methods/namespaces/possible bug

On 7/15/2008 2:11 PM, Kasper Daniel Hansen wrote:

Using

methods("plot")

 [1] plot.Date*          plot.HoltWinters*   plot.POSIXct*
 [4] plot.POSIXlt*       plot.TukeyHSD       plot.acf*
 [7] plot.data.frame*    plot.decomposed.ts* plot.default
[10] plot.dendrogram*    plot.density        plot.ecdf
[13] plot.factor*        plot.formula*       plot.hclust*
[16] plot.histogram*     plot.isoreg*        plot.lm
[19] plot.medpolish*     plot.mlm            plot.ppr*
[22] plot.prcomp*        plot.princomp*      plot.profile.nls*
[25] plot.spec           plot.spec.coherency plot.spec.phase
[28] plot.stepfun        plot.stl*           plot.table*
[31] plot.ts             plot.tskernel*
   Non-visible functions are asterisked
I don't see plot.function listed. As I read the man page for  
methods I  would say that the search is just looking for functions  
with the right  type of name.

In a package with a NAMESPACE (like the graphics package, where  
plot.function lives), a function needs to be declared to be an  
S3method to show up in this list.  plot.function is not declared as  
an S3 method.

I don't know the reason for this, but I assume it's intentional:   
take a look at the plot() generic:  it has special case code to  
handle functions.

So if this is a bug, I think it's a documentation bug in the ? 
plot.function man page, where plot.function should be documented to  
act a lot like an S3 method, but not identically like one:  notice  
the special handling of the y axis label.

If I define a plot.function in my global workspace,  
methods("plot")  picks it up

plot.function = function() {print("blah")}
methods("plot")

 [1] plot.Date*          plot.HoltWinters*   plot.POSIXct*
 [4] plot.POSIXlt*       plot.TukeyHSD       plot.acf*
 [7] plot.data.frame*    plot.decomposed.ts* plot.default
[10] plot.dendrogram*    plot.density        plot.ecdf
[13] plot.factor*        plot.formula*       plot.function
[16] plot.hclust*        plot.histogram*     plot.isoreg*
[19] plot.lm             plot.medpolish*     plot.mlm
[22] plot.ppr*           plot.prcomp*        plot.princomp*
[25] plot.profile.nls*   plot.spec           plot.spec.coherency
[28] plot.spec.phase     plot.stepfun        plot.stl*
[31] plot.table*         plot.ts             plot.tskernel*

Functions declared in the global workspace are handled by patterns  
on the name, since you can't declare things there:  there's no  
NAMESPACE file.

   Non-visible functions are asterisked
Based on this, I think that methods("plot") should return   
plot.function, so I am almost ready to take the bug word in my mouth.
When I debug the methods function it gets to the line
  S3reg <- ls(get(".__S3MethodsTable__.", envir = defenv), pattern  
=  name)
where it searches the .__S3MethodsTable__. object. Consulting the  
help  page it seems that this object is part of the namespace  
functionality.
My guess is that something goes wrong because function is a  
reserved  word?

I don't think so.

Duncan Murdoch
	

Kasper
This has been tested under R-2.7.1 on Mac OS X and under a not too   
recent version of R-devel under x86_64. My sessionInfo for the Mac   
version is

sessionInfo()

R version 2.7.1 (2008-06-23)
i386-apple-darwin8.10.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
loaded via a namespace (and not attached):
[1] tools_2.7.1