[R] Surv object in data.frame and Design package

[Thomas Lumley]

On Thu, 16 Mar 2006, Heinz Tuechler wrote:

> Dear All,
>
> there seems to be some strange influence of the Design package on
> data.frame. If I build a data.frame containing a Surv object without
> loading the package Design, the data frame is usable to coxph. If instead I
> just load Design and build a data.frame afterwards, the naming of the Surv
> object is different and it does not work with coxph.
> (In my real application I loaded Design to use the ie.setup function.)
> Even if I detach Design I cannot build a data.frame as before loading
> Design. If I include the Surv object with the I() function it seems to
> work, but then there appeare the problems discussed in the posting from
> yesterday "Surv object in data.frame".
> The problem is solvable, but I was surprised of the unexpected
> difficulties, especially that detaching Design did not solve the problem.
>
> Is it wrong to expect that R works after detaching a package as before
> loading it?

It's not as strange as all that. The Design package requires the Hmisc 
package, which you did not detach.  Hmisc contains an implementation of 
as.data.frame.Surv that doesn't work with data.frame()

Unfortunately the Hmisc implementation overrides the survival one, 
irrespective of the order in which the packages are loaded (at least from 
the viewpoint of getS3method()).

For code internal to the survival package the namespace system ensures 
that survival:::as.data.frame.Surv is called, but data.frame() is not part 
of the survival package and sees the Hmisc version.

I would have expected that S3 methods registered in NAMESPACE would 
override those based on the function name, but it seems to be the other 
way around.


Also, when you detached "Design" you also detached "survival". If "Design" 
rather than "Hmisc" had been the source of the problem this still wouldn't 
have worked as no as.data.frame method for Surv objects would have been 
available.


 	-thomas