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, ripley at 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
