This is actually all accomplished by calling the
   routines mnbrak and brent .*/
 int ncom;   int ncom; 
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
Line 1156  void linmin(double p[], double xi[], int Line 1597  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 1165  void linmin(double p[], double xi[], int Line 1608  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);     /* xxss=1; /\* 1 and using scale *\/ */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     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); 
 }   } 
   
 char *asc_diff_time(long time_sec, char ascdiff[])  
 {  
   long sec_left, days, hours, minutes;  
   days = (time_sec) / (60*60*24);  
   sec_left = (time_sec) % (60*60*24);  
   hours = (sec_left) / (60*60) ;  
   sec_left = (sec_left) %(60*60);  
   minutes = (sec_left) /60;  
   sec_left = (sec_left) % (60);  
   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);    
   return ascdiff;  
 }  
   
 /*************** powell ************************/  /*************** powell ************************/
   /*
   Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
Line 1202  void powell(double p[], double **xi, int Line 1680  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 1212  void powell(double p[], double **xi, int Line 1691  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
       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; 
     last_time=curr_time;      rlast_time=rcurr_time;
     (void) gettimeofday(&curr_time,&tzp);      /* (void) gettimeofday(&curr_time,&tzp); */
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);      rcurr_time = time(NULL);  
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);      curr_time = *localtime(&rcurr_time);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
    for (i=1;i<=n;i++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        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 1230  void powell(double p[], double **xi, int Line 1712  void powell(double p[], double **xi, int
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){      if(*iter <=3){
       tm = *localtime(&curr_time.tv_sec);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tm));        strcpy(strcurr,asctime(&tml));
 /*       asctime_r(&tm,strcurr); */        rforecast_time=rcurr_time; 
       forecast_time=curr_time;   
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         tmf = *localtime(&forecast_time.tv_sec);          forecast_time = *localtime(&rforecast_time);
 /*      asctime_r(&tmf,strfor); */          strcpy(strfor,asctime(&forecast_time));
         strcpy(strfor,asctime(&tmf));  
         itmp = strlen(strfor);          itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';          strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { /* For each direction i */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf \n",*fret);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficlog,"fret=%lf \n",*fret);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #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 1274  void powell(double p[], double **xi, int Line 1759  void powell(double p[], double **xi, int
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p=%.12e",p[j]);          printf(" p(%d)=%.12e",j,p[j]);
         fprintf(ficlog," p=%.12e",p[j]);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     }       } /* end loop on each direction i */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
       /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
       /* New value of last point Pn is not computed, P(n-1) */
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
         /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
         /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
         /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
         /* decreased of more than 3.84  */
         /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
         /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
         /* By adding 10 parameters more the gain should be 18.31 */
   
         /* Starting the program with initial values given by a former maximization will simply change */
         /* the scales of the directions and the directions, because the are reset to canonical directions */
         /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
         /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
       k[0]=1;        k[0]=1;
Line 1311  void powell(double p[], double **xi, int Line 1811  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++) {       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 */
     if (fptt < fp) {   #ifdef POWELLF1F3
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);   #else
       if (t < 0.0) {       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         linmin(p,xit,n,fret,func);   #endif
         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   #ifdef NRCORIGINAL
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
   #else
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
         t= t- del*SQR(fp-fptt);
   #endif
         directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
   #ifdef DEBUG
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
         fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
         printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   #endif
   #ifdef POWELLORIGINAL
         if (t < 0.0) { /* Then we use it for new direction */
   #else
         if (directest*t < 0.0) { /* Contradiction between both tests */
           printf("directest= %.12lf, 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++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n];             printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           xi[j][n]=xit[j];             if(j % ncovmodel == 0)
               printf("\n");
         }          }
   #endif
           for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
             xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
           }
           printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
 #ifdef DEBUG  #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);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 1337  void powell(double p[], double **xi, int Line 1891  void powell(double p[], double **xi, int
         printf("\n");          printf("\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       }        } /* end of t or directest negative */
     }   #ifdef POWELLF1F3
   }   #else
       } /* end if (fptt < fp)  */
   #endif
     } /* loop iteration */ 
 }   } 
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
Line 1348  double **prevalim(double **prlim, int nl Line 1905  double **prevalim(double **prlim, int nl
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached */
     
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=50 ; /* Max number of years to converge */
     
   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++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     
    cov[1]=1.;    cov[1]=1.;
      
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     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]][codtabm(ij,Tvar[k])]; */
       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
     }        /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      }
     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
       for (k=1; k<=cptcovprod;k++) /* Useless */
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d 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 1400  double **prevalim(double **prlim, int nl Line 1962  double **prevalim(double **prlim, int nl
       }        }
       maxmin=max-min;        maxmin=max-min;
       maxmax=FMAX(maxmax,maxmin);        maxmax=FMAX(maxmax,maxmin);
     }      } /* j loop */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       return prlim;        return prlim;
     }      }
   }    } /* age loop */
     return prlim; /* should not reach here */
 }  }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
Line 1426  double **pmij(double **ps, double *cov, Line 1989  double **pmij(double **ps, double *cov,
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
   int i,j,j1, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){        for(j=1; j<i;j++){
Line 1528  double ***hpxij(double ***po, int nhstep Line 2091  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 1541  double ***hpxij(double ***po, int nhstep Line 2105  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]][codtabm(ij,k)];
       for (k=1; k<=cptcovage;k++)          /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
           /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
Line 1568  double ***hpxij(double ***po, int nhstep Line 2139  double ***hpxij(double ***po, int nhstep
   return po;    return po;
 }  }
   
   #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
     double *xt;
     int j;
     myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
    free_vector(xt,1,n);
     return fret;
   }
   #endif
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
Line 1580  double func( double *x) Line 2170  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]);*/
   /*for(i=1;i<imx;i++)     /*for(i=1;i<imx;i++) 
     printf(" %d\n",s[4][i]);      printf(" %d\n",s[4][i]);
   */    */
   
     ++countcallfunc;
   
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
Line 1598  double func( double *x) Line 2192  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 1611  double func( double *x) Line 2205  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 1665  double func( double *x) Line 2262  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 1697  double func( double *x) Line 2313  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 1710  double func( double *x) Line 2330  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 1731  double func( double *x) Line 2354  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 1740  double func( double *x) Line 2363  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 1761  double func( double *x) Line 2387  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 1770  double func( double *x) Line 2396  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 1796  double func( double *x) Line 2425  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 1805  double func( double *x) Line 2434  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 1843  double funcone( double *x) Line 2475  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 1854  double funcone( double *x) Line 2487  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 1863  double funcone( double *x) Line 2496  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 1939  void likelione(FILE *ficres,double p[], Line 2576  void likelione(FILE *ficres,double p[],
   int k;    int k;
   
   if(*globpri !=0){ /* Just counts and sums, no printings */    if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ilk");       strcpy(fileresilk,"ILK_"); 
     strcat(fileresilk,fileres);      strcat(fileresilk,fileres);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
Line 1956  void likelione(FILE *ficres,double p[], Line 2593  void likelione(FILE *ficres,double p[],
   *fretone=(*funcone)(p);    *fretone=(*funcone)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm,"\n<br>File of contributions to the likelihood (if mle=1): <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fflush(fichtm);       fflush(fichtm); 
   }     } 
   return;    return;
Line 1967  void likelione(FILE *ficres,double p[], Line 2604  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter;    int i,j, iter=0;
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
   /*  char filerespow[FILENAMELENGTH];*/    /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(filerespow,"pow");     strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);    strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", filerespow);      printf("Problem with resultfile: %s\n", filerespow);
Line 1988  void mlikeli(FILE *ficres,double p[], in Line 2637  void mlikeli(FILE *ficres,double p[], in
     for(j=1;j<=nlstate+ndeath;j++)      for(j=1;j<=nlstate+ndeath;j++)
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");    fprintf(ficrespow,"\n");
   #ifdef POWELL
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,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 = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
Line 2004  void hesscov(double **matcov, double p[] Line 2680  void hesscov(double **matcov, double p[]
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    double **hess;
   int i, j,jk;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
Line 2138  double hessii(double x[], double delta, Line 2814  double hessii(double x[], double delta,
         k=kmax;          k=kmax;
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         k=kmax; l=lmax*10.;          k=kmax; l=lmax*10;
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
Line 2153  double hessii(double x[], double delta, Line 2829  double hessii(double x[], double delta,
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k;
Line 2261  void lubksb(double **a, int n, int *indx Line 2937  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 ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
Line 2277  void  freqsummary(char fileres[], int ia Line 2953  void  freqsummary(char fileres[], int ia
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileresp,"p");    strcpy(fileresp,"P_");
   strcat(fileresp,fileres);    strcat(fileresp,fileresu);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
Line 2292  void  freqsummary(char fileres[], int ia Line 2968  void  freqsummary(char fileres[], int ia
   
   first=1;    first=1;
   
   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   /*    j1++;    /*    j1++; */
 */  
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
Line 2314  void  freqsummary(char fileres[], int ia Line 2989  void  freqsummary(char fileres[], int ia
         bool=1;          bool=1;
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<=cptcoveff; z1++)                   for (z1=1; z1<=cptcoveff; z1++)       
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
               bool=0;                bool=0;
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             }               } 
         }          }
     
Line 2349  void  freqsummary(char fileres[], int ia Line 3024  void  freqsummary(char fileres[], int ia
       pstamp(ficresp);        pstamp(ficresp);
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresp, "**********\n#");          fprintf(ficresp, "**********\n#");
         fprintf(ficlog, "\n#********** Variable ");           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficlog, "**********\n#");          fprintf(ficlog, "**********\n#");
       }        }
       for(i=1; i<=nlstate;i++)         for(i=1; i<=nlstate;i++) 
Line 2449  void prevalence(double ***probs, double Line 3124  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, k1, i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   double ***freq; /* Frequencies */  
   double *pp, **prop;    double **prop;
   double pos,posprop;     double posprop; 
   double  y2; /* in fractional years */    double  y2; /* in fractional years */
   int iagemin, iagemax;    int iagemin, iagemax;
   int first; /** to stop verbosity which is redirected to log file */    int first; /** to stop verbosity which is redirected to log file */
Line 2480  void prevalence(double ***probs, double Line 3155  void prevalence(double ***probs, double
         bool=1;          bool=1;
         if  (cptcovn>0) {          if  (cptcovn>0) {
           for (z1=1; z1<=cptcoveff; z1++)             for (z1=1; z1<=cptcoveff; z1++) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
               bool=0;                bool=0;
         }           } 
         if (bool==1) {           if (bool==1) { 
Line 2543  void  concatwav(int wav[], int **dh, int Line 3218  void  concatwav(int wav[], int **dh, int
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
   jmin=1e+5;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
Line 2672  void tricode(int *Tvar, int **nbcode, in Line 3347  void tricode(int *Tvar, int **nbcode, in
 {  {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   /* Boring subroutine which should only output nbcode[Tvar[j]][k]     * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   /* nbcode[Tvar[j]][1]=      * nbcode[Tvar[j]][1]= 
   */    */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 2685  void tricode(int *Tvar, int **nbcode, in Line 3360  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 2712  void tricode(int *Tvar, int **nbcode, in Line 3387  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 2783  void evsij(double ***eij, double x[], in Line 3479  void evsij(double ***eij, double x[], in
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
Line 3102  void varevsij(char optionfilefiname[], d Line 3798  void varevsij(char optionfilefiname[], d
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /* double **newm;*/    /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double **dnewmp,**doldmp;    double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k;
   double *xp;    double *xp;
   double **gp, **gm;  /* for var eij */    double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */    double ***gradg, ***trgradg; /*for var eij */
Line 3123  void varevsij(char optionfilefiname[], d Line 3822  void varevsij(char optionfilefiname[], d
   
   if(popbased==1){    if(popbased==1){
     if(mobilav!=0)      if(mobilav!=0)
       strcpy(digitp,"-populbased-mobilav-");        strcpy(digitp,"-POPULBASED-MOBILAV_");
     else strcpy(digitp,"-populbased-nomobil-");      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
   }    }
   else     else 
     strcpy(digitp,"-stablbased-");      strcpy(digitp,"-STABLBASED_");
   
   if (mobilav!=0) {    if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 3137  void varevsij(char optionfilefiname[], d Line 3836  void varevsij(char optionfilefiname[], d
     }      }
   }    }
   
   strcpy(fileresprobmorprev,"prmorprev");     strcpy(fileresprobmorprev,"PRMORPREV-"); 
   sprintf(digit,"%-d",ij);    sprintf(digit,"%-d",ij);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
Line 3160  void varevsij(char optionfilefiname[], d Line 3859  void varevsij(char optionfilefiname[], d
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficgp,"\n# Routine varevsij");
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/    fprintf(ficgp,"\nunset title \n");
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */  /*   } */
Line 3372  void varevsij(char optionfilefiname[], d Line 4072  void varevsij(char optionfilefiname[], d
   free_vector(gmp,nlstate+1,nlstate+ndeath);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
     fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) 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.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
 */  */
 /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);    free_matrix(doldm,1,nlstate,1,nlstate);
Line 3405  void varprevlim(char fileres[], double * Line 4107  void varprevlim(char fileres[], double *
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;  
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   int k, cptcode;  
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
Line 3487  void varprevlim(char fileres[], double * Line 4188  void varprevlim(char fileres[], double *
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;    int k2, l2, j1,  z1;
   int k=0,l, cptcode;    int k=0, l;
   int first=1, first1, first2;    int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 3497  void varprob(char optionfilefiname[], do Line 4198  void varprob(char optionfilefiname[], do
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double **mu;    double **mu;
   double age,agelim, cov[NCOVMAX+1];    double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char fileresprob[FILENAMELENGTH];
Line 3505  void varprob(char optionfilefiname[], do Line 4206  void varprob(char optionfilefiname[], do
   char fileresprobcor[FILENAMELENGTH];    char fileresprobcor[FILENAMELENGTH];
   double ***varpij;    double ***varpij;
   
   strcpy(fileresprob,"prob");     strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);    strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);      printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   strcpy(fileresprobcov,"probcov");     strcpy(fileresprobcov,"PROBCOV_"); 
   strcat(fileresprobcov,fileres);    strcat(fileresprobcov,fileres);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);      printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }    }
   strcpy(fileresprobcor,"probcor");     strcpy(fileresprobcor,"PROBCOR_"); 
   strcat(fileresprobcor,fileres);    strcat(fileresprobcor,fileres);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);      printf("Problem with resultfile: %s\n", fileresprobcor);
Line 3560  void varprob(char optionfilefiname[], do Line 4261  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> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
   file %s<br>\n",optionfilehtmcov);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\  
 and drawn. It helps understanding how is the covariance between two incidences.\  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 3584  To be simple, these graphs help to under Line 4284  To be simple, these graphs help to under
     /*j1++;*/      /*j1++;*/
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");           fprintf(ficresprob, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprob, "**********\n#\n");          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");           fprintf(ficresprobcov, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcov, "**********\n#\n");          fprintf(ficresprobcov, "**********\n#\n");
                   
         fprintf(ficgp, "\n#********** Variable ");           fprintf(ficgp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "**********\n#\n");          fprintf(ficgp, "**********\n#\n");
                   
                   
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   
         fprintf(ficresprobcor, "\n#********** Variable ");              fprintf(ficresprobcor, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "**********\n#");              fprintf(ficresprobcor, "**********\n#");    
       }        }
               
Line 3610  To be simple, these graphs help to under Line 4310  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]][codtabm(j1,k)];
             /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(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]]][codtabm(ij,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]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                   
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
Line 3768  To be simple, these graphs help to under Line 4472  To be simple, these graphs help to under
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   if(first==1){                    if(first==1){
                     first=0;                      first=0;
                       fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                     fprintf(ficgp,"\nset parametric;unset label");                      fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter png small size 320, 240");                      fprintf(ficgp,"\nset ter svg size 640, 480");
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                      fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                      fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
Line 3795  To be simple, these graphs help to under Line 4500  To be simple, these graphs help to under
                   }/* if first */                    }/* if first */
                 } /* age mod 5 */                  } /* age mod 5 */
               } /* end loop age */                } /* end loop age */
               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
               first=1;                first=1;
             } /*l12 */              } /*l12 */
           } /* k12 */            } /* k12 */
         } /*l1 */          } /*l1 */
       }/* k1 */        }/* k1 */
       /* } /* loop covariates */        /* } */ /* loop covariates */
   }    }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
Line 3817  To be simple, these graphs help to under Line 4522  To be simple, these graphs help to under
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int estepm ,\                    int popforecast, int estepm ,\
Line 3830  void printinghtml(char fileres[], char t Line 4535  void printinghtml(char fileres[], char t
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n",     <a href=\"%s\">%s</a> <br>\n",
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));             estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Population projections by age and states: \   - Population projections by age and states: \
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
Line 3852  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4557  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]][codtabm(jj1,cpt)]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
   <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \       fprintf(fichtm,"<br>\n- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
 <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);    incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
        /* Period (stable) prevalence in each health state */  divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
        for(cpt=1; cpt<nlstate;cpt++){  <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
          fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \       /* Survival functions (period) in state j */
 <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);       for(cpt=1; cpt<=nlstate;cpt++){
        }         fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.\
    <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
        }
        /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }       }
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* 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(fileresu,"PROB_"),subdirf2(fileresu,"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",
          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));           subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));           subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));           estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));           estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));           subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 3926  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4656  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]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\  prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
 <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  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.svg<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
  fflush(fichtm);   fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;    int ng=0;
     int vpopbased;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 3970  void printinggnuplot(char fileres[], cha Line 4701  void printinggnuplot(char fileres[], cha
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */      for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
      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 svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else        fprintf(ficgp," \%%*lf (\%%*lf)");         else        fprintf(ficgp," %%*lf (%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
    }       fprintf(ficgp,"\nset out \n");
   }      } /* k1 */
     } /* cpt */
   /*2 eme*/    /*2 eme*/
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);      fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);      for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             if(vpopbased==0)
     for (i=1; i<= nlstate+1 ; i ++) {          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
       k=2*i;        else
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);          fprintf(ficgp,"\nreplot ");
       for (j=1; j<= nlstate+1 ; j ++) {        for (i=1; i<= nlstate+1 ; i ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          k=2*i;
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            else fprintf(ficgp," %%*lf (%%*lf)");
       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 ++) {          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficgp,"\" t\"\" w l lt 0,");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);            else fprintf(ficgp," %%*lf (%%*lf)");
       for (j=1; j<= nlstate+1 ; j ++) {          }   
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficgp,"\" t\"\" w l lt 0,");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       else fprintf(ficgp,"\" t\"\" w l lt 0,");            else fprintf(ficgp," %%*lf (%%*lf)");
     }          }   
   }          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
             else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         } /* state */
       } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
     } /* k1 */
   /*3eme*/    /*3eme*/
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       fprintf(ficgp,"set ter png small size 320, 240\n\        fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 4045  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4782  plot [%.f:%.f] \"%s\" every :::%d::%d u
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                   
       }         } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
     /* Survival functions (period) from state i in state j by initial state i */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate+ndeath ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         k=3;
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           if(j==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(cpt-1) +j;
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
           /* for (i=2; i<= nlstate+ndeath ; i ++) */
           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficgp,", '' ");
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           l=(nlstate+ndeath)*(cpt-1) +j;
           if(j < nlstate)
             fprintf(ficgp,"$%d +",k+l);
           else
             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
   /* CV preval stable (period) */    /* CV preval stable (period) */
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) {      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;        k=3;
       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter png small size 320, 240\n\  set ter svg size 640, 480\n\
 unset log y\n\  unset log y\n\
 plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
               for (i=1; i<= nlstate ; i ++){
       for (i=1; i< nlstate ; i ++)          if(i==1)
         fprintf(ficgp,"+$%d",k+i+1);            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          else
                   fprintf(ficgp,", '' ");
       l=3+(nlstate+ndeath)*cpt;          l=(nlstate+ndeath)*(i-1)+1;
       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
       for (i=1; i< nlstate ; i ++) {          for (j=2; j<= nlstate ; j ++)
         l=3+(nlstate+ndeath)*cpt;            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       }        } /* nlstate */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);           fprintf(ficgp,"\nset out\n");
     }       } /* end cpt state*/ 
   }      } /* 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;*/
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
     fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
     fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
     fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
     fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
     fprintf(ficgp,"#\n");
      for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
        fprintf(ficgp,"# ng=%d\n",ng);
        fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);          fprintf(ficgp,"#    jk=%d\n",jk);
        if (ng==2)         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
          fprintf(ficgp,"\nset ter svg size 640, 480 ");
          if (ng==1){
            fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
            fprintf(ficgp,"\nunset log y");
          }else if (ng==2){
            fprintf(ficgp,"\nset ylabel \"Probability\"\n");
            fprintf(ficgp,"\nset log y");
          }else if (ng==3){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else           fprintf(ficgp,"\nset log y");
          fprintf(ficgp,"\nset title \"Probability\"\n");         }else
        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);           fprintf(ficgp,"\nunset title ");
          fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;         i=1;
        for(k2=1; k2<=nlstate; k2++) {         for(k2=1; k2<=nlstate; k2++) {
          k3=i;           k3=i;
          for(k=1; k<=(nlstate+ndeath); k++) {           for(k=1; k<=(nlstate+ndeath); k++) {
            if (k != k2){             if (k != k2){
              if(ng==2)               switch( ng) {
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);               case 1:
              else                 if(nagesqr==0)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                  break;
                case 2: /* ng=2 */
                  if(nagesqr==0)
                    fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                  else /* nagesqr =1 */
                      fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                  break;
                case 3:
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                  break;
                }
              ij=1;/* To be checked else nbcode[0][0] wrong */               ij=1;/* To be checked else nbcode[0][0] wrong */
              for(j=3; j <=ncovmodel; j++) {               for(j=3; j <=ncovmodel-nagesqr; j++) {
                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */                 if(ij <=cptcovage) { /* Bug valgrind */
                /*        ij++; */                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                /* } */                     fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                /* else */                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                     ij++;
                    }
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
              }               }
              fprintf(ficgp,")/(1");               if(ng != 1){
                  fprintf(ficgp,")/(1");
                             
              for(k1=1; k1 <=nlstate; k1++){                    for(k1=1; k1 <=nlstate; k1++){ 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                   if(nagesqr==0)
                ij=1;                     fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                for(j=3; j <=ncovmodel; j++){                   else /* nagesqr =1 */
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */                     fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                  /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */                   
                  /*   ij++; */                   ij=1;
                  /* } */                   for(j=3; j <=ncovmodel-nagesqr; j++){
                  /* else */                     if(ij <=cptcovage) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                       if((j-2)==Tage[ij]) { /* Bug valgrind */
                          fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                          /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                          ij++;
                        }
                      }
                      else
                        fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                    }
                    fprintf(ficgp,")");
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
                  if(ng ==2)
                    fprintf(ficgp," t \"p%d%d\" ", k2,k);
                  else /* ng= 3 */
                    fprintf(ficgp," t \"i%d%d\" ", k2,k);
                }else{ /* end ng <> 1 */
                  fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
              }               }
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
              i=i+ncovmodel;               i=i+ncovmodel;
            }             }
          } /* end k */           } /* end k */
        } /* end k2 */         } /* end k2 */
          fprintf(ficgp,"\n set out\n");
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
  avoid:   /* avoid: */
    fflush(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
Line 4187  int movingaverage(double ***probs, doubl Line 5050  int movingaverage(double ***probs, doubl
   
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
   int *popage;  
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
Line 4205  prevforecast(char fileres[], double anpr Line 5067  prevforecast(char fileres[], double anpr
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
   strcpy(fileresf,"f");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileresu);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
Line 4255  prevforecast(char fileres[], double anpr Line 5117  prevforecast(char fileres[], double anpr
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf,"******\n");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
Line 4279  prevforecast(char fileres[], double anpr Line 5141  prevforecast(char fileres[], double anpr
             if (h*hstepm/YEARM*stepm ==yearp) {              if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");                fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++)                 for(j=1;j<=cptcoveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 4311  prevforecast(char fileres[], double anpr Line 5173  prevforecast(char fileres[], double anpr
 }  }
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
Line 4329  populforecast(char fileres[], double anp Line 5191  populforecast(char fileres[], double anp
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"POP_"); 
   strcat(filerespop,fileres);    strcat(filerespop,fileresu);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", filerespop);      printf("Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
Line 4377  populforecast(char fileres[], double anp Line 5239  populforecast(char fileres[], double anp
       k=k+1;        k=k+1;
       fprintf(ficrespop,"\n#******");        fprintf(ficrespop,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficrespop,"******\n");        fprintf(ficrespop,"******\n");
       fprintf(ficrespop,"# Age");        fprintf(ficrespop,"# Age");
Line 4488  void prwizard(int ncovmodel, int nlstate Line 5350  void prwizard(int ncovmodel, int nlstate
   
   /* Wizard to print covariance matrix template */    /* Wizard to print covariance matrix template */
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;    int i,j, k, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;    int numlinepar;
   
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 4683  double gompertz_f(const gsl_vector *v, v Line 5545  double gompertz_f(const gsl_vector *v, v
 #endif  #endif
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,  double p[],double **matcov,double agemortsup){                    int imx,  double p[],double **matcov,double agemortsup){
   int i,k;    int i,k;
Line 4692  void printinghtmlmort(char fileres[], ch Line 5554  void printinghtmlmort(char fileres[], ch
   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
   for (i=1;i<=2;i++)     for (i=1;i<=2;i++) 
     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));      fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");    fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
   fprintf(fichtm,"</ul>");    fprintf(fichtm,"</ul>");
   
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
Line 4707  fprintf(fichtm,"<ul><li><h4>Life table</ Line 5569  fprintf(fichtm,"<ul><li><h4>Life table</
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;    int ng;
   
   
Line 4721  void printinggnuplotmort(char fileres[], Line 5583  void printinggnuplotmort(char fileres[],
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   fprintf(ficgp,"set out \"graphmort.png\"\n ");     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");     fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
   /* fprintf(ficgp, "set size 0.65,0.65\n"); */    /* fprintf(ficgp, "set size 0.65,0.65\n"); */
   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
Line 4735  int readdata(char datafile[], int firsto Line 5597  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i, j, n;    int i=0, j=0, n=0;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[80], strb[80];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;    int lstra;
   
   
   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 4766  int readdata(char datafile[], int firsto Line 5628  int readdata(char datafile[], int firsto
       continue;        continue;
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     for (j=0; line[j]!='\0';j++){      strcpy(line, linetmp);
       line[j]=linetmp[j];  
     }  
       
   
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
Line 4789  int readdata(char datafile[], int firsto Line 5649  int readdata(char datafile[], int firsto
               
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }        }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;          month=99;
         year=9999;          year=9999;
       }else{        }else{
Line 4805  int readdata(char datafile[], int firsto Line 5665  int readdata(char datafile[], int firsto
     } /* ENd Waves */      } /* ENd Waves */
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.",dummy) != 0){      else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }else{
Line 4820  int readdata(char datafile[], int firsto Line 5680  int readdata(char datafile[], int firsto
     strcpy(line,stra);      strcpy(line,stra);
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.", dummy) != 0){      else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }else{
Line 4907  int readdata(char datafile[], int firsto Line 5767  int readdata(char datafile[], int firsto
   fclose(fic);    fclose(fic);
     
   return (0);    return (0);
   endread:    /* endread: */
     printf("Exiting readdata: ");      printf("Exiting readdata: ");
     fclose(fic);      fclose(fic);
     return (1);      return (1);
Line 4920  void removespace(char *str) { Line 5780  void removespace(char *str) {
   do    do
     while (*p2 == ' ')      while (*p2 == ' ')
       p2++;        p2++;
   while (*p1++ = *p2++);    while (*p1++ == *p2++);
 }  }
   
 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 4938  int decodemodel ( char model[], int last Line 5799  int decodemodel ( char model[], int last
  */   */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int i1, 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 4964  int decodemodel ( char model[], int last Line 5817  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]][codtabm(ij,Tvar[k])]; */
         /*        } */
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
         /*
          * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
         for(k=cptcovt; k>=1;k--) /**< Number of covariates */
         Tvar[k]=0;          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 5087  int decodemodel ( char model[], int last Line 5976  int decodemodel ( char model[], int last
   
   
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   endread:    /*endread:*/
     printf("Exiting decodemodel: ");      printf("Exiting decodemodel: ");
     return (1);      return (1);
 }  }
   
 calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {
   int i, m;    int i, m;
   
Line 5103  calandcheckages(int imx, int maxwav, dou Line 5992  calandcheckages(int imx, int maxwav, dou
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         *nberr++;          *nberr = *nberr + 1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         *nberr++;          (*nberr)++;
         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
Line 5122  calandcheckages(int imx, int maxwav, dou Line 6011  calandcheckages(int imx, int maxwav, dou
     for(m=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){        if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0)            if(agedc[i]>0){
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             else {              }else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 nbwarn++;                  nbwarn++;
                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
Line 5134  calandcheckages(int imx, int maxwav, dou Line 6023  calandcheckages(int imx, int maxwav, dou
                 agev[m][i]=-1;                  agev[m][i]=-1;
               }                }
             }              }
             } /* agedc > 0 */
         }          }
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a month */                                   years but with the precision of a month */
Line 5146  calandcheckages(int imx, int maxwav, dou Line 6036  calandcheckages(int imx, int maxwav, dou
           }            }
           else if(agev[m][i] >*agemax){            else if(agev[m][i] >*agemax){
             *agemax=agev[m][i];              *agemax=agev[m][i];
             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);              /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
Line 5164  calandcheckages(int imx, int maxwav, dou Line 6054  calandcheckages(int imx, int maxwav, dou
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
         *nberr++;          (*nberr)++;
         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         return 1;          return 1;
Line 5184  calandcheckages(int imx, int maxwav, dou Line 6074  calandcheckages(int imx, int maxwav, dou
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
   return (0);    return (0);
   endread:   /* endread:*/
     printf("Exiting calandcheckages: ");      printf("Exiting calandcheckages: ");
     return (1);      return (1);
 }  }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         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:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) fprintf(ficlog, " for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
            if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- 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,fileresu);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \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,codtabm(cptcod,cptcov));
           fprintf(ficrespl,"#******");
           printf("#******");
           fprintf(ficlog,"#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\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]][codtabm(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,fileresu);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
Line 5204  int main(int argc, char *argv[]) Line 6429  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   int linei, month, year,iout;  
   int jj, ll, li, lj, lk, imk;    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;
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb, agefin,hf;    double agedeb=0.;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   
   double fret;    double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */    double fret;
     double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char **bp, *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int c,  h , cpt, c2;
   int c,  h , cpt,l;    int jl=0;
   int ju,jl, mi;    int i1, j1, jk, stepsize=0;
   int i1,j1, jk,aa,bb, stepsize, ij;    int count=0;
   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;   
     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int 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, fage, 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 5255  int main(int argc, char *argv[]) Line 6483  int main(int argc, char *argv[])
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;    double *epj, vepp;
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
   
   char z[1]="c", occ;    char z[1]="c";
   
   /*char  *strt;*/    /*char  *strt;*/
   char strtend[80];    char strtend[80];
   
   long total_usecs;  
    
 /*   setlocale (LC_ALL, ""); */  /*   setlocale (LC_ALL, ""); */
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 /*   textdomain (PACKAGE); */  /*   textdomain (PACKAGE); */
Line 5275  int main(int argc, char *argv[]) Line 6502  int main(int argc, char *argv[])
 /*   setlocale (LC_MESSAGES, ""); */  /*   setlocale (LC_MESSAGES, ""); */
   
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   (void) gettimeofday(&start_time,&tzp);    rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
   curr_time=start_time;    curr_time=start_time;
   tm = *localtime(&start_time.tv_sec);    /*tml = *localtime(&start_time.tm_sec);*/
   tmg = *gmtime(&start_time.tv_sec);    /* strcpy(strstart,asctime(&tml)); */
   strcpy(strstart,asctime(&tm));    strcpy(strstart,asctime(&start_time));
   
 /*  printf("Localtime (at start)=%s",strstart); */  /*  printf("Localtime (at start)=%s",strstart); */
 /*  tp.tv_sec = tp.tv_sec +86400; */  /*  tp.tm_sec = tp.tm_sec +86400; */
 /*  tm = *localtime(&start_time.tv_sec); */  /*  tm = *localtime(&start_time.tm_sec); */
 /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
 /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
 /*   tmg.tm_hour=tmg.tm_hour + 1; */  /*   tmg.tm_hour=tmg.tm_hour + 1; */
 /*   tp.tv_sec = mktime(&tmg); */  /*   tp.tm_sec = mktime(&tmg); */
 /*   strt=asctime(&tmg); */  /*   strt=asctime(&tmg); */
 /*   printf("Time(after) =%s",strstart);  */  /*   printf("Time(after) =%s",strstart);  */
 /*  (void) time (&time_value);  /*  (void) time (&time_value);
Line 5299  int main(int argc, char *argv[]) Line 6528  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);
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]=='\n')      if(pathr[i-1]=='\n')
       pathr[i-1]='\0';        pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){     for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);        printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
Line 5332  int main(int argc, char *argv[]) Line 6568  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){
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);      printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
     /* fclose(ficlog); */      /* fclose(ficlog); */
 /*     exit(1); */  /*     exit(1); */
Line 5349  int main(int argc, char *argv[]) Line 6590  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 5357  int main(int argc, char *argv[]) Line 6598  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\
  optionfile=%s\n\   optionfile=%s\n\
  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(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);
   fflush(ficlog);    fflush(ficlog);
 /*   (void) gettimeofday(&curr_time,&tzp); */  /*   (void) gettimeofday(&curr_time,&tzp); */
 /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */  /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /* Main ---------arguments file --------*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
     fflush(ficlog);      fflush(ficlog);
     goto end;      /* goto end; */
       exit(70); 
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
Line 5398  int main(int argc, char *argv[]) Line 6644  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]", model)) !=EOF){
       if (num_filled == 0)
               model[0]='\0';
       else if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
           strcpy(model,modeltemp); 
         }
       }
       /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
     }
     /* 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 5432  int main(int argc, char *argv[]) Line 6755  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 5450  int main(int argc, char *argv[]) Line 6772  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 5485  int main(int argc, char *argv[]) Line 6807  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 5493  run imach with mle=-1 to get a correct t Line 6815  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 5532  run imach with mle=-1 to get a correct t Line 6854  run imach with mle=-1 to get a correct t
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){          if ( (i1-i) * (j1-j) != 0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
Line 5575  run imach with mle=-1 to get a correct t Line 6897  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 5596  run imach with mle=-1 to get a correct t Line 6928  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 5612  run imach with mle=-1 to get a correct t Line 6945  run imach with mle=-1 to get a correct t
     strcat(rfileres,".");    /* */      strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */      strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {      if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      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 5634  run imach with mle=-1 to get a correct t Line 6968  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 5669  run imach with mle=-1 to get a correct t Line 7004  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 5712  run imach with mle=-1 to get a correct t Line 7050  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
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/    /* 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) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    h=0;
   
   
Line 5725  run imach with mle=-1 to get a correct t Line 7067  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 5743  run imach with mle=-1 to get a correct t Line 7080  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_");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
Line 5789  run imach with mle=-1 to get a correct t Line 7142  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)
     strcat(optionfilehtm,"-mort");      strcat(optionfilehtm,"-MORT_");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm);      printf("Problem with %s \n",optionfilehtm);
Line 5831  Title=%s <br>Datafile=%s Firstpass=%d La Line 7186  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 5854  Interval (in months) between two waves: Line 7214  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 5901  Interval (in months) between two waves: Line 7261  Interval (in months) between two waves:
           
 #ifdef GSL  #ifdef GSL
     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");      printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
 #elsedef  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif  #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"POW-MORT_"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileresu);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }      }
 #ifdef GSL  #ifdef GSL
     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");      fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
 #elsedef  #else
     fprintf(ficrespow,"# Powell\n# iter -2*LL");      fprintf(ficrespow,"# Powell\n# iter -2*LL");
 #endif  #endif
     /*  for (i=1;i<=nlstate;i++)      /*  for (i=1;i<=nlstate;i++)
Line 5947  Interval (in months) between two waves: Line 7307  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 6016  Interval (in months) between two waves: Line 7376  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 6050  Interval (in months) between two waves: Line 7411  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\
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else
         printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
Line 6065  Interval (in months) between two waves: Line 7433  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 6098  Interval (in months) between two waves: Line 7467  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 6114  Interval (in months) between two waves: Line 7483  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 6241  Interval (in months) between two waves: Line 7628  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 6269  Interval (in months) between two waves: Line 7657  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 6293  Interval (in months) between two waves: Line 7682  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(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
           
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\                   model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                   jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
               
Line 6314  Interval (in months) between two waves: Line 7711  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 6323  Interval (in months) between two waves: Line 7725  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 6341  Interval (in months) between two waves: Line 7744  Interval (in months) between two waves:
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
       /*      }  */        /*      }  */
       /*      else{ */        /*      else{ */
Line 6350  Interval (in months) between two waves: Line 7753  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 6370  Interval (in months) between two waves: Line 7774  Interval (in months) between two waves:
   
     /*---------- Health expectancies, no variances ------------*/      /*---------- Health expectancies, no variances ------------*/
   
     strcpy(filerese,"e");      strcpy(filerese,"E_");
     strcat(filerese,fileres);      strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
Line 6384  Interval (in months) between two waves: Line 7788  Interval (in months) between two waves:
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }          }
         fprintf(ficreseij,"******\n");          fprintf(ficreseij,"******\n");
   
Line 6401  Interval (in months) between two waves: Line 7805  Interval (in months) between two waves:
     /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
   
   
     strcpy(filerest,"t");      strcpy(filerest,"T_");
     strcat(filerest,fileres);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
Line 6411  Interval (in months) between two waves: Line 7815  Interval (in months) between two waves:
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
     strcpy(fileresstde,"stde");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileres);      strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
Line 6420  Interval (in months) between two waves: Line 7824  Interval (in months) between two waves:
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"cve");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileres);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
Line 6429  Interval (in months) between two waves: Line 7833  Interval (in months) between two waves:
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"v");      strcpy(fileresv,"V_");
     strcat(fileresv,fileres);      strcat(fileresv,fileresu);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
Line 6444  Interval (in months) between two waves: Line 7848  Interval (in months) between two waves:
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");          fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
   
         fprintf(ficresstdeij,"\n#****** ");          fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");          fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }          }
         fprintf(ficresstdeij,"******\n");          fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");          fprintf(ficrescveij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");          fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");          fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
Line 6473  Interval (in months) between two waves: Line 7877  Interval (in months) between two waves:
   
   
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms; /* Segmentation fault */            oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);            cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");            fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           if(vpopbased==1)            if(vpopbased==1)
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);              fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
           else            else
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");              fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
           fprintf(ficrest,"# Age e.. (std) ");            fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
             /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
           epj=vector(1,nlstate+1);            epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){            for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */
             if (vpopbased==1) {              if (vpopbased==1) {
               if(mobilav ==0){                if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)                  for(i=1; i<=nlstate;i++)
Line 6497  Interval (in months) between two waves: Line 7902  Interval (in months) between two waves:
               }                }
             }              }
                   
             fprintf(ficrest," %4.0f",age);              fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
               /* printf(" age %4.0f ",age); */
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {                for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];                  epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                  /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
               }                }
               epj[nlstate+1] +=epj[j];                epj[nlstate+1] +=epj[j];
             }              }
               /* printf(" age %4.0f \n",age); */
   
             for(i=1, vepp=0.;i <=nlstate;i++)              for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)                for(j=1;j <=nlstate;j++)
Line 6536  Interval (in months) between two waves: Line 7944  Interval (in months) between two waves:
       
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
   
     strcpy(fileresvpl,"vpl");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileres);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
Line 6550  Interval (in months) between two waves: Line 7958  Interval (in months) between two waves:
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");          fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvpl,"******\n");          fprintf(ficresvpl,"******\n");
               
         varpl=matrix(1,nlstate,(int) bage, (int) fage);          varpl=matrix(1,nlstate,(int) bage, (int) fage);
Line 6566  Interval (in months) between two waves: Line 7974  Interval (in months) between two waves:
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
  endfree:   /* endfree:*/
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
Line 6580  Interval (in months) between two waves: Line 7988  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);
     free_ivector(Tage,1,NCOVMAX);      free_ivector(Tage,1,NCOVMAX);
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);      /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
Line 6600  Interval (in months) between two waves: Line 8009  Interval (in months) between two waves:
   }    }
   printf("See log file on %s\n",filelog);    printf("See log file on %s\n",filelog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
   (void) gettimeofday(&end_time,&tzp);    /*(void) gettimeofday(&end_time,&tzp);*/
   tm = *localtime(&end_time.tv_sec);    rend_time = time(NULL);  
   tmg = *gmtime(&end_time.tv_sec);    end_time = *localtime(&rend_time);
   strcpy(strtend,asctime(&tm));    /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   /*  printf("Total time was %d uSec.\n", total_usecs);*/    /*  printf("Total time was %d uSec.\n", total_usecs);*/
 /*   if(fileappend(fichtm,optionfilehtm)){ */  /*   if(fileappend(fichtm,optionfilehtm)){ */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
Line 6623  Interval (in months) between two waves: Line 8033  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");
 #ifndef UNIX  #ifdef _WIN32
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);    sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 #endif  #endif
   if(!stat(plotcmd,&info)){    if(!stat(plotcmd,&info)){
     printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);      printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     if(!stat(getenv("GNUPLOTBIN"),&info)){      if(!stat(getenv("GNUPLOTBIN"),&info)){
       printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);        printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #ifdef UNIX  #ifdef __unix
     strcpy(plotcmd,GNUPLOTPROGRAM);      strcpy(plotcmd,GNUPLOTPROGRAM);
     if(!stat(plotcmd,&info)){      if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);        printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #endif  #endif
Line 6649  Interval (in months) between two waves: Line 8065  Interval (in months) between two waves:
     strcpy(pplotcmd,plotcmd);      strcpy(pplotcmd,plotcmd);
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("\n Problem with gnuplot\n");      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
   }    }
   printf(" Wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {
     /* chdir(path); */      /* chdir(path); */
     printf("\nType e to edit output files, g to graph again and q for exiting: ");      printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
     scanf("%s",z);      scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */  /*     if (z[0] == 'c') system("./imach"); */
     if (z[0] == 'e') {      if (z[0] == 'e') {
       printf("Starting browser with: %s",optionfilehtm);fflush(stdout);  #ifdef __APPLE__
       system(optionfilehtm);        sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
     }      }
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   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.1.147  
changed lines
  Added in v.1.201


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