From jmc at r-project.org  Thu Mar  5 18:08:57 2009
From: jmc at r-project.org (John Chambers)
Date: Thu, 05 Mar 2009 09:08:57 -0800
Subject: [Rd] methods package
In-Reply-To: <200903050115.n251Frjs006726@yacko.mayo.edu>
References: <200903050115.n251Frjs006726@yacko.mayo.edu>
Message-ID: <49B00729.6040008@r-project.org>

Hi Terry,

Terry Therneau wrote:
>   I'm working on the next version of coxme, one step of which is converting
> the bdsmatrix library from Splus to R.  Actually, it is a conversion from
> S4 methods as first described in the Green book to S4 methods as they 
> currently exist.  Mostly it's going ok, but not entirely.
>
>   1. The biggest issue is lack of documentation.  The online help pages have
> not been a help; they keep saying it's "as found in the green book - almost".
> I've looked for the package on CRAN in the hopes for more there, but can't
> find it.  Perchance there is something obvious that I am missing?
>   
Well, one is that there is a 2008 book, "Software for Data Analysis", 
that I wrote partly to describe this and other topics from an R 
perspective.  It's a reference on most pages of documentation related to 
methods (in R version 2.8.1; you should be using that and/or the r-devel 
version if you're revising a package).

John

>   2. The changes are small but numerous.  The current one that has me puzzled
> is a method for addition:
>    setMethod(Ops, signature=c('numeric', 'bdsmatrix'), ....
>
> Let xmat be ordinary and bmat be a bdsmatrix.  In the old code "xmat + bmat"
> fell to this method (which knows what to do), in the current R I get
> failure due to no method found.  is.numeric(xmat) is TRUE.
>    What is the fix?
>
>  3. In the green book the examples used .Dim and .Dimnames slots, the Matrix
> library uses Dim and Dimnames.  Is there a good reason to choose one or the
> other?
>
>   I'll be out of town for the next few days (son's wedding) so instant response
> is not necessary.
>
> 	Terry Therneau
>
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>
>



[Rd] methods package
John Chambers