Duncan,
I agree completely with "don't use attach"; if I could get all the
users of the survival package to agree as well the problem in question
would go away :-) I'm thinking about ways to add more effective error
surveillance.
Your suggestion was not horribly complex and I'll look into it
further. My first foray failed because what I want (I think) is the
environment that they had when the first ">" came up. I tried baseenv
in a spot, but then my code couldn't find the model.frame function.
Terry T.
On 05/17/2012 05:00 AM, Duncan wrote:
On 12-05-16 4:59 PM, Terry Therneau wrote:
> I've been tracking down a survival problem from R-help today. A short
> version of the primary issue is reconstructed by the following simple
> example:
>
> library(survival)
> attach(lung)
> fit<- coxph(Surv(time, status) ~ log(age))
> predict(fit, newdata=data.frame(abe=45))
>
> Note the typo in the last line of "abe" instead of "age". Instead of an
> error message, this returns predictions for all the subjects since
> model.frame matches "age" by searching more widely. I'd prefer the error.
> I suspect this is hard -- I'd like it to not see the attached lung data
> set, but still be able to find the log function.
> Is there a not-horribly-complex solution?
The best solution is to not use attach(), use data=lung in the fit.
I think if you want to use attach but limit the search, you need
something like
predict(fit, newdata=list2env(data.frame(abe=45), parent=baseenv()))
but I don't think that meets your "not horribly complex" criterion.
Duncan Murdoch
>
> I also tried to change the primary function to lm instead of coxph. It
> has the same problem, but does print a warning that the newdata and
> results have different lengths (which I will incorporate).
>
> Terry T.
>
>
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