[Rd] methods/namespaces/possible bug

[Kasper Daniel Hansen]

On Jul 15, 2008, at 12:00 PM, Duncan Murdoch wrote:

> 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.

Let me just state that if I do

plot(sin)

plot.function gets called. This looks to me (as a somewhat experienced  
R user) as a clear case of method dispatching. I call something that I  
think most of us think of as a generic, with a function argument and I  
cannot see that possibility when I do a methods("plot"). This use case  
is not entirely far out - I have just been teaching and wanted to show  
how I could see what happened when I called plot on sin and lo and  
behold, plot.function is not in the list of methods("plot")

I can see that there is special code in plot for handling dispatching  
on a function. I can see that is it handled differently (ie. not with  
a call to UseMethod) but from my point of view, the call
   plot(sin)
looks and feels like methods dispatching. I would say plot is a generic.

Finally the help page for plot.function states
## S3 method for class 'function':
      plot(x, y = 0, to = 1, from = y, xlim = NULL, ...)

So I think something should be cleaned up here.

Kasper

> 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
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