rstanarm::stan_clogit to estimate the effect of a certain intervention on mortality. In short, our design is a matched risk-set case-control study with 1 case and 5 controls per risk set/stratum. I used
rms::rcs as suggested previously but I’m now struggling a bit with getting conditional effects of the splines.
brms (which has the nice
conditional_effects function) doesn’t support the conditional logistic likelihood, as far as I know, which is why I’m sticking with
rstanarm. It is possible to re-cast the conditional logistic regression as a Cox regression, but that requires defining the strata, and I can’t seem to find out how to do that in
I feel like I’m missing something obvious, but since I’m quite stuck, I wanted to reach out to the community and hopefully get some pointers on moving forwards with this.
So, to continue with the example from my other post:
library(dplyr) library(rstanarm) library(rms) dat <- arrange(infert, stratum) %>% filter(parity <= 2) # yields 1 case and 2 controls per stratum post <- stan_clogit(case ~ rcs(age) + spontaneous + induced, strata = stratum, data = dat, QR = TRUE)
As per the
Drawing from the posterior predictive distribution at interesting values of the predictors also lets us visualize how a manipulation of a predictor affects (a function of) the outcome(s).
All good, but the Details section specifies,
For models estimated with
stan_clogit, the number of successes per stratum is ostensibly fixed by the research design. Thus, when doing posterior prediction with new data, the
data.framepassed to the
newdataargument must contain an outcome variable and a stratifying factor, both with the same name as in the original
data.frame. Then, the posterior predictions will condition on this outcome in the new data.
My question is, then, if I wanted to see how age affects the outcome (e.g. over a grid in [18:45]) for women with
spontaneous = 0 and
induced = 0, how would I go about it? That is, what
newdata should I give the
posterior_predict? Or am I completely off track and need to do something else? I’m running rstanarm v2.18.2.