R help - Mar 2007 - Over-writing functions from other packages? What is a good strategy??

I am writing a package which uses the Rgraphviz package which in turn uses the
graph package, but my question does not (I believe) pertain specifically to the
these packages so therefore I dare to post the question here:
 
I my package I have a function "edges" which works on some graphs I
have defined. However, there is also a function "edges" (or rather a
generic method) in the graph package (seemingly written in S4). When I load my
package the Rgraphviz package is automatically loaded, but this means that the
edges method of the the graph package "overrides" the edge function in
my package.
 
Is there a way of avoiding this? If there is, I guess that it is a dangerous
path to take? But if so, what else is a good strategy to take?
 
Regards
S?ren

Could you call yours Edges?

On 3/20/07, S?ren H?jsgaard <Soren.Hojsgaard at agrsci.dk>
wrote:
> I am writing a package which uses the Rgraphviz package which in turn uses
the graph package, but my question does not (I believe) pertain specifically to
the these packages so therefore I dare to post the question here:
>
> I my package I have a function "edges" which works on some graphs
I have defined. However, there is also a function "edges" (or rather a
generic method) in the graph package (seemingly written in S4). When I load my
package the Rgraphviz package is automatically loaded, but this means that the
edges method of the the graph package "overrides" the edge function in
my package.
>
> Is there a way of avoiding this? If there is, I guess that it is a
dangerous path to take? But if so, what else is a good strategy to take?
>
> Regards
> S?ren
>
> ______________________________________________
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S?ren H?jsgaard <Soren.Hojsgaard at agrsci.dk> writes:
> I am writing a package which uses the Rgraphviz package which in
> turn uses the graph package, but my question does not (I believe)
> pertain specifically to the these packages so therefore I dare to
> post the question here:
>  
> I my package I have a function "edges" which works on some graphs
I
> have defined. However, there is also a function "edges" (or
rather a
> generic method) in the graph package (seemingly written in S4).
Yes, edges is a generic function defined by the graph package.  With
methods for various graph representation classes.
> I load my package the Rgraphviz package is automatically loaded, but
> this means that the edges method of the the graph package
> "overrides" the edge function in my package.
>  
> Is there a way of avoiding this? If there is, I guess that it is a
> dangerous path to take? But if so, what else is a good strategy to
> take?
I'm pretty sure this is resolved by adding a NAMESPACE file to your
package (see the Writing R Extensions Manual for details).

I made a little test package that has Rgraphviz in Depends, defines an
edges function and exports it in its NAMESPACE file.  When I load this
package, edges is the one from my test package and graph::edges is the
one from graph.

It won't solve your problem in general, but I will also look into
having Rgraphviz only import graph and not Depend on it.  This would
avoid graph::edges polluting the search path when Rgraphviz gets
loaded.  This is a reason that import might be preferred over Depends
for packages that have namespaces.

Finally, if you were depending on graph and not Rgraphviz, then you
could rename graph::edges when you import it in your NAMESPACE file:

  importFrom("graph", someOtherName=edges)

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org

Gabor Grothendieck wrote:
>
> Could you call yours Edges?
>
Is it a good idea to have two different functions, whose name
differs by case sensitivity? I believe this is a shortcut to
Chaos :-)

IMHO, case sensitivity should _only_ be used for aesthetical
purposes, else it may result in errors that are very difficult
to find. Of course, YKMV.[*]

Alberto Monteiro
 
[*] I always use S.I. units :-)

Sometimes but its also easy to forget about simple solutions.

On 3/21/07, Alberto Monteiro <albmont at centroin.com.br>
wrote:
> Gabor Grothendieck wrote:
> >
> > Could you call yours Edges?
> >
> Is it a good idea to have two different functions, whose name
> differs by case sensitivity? I believe this is a shortcut to
> Chaos :-)
>
> IMHO, case sensitivity should _only_ be used for aesthetical
> purposes, else it may result in errors that are very difficult
> to find. Of course, YKMV.[*]
>
> Alberto Monteiro
>
> [*] I always use S.I. units :-)
>
>