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

From: Dan Davison <davison@stats.ox.ac.uk>
To: "Charles C. Berry" <cberry@tajo.ucsd.edu>
Cc: emacs-orgmode <emacs-orgmode@gnu.org>,
	Rainer M Krug <r.m.krug@gmail.com>
Subject: Re: [babel] Writing R-packages the org way?
Date: Fri, 08 Oct 2010 13:10:09 +0100	[thread overview]
Message-ID: <87fwwglwbi.fsf@stats.ox.ac.uk> (raw)
In-Reply-To: <Pine.LNX.4.64.1010071949470.29985@tajo.ucsd.edu> (Charles C. Berry's message of "Thu, 7 Oct 2010 21:29:59 -0700")

Hi Chuck,

I agree about making use of existing ESS tools and that a more
traditional Org approach might be appropriate.

> If you do decide to go all in for a 'one org file makes one package'
> approach, you might try to get Rd language support added, so you can
> edit Rd directly in an Org Src buffer in Rd-mode.

No extra code is needed to get editing support for languages.

#+begin_src XXX

provides an edit buffer in XXX-mode automatically, with no special
customization. Also fontification in the org buffer works automatically
if `org-src-fontify-natively' is set.

Dan

> And get
> org-babel-Rd-evaluate to run Rd-preview-help or call Rd2HTML or
> whatnot.
>
> HTH,
>
> Chuck
>
>> Then, to insert a template, you can use
>>
>> #+call: R-pkg-template(function_name="do.something") :results output org raw
>>
>> which should give something like this:
>>
>> --8<---------------cut here---------------start------------->8---
>> #+results: R-pkg-template(function_name="do.something")
>> * do.something
>> ** Help
>> *** Title
>>    this is do.something title
>> *** Description
>>    do.something does this...
>> *** Usage
>>    do.something(arg1, arg2, ...)
>> *** Arguments
>>    arg1: the first argument
>> *** Examples
>>    do.something(arg1 = x, arg2 = y)
>> ** Definition
>>    begin_src R :tangle R/package.R
>>    do.something <- function(arg1, arg2) {
>>
>>    }
>> --8<---------------cut here---------------end--------------->8---
>>
>> While playing about you may want to get rid of the "raw" directive so
>> that the results will automatically be replaced on repeated evaluations.
>>
>> Dan
>>
>>>
>>>
>>>
>>>>
>>>>>>  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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>
> Charles C. Berry                            (858) 534-2098
>                                             Dept of Family/Preventive Medicine
> E mailto:cberry@tajo.ucsd.edu	            UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>
>
>
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