Request: Suggestions for "good teaching" packages, esp. with C code
Hi Paul, You might want to post this to the teaching list (R-sig-teaching). I'd look at packages written by old-timers and R Core. I've also found that most Bioconductor packages follow the guidelines you mention and many other excellent habits very well. I agree with you that these are very important things to teach. Seb On Tue, 15 Feb 2011 12:04:42 -0600,
Paul Johnson <pauljohn32 at gmail.com> wrote:
Hello, I am looking for CRAN packages that don't teach bad habits. Can I have suggestions?
I don't mean the recommended packages that come with R, I mean the contributed ones. I've been sampling a lot of examples and am surprised that many ignore seemingly agreed-upon principles of R coding. In r-devel, almost everyone seems to support the "functional programming" theme in Chambers's book on Software For Data Analysis, but when I go look at randomly selected packages, programmers don't follow that advice.
In particular:
1. Functions must avoid "mystery variables from nowhere."
Consider a function's code, it should not be necessary to say "what's variable X?" and go hunting in the commands that lead up to the function call. If X is used in the function, it should be in a named argument, or extracted from one of the named arguments. People who rely on variables floating around in the user's environment are creating hard-to-find bugs.
2. We don't want functions with indirect effects (no <<- ), almost always.
3. Code should be vectorized where possible, C style for loops over vector members should be avoided.
4. We don't want gratuitous use of "return" at the end of functions. Why do people still do that?
5. Neatness counts. Code should look nice! Check out how beautiful the functions in MASS look! I want code with spaces and " <- " rather than everything jammed together with "=".
I don't mean to criticize any particular person's code in raising this point. For teaching exemples, where to focus?
Here's one candidate I've found:
MNP. as far as I can tell, it meets the first 4 requirements. And it has some very clear C code with it as well. I'm only hesitant there because I'm not entirely sure that a package's C code should introduce its own functions for handling vectors and matrices, when some general purpose library might be more desirable. But that's a small point, and clarity and completeness counts a great deal in my opinion.
Seb