The ridge() function was put into the survival package as a simple
example of what a user could do with penalized functions. It's not a
"serious" function, and I'd be open to any suggestions for change.
Actually, for any L2 penalty + Cox model one is now better off using
coxme as the maximization process is much better thought out there. I'd
be happy to remove ridge from survival -- except that there are bound to
be lots of folks using the function and any such changes (even good
ones) to the survival package are fraught with peril.
Duncan: this raises a larger point. I've often wished that I could have
"namespace" like rules apply to formulas. Using survival again, when I
implemented gam-like smooths I had to create "pspline" rather than use
the more natural "s()" notation. In survival, it would be good to do
this for ridge, cluster, pspline, and frailty; all of whom depend deeply
on a coxph context. It would also solve a frailty() problem of long
standing, that when used in survreg only a subset of the frailty options
make sense; this is documented in the help file but catches users again
and again.
Terry Therneau
On Fri, 2011-11-25 at 12:00 +0100, r-devel-requ...@r-project.org wrote:
> > In my genridge package, I define a function ridge() for ridge
> > regression, creating objects of class 'ridge'
> > that I intend to enhance.
> >
> > In a documentation example, I want to use some functions from the
> car
> > package. However, that package
> > requires survival, which also includes a ridge() function, for coxph
> > models. So, once I require(car)
> > my ridge() function is masked, which means I have to use the awkward
> > form below in my .Rd files.
> >
> > ridgemod<- genridge::ridge(...)
> >
> > I tried to detach survival, but that doesn't work:
> >
> > > detach("package:survival")
> > Error: package ?survival? is required by ?car? so will not be
> detached
> >
> > I don't see any solution to this, other than
> > (a) renaming my ridge() to something else -- don't want to do this
> > (b) use \dontrun{} for the examples that use car
> >
> > Or, is there some other way?
>
> Not really. I'd say the renaming is the preferred way to go, but you
> might also be able to convince Terry Therneau (survival author) to
> make
> ridge() a generic, so your method is called for your objects, and his
> is
> called for others.
>
> Duncan Murdoch
>
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