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Diff for /imach/src/imach.c between versions 1.305 and 1.309

version 1.305, 2021/02/20 15:28:30 version 1.309, 2021/05/20 12:39:14
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.309  2021/05/20 12:39:14  brouard
     Summary: Version 0.99r24
   
     Revision 1.308  2021/03/31 13:11:57  brouard
     Summary: Version 0.99r23
   
   
     * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
   
     Revision 1.307  2021/03/08 18:11:32  brouard
     Summary: 0.99r22 fixed bug on result:
   
     Revision 1.306  2021/02/20 15:44:02  brouard
     Summary: Version 0.99r21
   
     * imach.c (Module): Fix bug on quitting after result lines!
     (Module): Version 0.99r21
   
   Revision 1.305  2021/02/20 15:28:30  brouard    Revision 1.305  2021/02/20 15:28:30  brouard
   * imach.c (Module): Fix bug on quitting after result lines!    * imach.c (Module): Fix bug on quitting after result lines!
   
Line 1139  typedef struct { Line 1157  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="May 2019,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020";  char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
 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 5256  void  concatwav(int wav[], int **dh, int Line 5274  void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */      mi=0;  /* First valid wave */
     mli=0; /* Last valid wave */      mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;  /* Loop on waves */
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state or unknown state  */
       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
         mli=m-1;/* mw[++mi][i]=m-1; */          mli=m-1;/* mw[++mi][i]=m-1; */
       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
         mw[++mi][i]=m;          mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
         mli=m;          mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */        if(m < lastpass){ /* m < lastpass, standard case */
         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
       else{ /* m >= lastpass, eventual special issue with warning */        else{ /* m = lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
         break;          break;
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);              printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
           }            }
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);            fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
           mw[++mi][i]=m;            mw[++mi][i]=m; /* Valid transition with unknown status */
           mli=m;            mli=m;
         }          }
         if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
           nbwarn++;            nbwarn++;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
           }            }
Line 5307  void  concatwav(int wav[], int **dh, int Line 5325  void  concatwav(int wav[], int **dh, int
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) {  /* Date of death is known */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
           nbwarn++;            nbwarn++;
           if(firstfiv==0){            if(firstfiv==0){
             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             firstfiv=1;              firstfiv=1;
           }else{            }else{
             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
           }            }
         }else{ /* Death occured afer last wave potential bias */              s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
           }else{ /* Month of Death occured afer last wave month, potential bias */
           nberr++;            nberr++;
           if(firstwo==0){            if(firstwo==0){
             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );              printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             firstwo=1;              firstwo=1;
           }            }
           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
         }          }
       }else{ /* if date of interview is unknown */        }else{ /* if date of interview is unknown */
         /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){          if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
           firstfour=1;            firstfour=1;
         }          }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );          fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
       }        }
     } /* end if date of death is known */      } /* end if date of death is known */
 #endif  #endif
     wav[i]=mi; /* mi should be the last effective wave (or mli) */      wav[i]=mi; /* mi should be the last effective wave (or mli),  */
     /* wav[i]=mw[mi][i]; */      /* wav[i]=mw[mi][i];   */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
Line 9585  int decoderesult ( char resultline[], in Line 9604  int decoderesult ( char resultline[], in
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   removefirstspace(&resultline);    removefirstspace(&resultline);
   printf("decoderesult:%s\n",resultline);  
   
   if (strstr(resultline,"v") !=0){    if (strstr(resultline,"v") !=0){
     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);      printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 9600  int decoderesult ( char resultline[], in Line 9618  int decoderesult ( char resultline[], in
     TKresult[nres]=0; /* Combination for the nresult and the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     return (0);      return (0);
   }    }
       
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
Line 12411  Please run with mle=-1 to get a correct Line 12428  Please run with mle=-1 to get a correct
     }      }
             
     /* Results */      /* Results */
       endishere=0;
     nresult=0;      nresult=0;
       parameterline=0;
     do{      do{
       if(!fgets(line, MAXLINE, ficpar)){        if(!fgets(line, MAXLINE, ficpar)){
         endishere=1;          endishere=1;
         parameterline=14;          parameterline=15;
       }else if (line[0] == '#') {        }else if (line[0] == '#') {
         /* If line starts with a # it is a comment */          /* If line starts with a # it is a comment */
         numlinepar++;          numlinepar++;
Line 12428  Please run with mle=-1 to get a correct Line 12447  Please run with mle=-1 to get a correct
         parameterline=11;          parameterline=11;
       else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))        else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
         parameterline=12;          parameterline=12;
       else if(sscanf(line,"result:%[^\n]\n",modeltemp))        else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
         parameterline=13;          parameterline=13;
         }
       else{        else{
         parameterline=14;          parameterline=14;
       }        }
       switch (parameterline){         switch (parameterline){ /* =0 only if only comments */
       case 11:        case 11:
         if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){          if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
                   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);                    fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
Line 12481  Please run with mle=-1 to get a correct Line 12501  Please run with mle=-1 to get a correct
         }          }
         break;          break;
       case 13:        case 13:
         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){          num_filled=sscanf(line,"result:%[^\n]\n",resultline);
           if (num_filled == 0){          nresult++; /* Sum of resultlines */
             resultline[0]='\0';          printf("Result %d: result:%s\n",nresult, resultline);
             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);          if(nresult > MAXRESULTLINES){
             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);            printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
             break;            fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
           } else if (num_filled != 1){            goto end;
             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);          }
             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);          decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
           }          fprintf(ficparo,"result: %s\n",resultline);
           nresult++; /* Sum of resultlines */          fprintf(ficres,"result: %s\n",resultline);
           printf("Result %d: result=%s\n",nresult, resultline);          fprintf(ficlog,"result: %s\n",resultline);
           if(nresult > MAXRESULTLINES){          break;
             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);        case 14:
             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);          printf("Error: Unknown command '%s'\n",line);
             goto end;          fprintf(ficlog,"Error: Unknown command '%s'\n",line);
           }          if(ncovmodel >=2 && nresult==0 ){
           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */            printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
           fprintf(ficparo,"result: %s\n",resultline);            fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
           fprintf(ficres,"result: %s\n",resultline);  
           fprintf(ficlog,"result: %s\n",resultline);  
           break;  
         case 14:  
           printf("Error: Unknown command '%s'\n",line);  
           fprintf(ficlog,"Error: Unknown command '%s'\n",line);  
           if(ncovmodel >=2 && nresult==0 ){  
             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);  
             fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);  
           }  
           /* goto end; */  
           break;  
         default:  
           nresult=1;  
           decoderesult(".",nresult ); /* No covariate */  
         }          }
           /* goto end; */
           break;
         case 15:
           printf("End of resultlines.\n");
           fprintf(ficlog,"End of resultlines.\n");
           break;
         default: /* parameterline =0 */
           nresult=1;
           decoderesult(".",nresult ); /* No covariate */
       } /* End switch parameterline */        } /* End switch parameterline */
     }while(endishere==0); /* End do */      }while(endishere==0); /* End do */
           
Removed from v.1.305  
changed lines
  Added in v.1.309

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