From benjamin.hofner at fau.de  Mon Aug 26 17:20:10 2013
From: benjamin.hofner at fau.de (Benjamin Hofner)
Date: Mon, 26 Aug 2013 17:20:10 +0200
Subject: [Rd] legitimate use of :::
In-Reply-To: <521B6A8A.7040307@gmail.com>
References: <mailman.25.1377252007.21998.r-devel@r-project.org>
	<521B4F6C.3090101@imbe.med.uni-erlangen.de>
	<521B6A8A.7040307@gmail.com>
Message-ID: <521B722A.5050702@fau.de>

Dear Duncan,

thank you for the quick reply.

Am 26.08.2013 16:47, schrieb Duncan Murdoch:
> On 26/08/2013 8:51 AM, Benjamin Hofner wrote:
>> Hi,
>>
>> related to this important discussion I have several questions:
>>
>> What can I do to explicitly state that I want to use a certain,
>> *non-exported* generic function? The function I am currently talking of
>> is predict.smooth.spline from package stats. As I want to make shure
>> that *this* function is used I currently call
>> stats:::predict.smooth.spline() in my code, which now triggers a NOTE on
>> CRAN. Strange enough predict.smooth.spline even has a manual page but is
>> not exported (as is true for many other generic functions as well).
>
> Actually the standard name is that predict() is a generic function,
> predict.smooth.spline() is a method, but it's a good question.  Can you
> describe why you want to call that method on something that isn't a
> smooth.spline object?

Actually the object is a smooth.spline object but with additional 
attributes and more classes, i.e.,

class(mod)
[1] "opm_model"           "smooth.spline_model" "smooth.spline"

Now I have a specialized predict function predict.smooth.spline_model 
which in turn calls predict.smooth.spline.

I just tried to use NextMethod(generic = "predict", object, ...) and it 
seems to work. So this seems to be the desired solution. I tried this 
earlier and got error messages, perhaps because I omitted the argument 
generic. I guess the function then was confused what the generic is 
(predict or predict.smooth).

>>
>> Is it advisable to specify (S3) methods without exporting them? How can
>> I access exactly this function without using :::? And/or shouldn't we (R
>> Core in this instance but others - including myself) export all methods
>> (especially if a manual exists anyway)?
>
> The general reason for hiding methods is that it allows the author of
> the package to change the internal implementation of the class without
> worrying that it will break code that uses the method, i.e. it will stop
> usages such as yours.  So you need to explain why you are doing what you
> are doing.

I see no difference in these two ways to call the next generic function: 
In both cases I can (and do) specify further arguments, namely x for new 
data and deriv = 0. Thus in both cases I rely on the interface in the 
same way. I do not see any bonus for the package maintainer (both of the 
depending and dependent package). The interface stays the same and the 
class could change in both situations. Isn't a method always relying on 
the current implementation of a class? And isn't anything else more than 
unwanted? So again? Why hiding a method? The only reason I see is that 
one doesn't want to document the function properly.

>
>
>> A related question concerns the function stats:::n.knots. I want to use
>> this function to compute the number of knots for a spline (not
>> necessarily a smoothing spline as defined by smooth.spline were it is
>> originally used). The source of the function even states as a comment:
>> "## Namespace-hidden but at least available to programmeRs:" So I guess
>> this function can be considered to be stable and usable. Would it then
>> be possible for R Core to export this function?

Do I need to file a formal request for this issue?

>>
>> Finally, if one needs to copy a function (perhaps with minor
>> modifications), how does one properly state the authorship of the code
>> that one copies? Are there any guidelines, rules, ...? Is it sufficient
>> for small functions to state the original authorship as a comment in the
>> source? Is it necessary to state the authorship in the manual? Or is it
>> even required to state the quthorship in the DESCRITPION? I already did
>> an extensive search of the R-devel mailing list but couldn't find an
>> appropriate answer. And after all I do not want to spend hours and hours
>> thinking about licenses, authorship etc. but I want to produce nice and
>> usable code (but also want to mention the original authors
>> appropriately)!
>
> I would say that you should certainly state it in the man page, and have
> something in the DESCRIPTION file as well.  It might be something like
>
> Author:  Duncan Murdoch, with code from others (see the man pages)
>
> However, I just looked at rgl (a package I maintain), and I see we
> didn't do that.  We have a separate README file listing other credits.

This is a good solution. Do I need to specify the original License etc? 
And what about a helper function such as stats:::n.knots? This will not 
appear in the manual of my package. Is it sufficient in this case to 
document the authorship in the source (and perhaps a README as you 
suggested)?

>
> Duncan Murdoch
>
>>
>> Happy to learn more and read your thoughts and ideas about these issues.
>>
>> All the best,
>> Benjamin
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Benjamin



[Rd] legitimate use of :::
Benjamin Hofner