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

From: Dan Davison
Subject: [Orgmode] Re: [babel] Writing R-packages the org way?
Date: Thu, 07 Oct 2010 16:59:33 +0100
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.0.50 (gnu/linux)

Erik Iverson <address@hidden> writes:

> Dan Davison wrote:
>> Erik Iverson <address@hidden> 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) {
>>>     }
>>>> 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.
>> 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,

Yes perfectly, thanks. I had only thought of the solution you mention
involving writing Rd explicitly; I hadn't thought of Rd as an export

Well, anyone who wants to put Bastien's new export machinery to the
test, I'll have a texinfo and an Rd backend please.



> Erik > Dan
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