[Rd] Best practices in developing package: From a single file

Joris Meys jorismeys at gmail.com
Wed Jan 31 12:33:50 CET 2018

Dear Duncan,

With all respect, but I strongly disagree on your stance regarding roxygen2
for multiple reasons:

1. It is in my humble opinion not correct to evaluate a tool based on the
abuse of some users. It's not because people write packages with bad
documentation, that roxygen2 is to blame. I use roxygen2, and I care a
great deal about documentation. So I actually took a bit offense there.

2. Writing .Rd files directly means that you have to write out the usage
yourself, know the different tags needed for documenting different types of
generics and methods, and so forth. It means a lot more iterations to get
every tag right so that R CMD check does not complain any more. It requires
a more detailed knowledge of the entire Rd tag system compared to letting
roxygen2 do the standard work for you. So one could argue that the extra
knowledge required would actually hinder starting developers to write good
documentation as opposed to help them.

3. given your criticism, I'd like your opinion on where I can improve the
documentation of https://github.com/CenterForStatistics-UGent/pim. I'm
currently busy updating the help files for a next release on CRAN, so your
input is more than welcome.

I'm not going to force anyone to use roxygen2. But I personally find it
easier to have the function right below the documentation, so that any
change to the function can immediately be documented as well. You prefer to
do this by keeping that strictly separated, which is absolutely fine. It's
just not my prefered workflow. Different animal, different habits I guess.

On a sidenote: I had a lot of complaints about earlier iterations of
roxygen2 and the many changes to tags and their meanings, but the roxygen2
package matured in the meantime and has been a stable and reliable tool for
me the past years.

Kind regards

On Tue, Jan 30, 2018 at 8:53 PM, Duncan Murdoch <murdoch.duncan at gmail.com>

> On 30/01/2018 11:29 AM, Brian G. Peterson wrote:
>> On Tue, 2018-01-30 at 17:00 +0100, Suzen, Mehmet wrote:
>>> Dear R developers,
>>> I am wondering what are the best practices for developing an R
>>> package. I am aware of Hadley Wickham's best practice
>>> documentation/book (http://r-pkgs.had.co.nz/).  I recall a couple of
>>> years ago there were some tools for generating a package out of a
>>> single file, such as using package.skeleton, but no auto-generated
>>> documentation. Do you know a way to generate documentation and a
>>> package out of single R source file, or from an environment?
>> Mehmet,
>> This list is for development of the R language itself and closely
>> related tools.  There is a separate list, R-pkg-devel, for development
>> of packages.
>> Since you're here, I'll try to answer your question.
>> package.skeleton can create a package from all the R functions in a
>> specified environment.  So if you load all the functions that you want
>> in your new package into your R environment, then call
>> package.skeleton, you'll have a starting point.
>> At that point, I would probably recommend moving to RStudio, and using
>> RStudio to generate markdown comments for roxygen for all your newly
>> created function files.  Then you could finish off the documentation by
>> writing it in these roxygen skeletons or copying and pasting from
>> comments in your original code files.
> I'd agree about moving to RStudio, but I think Roxygen is the wrong
> approach for documentation.  package.skeleton() will have done the boring
> mechanical part of setting up your .Rd files; all you have to do is edit
> some content into them.  (Use prompt() to add a new file if you add a new
> function later, don't run package.skeleton() again.)
> This isn't the fashionable point of view, but I think it is easier to get
> good documentation that way than using Roxygen.  (It's easier to get bad
> documentation using Roxygen, but who wants that?)
> The reason I think this is that good documentation requires work and
> thought.  You need to think about the markup that will get your point
> across, you need to think about putting together good examples, etc.
> This is *harder* in Roxygen than if you are writing Rd files, because
> Roxygen is a thin front end to produce Rd files from comments in your .R
> files.  To get good stuff in the help page, you need just as much work as
> in writing the .Rd file directly, but then you need to add another layer on
> top to put in in a comment.  Most people don't bother.
> I don't know any packages with what I'd consider to be good documentation
> that use Roxygen.  It's just too easy to write minimal documentation that
> passes checks, so Roxygen users don't keep refining it.
> (There are plenty of examples of packages that write bad documentation
> directly to .Rd as well.  I just don't know of examples of packages with
> good documentation that use Roxygen.)
> Based on my criticism last week of git and Github, I expect to be called a
> grumpy old man for holding this point of view.  I'd actually like to be
> proven wrong.  So to anyone who disagrees with me:  rather than just
> calling me names, how about some examples of Roxygen-using packages that
> have good help pages with good explanations, and good examples in them?
> Back to Mehmet's question:  I think Hadley's book is pretty good, and I'd
> recommend most of it, just not the Roxygen part.
> Duncan Murdoch
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Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)

Biowiskundedagen 2017-2018

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