Brian,
So let me ask an r-core opinion. Should I change the default to model=TRUE? Survival
is heavily used and there is something to be said for consistency within the central
packages. Sometimes old habits die hard, and there is a "save memory" part of me that
hates to save a large object that likely won't be used. Not nearly as relevant today as
when I started my career.
I agree that the biggest issue with model=FALSE is when someone asks for predictions
from a saved fit, perhaps saved weeks ago, and the data has changed under our feet. I
have a check in predict.coxph that the number of rows in the data hasn't changed, but
there really is no defense.
Aside: This would mean in theory that I could also change the default to y= FALSE. I
discovered a few years ago that that won't fly, when I set the default for y to "not
model"; why keep redundant copies? Several other packages that depend on survival failed.
They assume fit$y is there, without checking. The iron chains of backwards compatability...
>1. The key line, in both model.frame.coxph and model.frame.lm is
> eval(fcall, env, parent.frame())
>
>and it appear (at least to me) that the parent.frame() part of this is
>effectively ignored when fcall is itself a reference to model.frame.
>I'd like to understand this better.
Way back (ca R 1.2.0) an advocate of lexical scoping changed
model.frame.lm to refer to an environment not a data frame for 'env'.
That pretty fundamental change means that your sort of example is not a
recommended way to do this: you are mixing scoping models.
This hasn't left me any wiser. Can you expand? As stated in another note the
real issue was
fit <- coxph(formula, data=nd)
predict(fit, type="expected")
within a user's function. They, not unreasonably, expected it to work without further
trickery. It fails because the model.frame call within predict.coxph cannot find "nd".
>2. The modeling functions coxph and survreg in the survival default to
>model=FALSE, originally in mimicry of lm and glm; I don't know when R
> changed the default to model=TRUE for lm and glm. One possible response
I am not sure R ever did: model = TRUE was the default 16 years ago at
the beginning of the CVS/SVN archive.
-- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics,
http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861
(self) 1
South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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