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Diff for /imach/src/imach.c between versions 1.119 and 1.123

version 1.119, 2006/03/15 17:42:26 version 1.123, 2006/03/20 10:52:43
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   
     * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
   
     Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
   
     Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
   
     * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
     Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
   Revision 1.119  2006/03/15 17:42:26  brouard    Revision 1.119  2006/03/15 17:42:26  brouard
   (Module): Bug if status = -2, the loglikelihood was    (Module): Bug if status = -2, the loglikelihood was
   computed as likelihood omitting the logarithm. Version O.98e    computed as likelihood omitting the logarithm. Version O.98e
Line 329  extern int errno; Line 360  extern int errno;
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite ";  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 404  char strcurr[80], strfor[80]; Line 435  char strcurr[80], strfor[80];
   
 char *endptr;  char *endptr;
 long lval;  long lval;
   double dval;
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
Line 1386  double func( double *x) Line 1418  double func( double *x)
   
         } else if  (s2==-2) {          } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += out[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
           lli= log(survp);            lli= log(survp);
         }          }
                   
 /*      else if  (s2==-4) { */          else if  (s2==-4) { 
 /*        for (j=3,survp=0. ; j<=nlstate; j++)  */            for (j=3,survp=0. ; j<=nlstate; j++)  
 /*          survp += out[s1][j]; */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /*        lli= survp; */            lli= log(survp); 
 /*      } */          } 
           
 /*      else if  (s2==-5) { */  
 /*        for (j=1,survp=0. ; j<=2; j++)  */  
 /*          survp += out[s1][j]; */  
 /*        lli= survp; */  
 /*      } */  
   
   
           else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
           
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
Line 1599  double funcone( double *x) Line 1631  double funcone( double *x)
         lli=log(out[s1][s2] - savm[s1][s2]);          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++) 
           survp += out[s1][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         lli= log(survp);          lli= log(survp);
       }else if (mle==1){        }else if (mle==1){
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
Line 3448  void printinghtml(char fileres[], char t Line 3480  void printinghtml(char fileres[], char t
  - 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(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
Line 4547  int main(int argc, char *argv[]) Line 4579  int main(int argc, char *argv[])
     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;
     exit(0);      exit(0);
   }    }
   else if(mle==-3) {    else if(mle==-3) {
Line 4577  int main(int argc, char *argv[]) Line 4610  int main(int argc, char *argv[])
         j++;          j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){          if ((i1 != i) && (j1 != j)){
           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 \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
         fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
Line 4801  int main(int argc, char *argv[]) Line 4836  int main(int argc, char *argv[])
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     lval=strtol(strb,&endptr,10);       dval=strtod(strb,&endptr); 
     if( strb[0]=='\0' || (*endptr != '\0')){      if( strb[0]=='\0' || (*endptr != '\0')){
       printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);        printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
       exit(1);        exit(1);
     }      }
     weight[i]=(double)(lval);       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
           
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
Line 4818  int main(int argc, char *argv[]) Line 4853  int main(int argc, char *argv[])
         exit(1);          exit(1);
       }        }
       if(lval <-1 || lval >1){        if(lval <-1 || lval >1){
         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);          printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
         exit(1);          exit(1);
       }        }
       covar[j][i]=(double)(lval);        covar[j][i]=(double)(lval);
Line 5114  int main(int argc, char *argv[]) Line 5157  int main(int argc, char *argv[])
     printf("Problem with %s \n",optionfilehtmcov), exit(0);      printf("Problem with %s \n",optionfilehtmcov), exit(0);
   }    }
   else{    else{
   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \    fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
 \n\  \n\
Line 5131  Title=%s <br>Datafile=%s Firstpass=%d La Line 5174  Title=%s <br>Datafile=%s Firstpass=%d La
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\   - Date and time at start: %s</ul>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\            optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\            optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
           fileres,fileres,\            fileres,fileres,\
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
Line 5896  Interval (in months) between two waves: Line 5939  Interval (in months) between two waves:
   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);    fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
   /*  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>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
   fclose(fichtm);    fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
   fclose(fichtmcov);    fclose(fichtmcov);
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
Removed from v.1.119  
changed lines
  Added in v.1.123

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