Suzen, Mehmet
2018-Jan-30 16:00 UTC
[Rd] Best practices in developing package: From a single file
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? Many thanks, Mehmet
Brian G. Peterson
2018-Jan-30 16:29 UTC
[Rd] Best practices in developing package: From a single file
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. Please address further discussion to the R-pkg-devel list. Regards, Brian
Duncan Murdoch
2018-Jan-30 19:53 UTC
[Rd] Best practices in developing package: From a single file
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
Suzen, Mehmet
2018-Jan-30 22:32 UTC
[Rd] Best practices in developing package: From a single file
Dear All, Thank you for all valuable input and sorry for the off-topic for the list. I will try R-pkg-devel for further related questions. I was actually after "one-go" auto-documentation in-line or out of comments from a single file/environment in a similar spirit to 'package.skeleton or an extension of it. My take-home message or summary from all responses do far. * Regarding documentation;Duncan Murdoch's wisdom "...to get good stuff in the help page, you need just as much work as in writing the .Rd file directly..". So there is no silver bullet in terms of auto-documentation, I gather, especially for considering if one uses more complex constructs, S4/S6 classes or Rcpp code behind.On the other hand, roxgen2 being the most comprehensive solution. * Lightweight solution to try out before moving to RStudio fully. I will give a try Dirk's 'pkgKitten' and 'inlinedocs' Malcolm mentioned. Interestingly, responses have reminded me Larry Wall's quote (https://en.wikipedia.org/wiki/There%27s_more_than_one_way_to_do_it), which I think really applies to R more than any language I encounter so far, from different class systems to different time-series representations, so richly democratised. Many regards, Mehmet On 30 January 2018 at 17:00, Suzen, Mehmet <mehmet.suzen at gmail.com> 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? > > Many thanks, > Mehmet
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