[BioC] formal methods and classes and capitalization conventions

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Wed Mar 26 08:43:39 MET 2003

> I'd like to raise the issue of a capitalization convention for naming
> objects in R. Almost everything in R used to be lowercase but recently
> there is increasing use of mixed upper/lower case to define names. There is
> potential for using the capitalizations to make code more self explanatory,
> but only if a consistent system is used.

Another discussion of this issue is in Henrik Bengtsson's contribution
to the DSC-2003.  He describes some rules and tools that optionally
enforce such conventions.  To find it, just Google DSC-2003 and go to
working papers/drafts.

I don't feel a strong need for such a convention at present, but voluntary
adoption of such a convention can be supported if we post a "voluntary
coding convention" document somewhere on the site.  If it turns out
that this is a valuable set of rules, and software tools that aid
in achieving compliance are available, then we might consider using this
convention for package evaluation and maintenance.

Examples of productivity benefits or references on this would be
of interest.  One alternative perspective is that a universal
convention is not necessary, but consistent coding practices within
packages can be encouraged.  The author can state his/her own convention
explicitly for the package.

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