From therneau at mayo.edu  Fri Nov 25 15:10:52 2011
From: therneau at mayo.edu (Terry Therneau)
Date: Fri, 25 Nov 2011 08:10:52 -0600
Subject: [Rd] How to deal with package conflicts
In-Reply-To: <mailman.21.1322218808.15358.r-devel@r-project.org>
References: <mailman.21.1322218808.15358.r-devel@r-project.org>
Message-ID: <1322230252.5806.15.camel@nemo>

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-request at 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
>



[Rd] How to deal with package conflicts
Terry Therneau