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Which R packages make good use of S4 classes? I'm looking for packages that use S4 appropriately (i.e. when the complexity of the underlying problem demands), are well written and well documented (so you can read the code and understand what's going on).
I'm interested because I'll be teaching S4 soon and I'd like to point students to good examples in practice so they can read the code to help them learn.
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The S4 system in R is a system for object oriented programing. Confusingly, R has support for at least 3 different systems for object oriented programming: S3, S4 and S5 (also known as reference classes).
Example 2: Creation of S4 object We can check if an object is an S4 object through the function isS4() . The function setClass() returns a generator function. This generator function (usually having same name as the class) can be used to create new objects. It acts as a constructor.
S4 Class is stricter, conventional, and closely related to Object-Oriented concepts. The classes are represented by the formal class definitions of S4. More specifically, S4 has setter and getter functions for methods and generics. As compared to the S3 class, S4 can be able to facilitate multiple dispatches.
The S3 and S4 software in R are two generations implementing functional object-oriented programming. S3 is the original, simpler for initial programming but less general, less formal and less open to validation. The S4 formal methods and classes provide these features but require more programming.
Thinking about this some more, maybe Matrix and/or lme4? Matrix does a lot of trickery with efficient representation of sparse matrices so this may be a worthwhile (though possibly heavy) example.
Else, given that all of BioConductor is done in S4, some of it is bound to be better than average :) I am sure Martin Morgan will pipe in with good examples.
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This doesn't exactly answer your question, but....
timeseries object and then compares it to the S3 representation. It's a very nice illustration (without being overly complex or too simple) of the differences between S3 and S4.ExpressionSet set object. In regards with using the Bioconductor packages, you might find that to fully appreciate the code - or even just to get started - you will have to a reasonable knowledge of biology. I suppose the same applies to complex statistics packages; you need to have a vague idea of what's going on to understand the reasons behind the code structure.
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