\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); + /* mu = \frac{w x}{\sum w} + var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 + */ + printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); + fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)
\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); } /* for (z1=1; z1<= nqtveff; z1++) { */ /* for(m=1;m<=lastpass;m++){ */ @@ -5253,33 +5298,33 @@ void concatwav(int wav[], int **dh, int for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ mi=0; /* First valid wave */ mli=0; /* Last valid wave */ - m=firstpass; - while(s[m][i] <= nlstate){ /* a live state */ + m=firstpass; /* Loop on waves */ + 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 */ 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 */ - 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; } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ 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 */ } - else{ /* m >= lastpass, eventual special issue with warning */ + else{ /* m = lastpass, eventual special issue with warning */ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING break; #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){ 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; } 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; } if(s[m][i]==-2){ /* Vital status is really unknown */ 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); 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); } @@ -5304,34 +5349,35 @@ void concatwav(int wav[], int **dh, int #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE else if ((int) andc[i] != 9999) { /* Date of death 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++; 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; }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++; 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; } - 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 */ /* death is known but not confirmed by death status at any wave */ 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; } - 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 */ #endif - wav[i]=mi; /* mi should be the last effective wave (or mli) */ - /* wav[i]=mw[mi][i]; */ + wav[i]=mi; /* mi should be the last effective wave (or mli), */ + /* wav[i]=mw[mi][i]; */ if(mi==0){ nbwarn++; if(first==0){ @@ -5466,6 +5512,8 @@ void concatwav(int wav[], int **dh, int if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ switch(Fixed[k]) { case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ + modmaxcovj=0; + modmincovj=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*/ ij=(int)(covar[Tvar[k]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i @@ -5479,8 +5527,10 @@ void concatwav(int wav[], int **dh, int else if (ij < modmincovj) modmincovj=ij; if (ij <0 || ij >1 ){ - printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i); - fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i); + printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); + fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); + fflush(ficlog); + exit(1); } if ((ij < -1) || (ij > NCOVMAX)){ printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); @@ -5555,6 +5605,16 @@ void concatwav(int wav[], int **dh, int break; } /* end switch */ } /* end dummy test */ + if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */ + 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*/ + if(isnan(covar[Tvar[k]][i])){ + printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); + fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); + fflush(ficlog); + exit(1); + } + } + } } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/ for (k=-1; k< maxncov; k++) Ndum[k]=0; @@ -9479,6 +9539,8 @@ int readdata(char datafile[], int firsto cutv(stra, strb, line, ' '); if(strb[0]=='.') { /* Missing value */ lval=-1; + coqvar[iv][i]=NAN; + covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ }else{ errno=0; /* what_kind_of_number(strb); */ @@ -9582,7 +9644,6 @@ int decoderesult ( char resultline[], in char stra[80], strb[80], strc[80], strd[80],stre[80]; removefirstspace(&resultline); - printf("decoderesult:%s\n",resultline); if (strstr(resultline,"v") !=0){ printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); @@ -9597,15 +9658,14 @@ int decoderesult ( char resultline[], in TKresult[nres]=0; /* Combination for the nresult and the model */ return (0); } - 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); - 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); + printf("ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); + fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); } for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ if(nbocc(resultsav,'=') >1){ cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' - resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */ + resultsav= V4=1 V5=25.1 V3=0 stra= V5=25.1 V3=0 strb= V4=1 */ cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ }else cutl(strc,strd,resultsav,'='); @@ -9630,7 +9690,9 @@ int decoderesult ( char resultline[], in } } if(match == 0){ - printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); + fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); + return 1; } } } @@ -9647,8 +9709,12 @@ int decoderesult ( char resultline[], in } if(match == 0){ printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); + return 1; }else if(match > 1){ printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); + return 1; } } @@ -12408,11 +12474,13 @@ Please run with mle=-1 to get a correct } /* Results */ + endishere=0; nresult=0; + parameterline=0; do{ if(!fgets(line, MAXLINE, ficpar)){ endishere=1; - parameterline=14; + parameterline=15; }else if (line[0] == '#') { /* If line starts with a # it is a comment */ numlinepar++; @@ -12425,12 +12493,13 @@ Please run with mle=-1 to get a correct parameterline=11; else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp)) parameterline=12; - else if(sscanf(line,"result:%[^\n]\n",modeltemp)) + else if(sscanf(line,"result:%[^\n]\n",modeltemp)){ parameterline=13; + } else{ parameterline=14; } - switch (parameterline){ + switch (parameterline){ /* =0 only if only comments */ 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)){ 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); @@ -12478,41 +12547,37 @@ Please run with mle=-1 to get a correct } break; case 13: - if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){ - if (num_filled == 0){ - resultline[0]='\0'; - printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); - 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); - break; - } else if (num_filled != 1){ - 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); - } - nresult++; /* Sum of resultlines */ - printf("Result %d: result=%s\n",nresult, resultline); - if(nresult > MAXRESULTLINES){ - printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); - fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); - goto end; - } - decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ - fprintf(ficparo,"result: %s\n",resultline); - 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); - } + num_filled=sscanf(line,"result:%[^\n]\n",resultline); + nresult++; /* Sum of resultlines */ + printf("Result %d: result:%s\n",nresult, resultline); + if(nresult > MAXRESULTLINES){ + 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); + 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); goto end; - break; - default: - nresult=1; - decoderesult(".",nresult ); /* No covariate */ } + if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ + fprintf(ficparo,"result: %s\n",resultline); + fprintf(ficres,"result: %s\n",resultline); + fprintf(ficlog,"result: %s\n",resultline); + } else + goto end; + 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; + 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 */ }while(endishere==0); /* End do */