[R] accessing source code in R packages

[Spencer Graves]

Dear Prof. Ripley:  Thanks.  This looks like a very useful summary. 
spencer graves

Prof Brian Ripley wrote:

> The original reply was deliberately (I guess) vague. (I've removed the 
> history, as attributions had already been removed, in violation of 
> copyright law. If you cite someone, you MUST credit the author.)
> 
> Sometimes a little knowledge is a dangerous thing, and we have had a 
> number of partially true answers.
> 
> Spreading confusion between the S4 classes of the 'methods' package and 
> the (sometimes called S3) classes of base R is also dangerous.  The R 
> documentation refers to S3 methods and classes unless otherwise stated 
> (and in the methods package documentation).  Please follow that lead.
> 
> On Thu, 22 Sep 2005, Spencer Graves wrote:
> 
>>       Is there general documentation on a procedure to follow to:
>>
>>       (a) Find what methods are available for a particular class of 
>> objects?
> 
> 
> ?methods, unless you mean an S4 class.
> 
> Be careful here: methods `for a particular class' are not all that might 
> be dispatched, as methods for classes the object inherits from may also 
> be used.  Thus "lm" methods may be invoked for "glm" objects, and you 
> may need to call methods() for all the classes the object inherits from.
> 
>>       (b) Find what classes of objects have methods defined for a 
>> partilar
>> generic function?
> 
> 
> ?methods, unless you mean S4 classes (and that help page leads you to the
> right place for those).
> 
>>       (c) Get the code that's actually used?
> 
> 
> getAnywhere() on the asterisked results of (a) or (b).
> 
> For a specific generic and a specific class, getS3method().
> 
> [There is a potential gap here as the "bar" method for class "foo" need 
> not be called foo.bar().  So guessing the name may not work, but 
> getS3method("foo", "bar") will.  AFAIK there are no live examples of this.]
> 
>>       For example, I recently needed to access numbers associated with an
>> object of class "lmer".  Sundar suggested I use with 'getMethod("show",
>> "summary.lmer")'.  However, this doesn't work with the example below.
> 
> 
> (I think that was intended to refer to the default method for princomp, 
> which is not an S4 generic in base R.
> 
>> methods("princomp")
> 
> [1] princomp.default* princomp.formula*
> 
>    Non-visible functions are asterisked
> 
>> getAnywhere("princomp.default")    # works
>> getS3Method("princomp", "default") # works
>> showMethods("princomp")
> 
> 
> Function "princomp":
>  <not a generic function>
> )
> 
> show() is an S4 generic, not an S3 generic.  ?methods points you to how 
> to explore S4 generics.
> 
>> library(lme4)
> 
> ... (and drink some coffee while you wait)
> 
>> methods(show)
> 
> no methods were found
> Warning message:
> function 'show' appears not to be generic in: methods(show)
> 
>> showMethods("show")
> 
> 
> Function "show":
> object = "ANY"
> object = "traceable"
> object = "ObjectsWithPackage"
> object = "MethodDefinition"
> object = "MethodWithNext"
> object = "genericFunction"
> object = "classRepresentation"
> object = "ddenseMatrix"
> object = "Matrix"
> object = "lmer"
> object = "summary.lmer"
> object = "VarCorr"
> object = "sparseMatrix"
> object = "lmList"
> 
>> selectMethod("show", "summary.lmer")
> 
> Method Definition:
> 
> function (object) ...
> 
> Here getMethod() will also work, but selectMethod() is more likely to 
> find `the code that's actually used'.
> 
> 

-- 
Spencer Graves, PhD
Senior Development Engineer
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