Re: [babel] Writing R-packages the org way?

From: Rainer M Krug <r.m.krug@gmail.com>
To: Erik Iverson <eriki@ccbr.umn.edu>
Cc: Dan Davison <davison@stats.ox.ac.uk>,
	emacs-orgmode <emacs-orgmode@gnu.org>
Subject: Re: [babel] Writing R-packages the org way?
Date: Thu, 7 Oct 2010 18:04:25 +0200	[thread overview]
Message-ID: <AANLkTimW4hmahYhfGJYT6bOM+zYb_sR88b1a6qQT4kSN@mail.gmail.com> (raw)
In-Reply-To: <4CADE357.1090803@ccbr.umn.edu>

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On Thu, Oct 7, 2010 at 5:12 PM, Erik Iverson <eriki@ccbr.umn.edu> wrote:

>
> Dan Davison wrote:
>
>> Erik Iverson <eriki@ccbr.umn.edu> writes:
>>
>>  Rainer M Krug wrote:
>>>
>>>> Hi
>>>>
>>>> I am about to write an R package, and as I am an org-mode and
>>>> org-babel user, I would (obviously) like to use org-mode for that.
>>>>
>>>> Is there a recommended way of writing an R package in org-babel, or
>>>> do I have effectively wrap the R code for the documentation
>>>> etc. into source blocks in babel?
>>>>
>>> That's what I do.  I've looked into converting an org-file to
>>> Roxygen or Rd markup, but never got very far.  My idea at the time
>>> was to do something like:
>>>
>>> * function1
>>> ** Help
>>> *** Title
>>>    this is function 1 title
>>> *** Description
>>>    function1 does this...
>>> *** Usage
>>>    function1(arg1, arg2, ...)
>>> *** Arguments
>>>    arg1: the first argument
>>> *** Examples
>>>    function1(arg1 = x, arg2 = y)
>>> **Definition
>>>    begin_src R :tangle R/package.R
>>>    function1 <- function(arg1, arg2) {
>>>
>>>    }
>>>
>>>
I like the idea of a kind of template, which takes the function name as a
parameter and expands it to the above described structure, but also
including one section for tests.
That would definitely be a starting point from which one could look into the
"problem" of the .Rd files. As I am not an emacs / elisp expert, how could
that be done (the template)?

>
>>>  Any suggestions how to best proceed?
>>>>
>>>> Dream: I would like to have one org file which contains everything
>>>> (documentation, code, other relevant files) and if I export or
>>>> tangle the file, I have the package ready.
>>>>
>>> Well, that functionality is essentially present with code blocks
>>> and tangling, except the documentation part.
>>>
>>
Exactly - and that is the part I would like to have.

>
>> Hi Erik,
>>
>> Would you mind expanding on that -- what are we missing for the
>> documentation part?
>>
>>
> Dan, by "except for the documentation part", I meant generating
> .Rd files (the LaTeX-like syntax) automatically from some org-syntax
> that does *not* depend on code blocks.  I.e., it would be cool to
> specify syntax like I have above for documentation.  Using org-mode
> headlines for each section like Description, Usage, Arguments, etc.
>
> Just like exporting to LaTeX generates sections, some process would
> use these headlines to generate the .Rd sections.
>
> That way, you don't have to use the .Rd syntax yourself.  No big deal,
> just a convenience feature.  I don't know how you'd specify to org-mode
> that a particular subtree was to generate .Rd syntax, and I don't know
> if it would be on export or tangling.
>
> An alternative is simply just to use code blocks of type Rd within
> org-mode and then tangle to .Rd files.  That's what I currently do.
>
> Hope that explains it,
> Erik
>
>
>  Dan
>>
>

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