[Rd] Request: Suggestions for "good teaching" packages, esp. with C code

Sebastian P. Luque spluque at gmail.com
Tue Feb 15 21:26:22 CET 2011

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.


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.


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