> I want use survfit() and basehaz() inside a function, but it doesn't
> work. Could you take a look at this problem. Thanks for your help.
Your problem has to do with environments, and these lines
fmla <- as.formula("Surv(time, event) ~ Z1 + Z2")
BaseFun <- function(x){
start.coxph <- coxph(x, phmmd)
...
survfit(start.coxph)
}
Basefun(fmla)
The survfit routine needs to reconstruct the model matrix, and by
default in R this is done in the context where the model formula was
first defined. Unfortunately this is outside the function, leading to
problems -- your argument "x" is is unknown in the outer envirnoment.
The solution is to add "model=TRUE" to the coxph call so that the model
frame is saved and survfit doesn't have to do reconstruction.
If you think this should work as is, well, so do I. I spent a lot of
time on this issue a few months ago and finally threw in the towel. The
interaction of environments with model.frame and model.matrix is subtle
and far from obvious. (Just to be clear: I didn't say "broken". Each
aspect of the process has well thought out reasons.) The standard
modeling functions lm, glm, etc changed their defaults from model=F to
model=T at some point. This costs some space & memory, but coxph may
need to do the same.
Terry T
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