Hello,
I am apparently confused about the use of an id parameter for an event
history/survival model, and why the EHA documentation for aftreg does
not specify one. All assistance and insights are appreciated.
Attempting to specifiy an id variable with the documentation example
generates an "overlapping intervals" error, so I sorted the original
mort dataframe and set subsequent entry times an id to the previous
exit time + 0.0001. This allowed me to see the affect of the id
parameter on the coefficients and significance tests, and prompted my
question. The code I used is shown below, with the results at the
bottom. Thanks in advance!
Mike
head(mort) ## data clearly contains multiple entries for some of the
dataframe ids
no.id.aft <- aftreg(Surv(enter, exit, event) ~ ses, data = mort) ##
Inital model
id.aft <- aftreg(Surv(enter, exit, event) ~ ses, data = mort, id=id)
## overlapping intervals error
mort.sort <- ## ensure records ordered
mort[
order(mort$id, mort$enter),]
## remove overlap
for (i in 2:nrow(mort.sort)){
if (mort.sort[i,'id'] == mort.sort[i-1,'id'])
mort.sort[i,'enter'] <- mort.sort[i-1, 'exit'] + 0.0001
}
no.id.aft.sort <- aftreg(Surv(enter, exit, event) ~ ses, data =
mort.sort) ## initial model on modified df
id.aft.sort <- aftreg(Surv(enter, exit, event) ~ ses, id=id, data =
mort.sort) ## with id parameter
#=== output ===========#
> no.id.aft.sort
Call:
aftreg(formula = Surv(enter, exit, event) ~ ses, data = mort.sort)
Covariate W.mean Coef Exp(Coef) se(Coef) Wald p
ses
lower 0.416 0 1 (reference)
upper 0.584 -0.347 0.707 0.089 0.000
log(scale) 3.603 36.704 0.065 0.000
log(shape) 0.331 1.393 0.058 0.000
Events 276
Total time at risk 17045
Max. log. likelihood -1391.4
LR test statistic 16.1
Degrees of freedom 1
Overall p-value 6.04394e-05
> id.aft.sort
Call:
aftreg(formula = Surv(enter, exit, event) ~ ses, data = mort.sort,
id = id)
Covariate W.mean Coef Exp(Coef) se(Coef) Wald p
ses
lower 0.416 0 1 (reference)
upper 0.584 -0.364 0.695 0.090 0.000
log(scale) 3.588 36.171 0.065 0.000
log(shape) 0.338 1.402 0.058 0.000
Events 276
Total time at risk 17045
Max. log. likelihood -1390.8
LR test statistic 17.2
Degrees of freedom 1
Overall p-value 3.3091e-05
>
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