version 1.215, 2015/12/16 08:52:24
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version 1.216, 2015/12/18 17:32:11
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Line 1
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.216 2015/12/18 17:32:11 brouard |
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Summary: 0.98r4 Warning and status=-2 |
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Version 0.98r4 is now: |
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- displaying an error when status is -1, date of interview unknown and date of death known; |
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- permitting a status -2 when the vital status is unknown at a known date of right truncation. |
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Older changes concerning s=-2, dating from 2005 have been supersed. |
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Revision 1.215 2015/12/16 08:52:24 brouard |
Revision 1.215 2015/12/16 08:52:24 brouard |
Summary: 0.98r4 working |
Summary: 0.98r4 working |
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Line 2446 double func( double *x)
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Line 2454 double func( double *x)
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/* else */ |
/* else */ |
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
/* lli=log(out[s1][s2] - savm[s1][s2]); */ |
/* #endif */ |
/* #endif */ |
lli=log(out[s1][s2] - savm[s1][s2]); |
lli=log(out[s1][s2] - savm[s1][s2]); |
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} else if (s2==-2) { |
} else if ( s2==-1 ) { /* alive */ |
for (j=1,survp=0. ; j<=nlstate; j++) |
for (j=1,survp=0. ; j<=nlstate; j++) |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
/*survp += out[s1][j]; */ |
/*survp += out[s1][j]; */ |
lli= log(survp); |
lli= log(survp); |
} |
} |
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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 += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
lli= log(survp); |
lli= log(survp); |
} |
} |
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else if (s2==-5) { |
else if (s2==-5) { |
for (j=1,survp=0. ; j<=2; j++) |
for (j=1,survp=0. ; j<=2; j++) |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
lli= log(survp); |
lli= log(survp); |
} |
} |
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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 2578 double func( double *x)
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Line 2583 double func( double *x)
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s2=s[mw[mi+1][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
if( s2 > nlstate){ |
if( s2 > nlstate){ |
lli=log(out[s1][s2] - savm[s1][s2]); |
lli=log(out[s1][s2] - savm[s1][s2]); |
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} else if ( s2==-1 ) { /* alive */ |
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for (j=1,survp=0. ; j<=nlstate; j++) |
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survp += out[s1][j]; |
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lli= log(survp); |
}else{ |
}else{ |
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ |
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */ |
} |
} |
Line 2685 double funcone( double *x)
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Line 2694 double funcone( double *x)
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s1=s[mw[mi][i]][i]; |
s1=s[mw[mi][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
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if(s2==-1){ |
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printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); |
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/* exit(1); */ |
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} |
bbh=(double)bh[mi][i]/(double)stepm; |
bbh=(double)bh[mi][i]/(double)stepm; |
/* bias is positive if real duration |
/* bias is positive if real duration |
* is higher than the multiple of stepm and negative otherwise. |
* is higher than the multiple of stepm and negative otherwise. |
*/ |
*/ |
if( s2 > nlstate && (mle <5) ){ /* Jackson */ |
if( s2 > nlstate && (mle <5) ){ /* Jackson */ |
lli=log(out[s1][s2] - savm[s1][s2]); |
lli=log(out[s1][s2] - savm[s1][s2]); |
} else if (s2==-2) { |
} else if ( s2==-1 ) { /* alive */ |
for (j=1,survp=0. ; j<=nlstate; j++) |
for (j=1,survp=0. ; j<=nlstate; j++) |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; |
lli= log(survp); |
lli= log(survp); |
Line 3613 void concatwav(int wav[], int **dh, int
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Line 3626 void concatwav(int wav[], int **dh, int
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mi=0; |
mi=0; |
m=firstpass; |
m=firstpass; |
while(s[m][i] <= nlstate){ /* a live state */ |
while(s[m][i] <= nlstate){ /* a live state */ |
if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) |
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; |
if(m >=lastpass) |
} |
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if(m >=lastpass){ |
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if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ |
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printf("Information! Unknown health 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.\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); |
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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.\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); |
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mw[++mi][i]=m; |
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} |
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if(s[m][i]==-2){ /* Vital status is really unknown */ |
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nbwarn++; |
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if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ |
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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); |
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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.\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); |
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} |
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break; |
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} |
break; |
break; |
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} |
else |
else |
m++; |
m++; |
}/* end while */ |
}/* end while */ |
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/* After last pass */ |
if (s[m][i] > nlstate){ /* In a death state */ |
if (s[m][i] > nlstate){ /* In a death state */ |
mi++; /* Death is another wave */ |
mi++; /* Death is another wave */ |
/* if(mi==0) never been interviewed correctly before death */ |
/* if(mi==0) never been interviewed correctly before death */ |
/* Only death is a correct wave */ |
/* Only death is a correct wave */ |
mw[mi][i]=m; |
mw[mi][i]=m; |
}else if (andc[i] != 9999) { /* A death occured after lastpass */ |
}else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */ |
m++; |
/* m++; */ |
mi++; |
/* mi++; */ |
s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */ |
/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */ |
mw[mi][i]=m; |
/* mw[mi][i]=m; */ |
nbwarn++; |
nberr++; |
if(firstwo==0){ |
if(firstwo==0){ |
printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m); |
printf("Error! Death for individual %ld line=%d occurred %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.\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 ); |
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %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.\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 ); |
firstwo=1; |
firstwo=1; |
} |
}else if(firstwo==1){ |
if(firstwo==1){ |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %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.\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 ); |
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); |
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} |
} |
} |
} |
wav[i]=mi; |
wav[i]=mi; |
Line 6625 int calandcheckages(int imx, int maxwav,
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Line 6654 int calandcheckages(int imx, int maxwav,
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for(m=2; (m<= maxwav); m++) { |
for(m=2; (m<= maxwav); m++) { |
if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
anint[m][i]=9999; |
anint[m][i]=9999; |
s[m][i]=-1; |
if (s[m][i] != -2) /* Keeping initial status of unknown vital status */ |
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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 + 1; |
*nberr = *nberr + 1; |
Line 8784 Please run with mle=-1 to get a correct
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Line 8814 Please run with mle=-1 to get a correct
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if((nberr >0) || (nbwarn>0)){ |
if((nberr >0) || (nbwarn>0)){ |
printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn); |
printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn); |
fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn); |
fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn); |
}else{ |
}else{ |
printf("End of Imach\n"); |
printf("End of Imach\n"); |
fprintf(ficlog,"End of Imach\n"); |
fprintf(ficlog,"End of Imach\n"); |