[TxMt] R, Sweave, markdown

Charilaos Skiadas cskiadas at gmail.com
Tue Apr 29 23:40:21 UTC 2008

On Apr 29, 2008, at 9:59 AM, baptiste auguie wrote:

> Hi again,
> I'm not very familiar with Sweave, but I was under the impression  
> that the principle of it –– actually, as a special case of noweb  
> files ––, would allow one to define new drivers without worrying  
> about the parsing. There is a LaTeX one, an HTML one, and I think  
> an OpenOffice thing one.
> I think the function Rtangle would extract and execute the R chunks  
> in any source file, it it then a matter of integrating the output  
> to the Markdown syntax.
> Maybe this is actually more a question to ask on the R-mailing list.

It certainly is possible to use Sweave with something other than  
LaTeX, but someone would have to write the driver. On the other hand,  
writing in Markdown with <<...>> .... @ blocks for the R and figure  
code should work just fine, you then just:
1) Run the file through MultiMarkdownToLaTeX to get a LaTeX file with  
these blocks still there. The tricky part here is getting  
MultimarkdownToLaTeX to not touch the <...>...@ blocks, though that  
should be doable I think. Perhaps someone more familiar with the  
script can tell us how to do that (I believe it would amount to  
adding some XSLT transformations?)
2) Pass the resulting LaTeX file through the standard Sweave process,  
to get a pdf
3) There's no step 3.

Of course, if you want something like an HTML output, that's another  
story, though shouldn't be too bad. Perhaps one can have a look at  
how the R help files (I believe they have a .Rd format) get converted  
to HTML help pages.
Also it would be nice to have the equivalent of \Sexpr{...}. Probably  
amounts to just another XSLT transformation.

Just some thoughts
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

> cheers,
> baptiste
> --- En date de : Lun 28.4.08, Hans-Jörg Bibiko <bibiko at eva.mpg.de>  
> a écrit :
>> De: Hans-Jörg Bibiko <bibiko at eva.mpg.de>
>> Objet: Re: [TxMt] R, Sweave, markdown
>> À: "TextMate users" <textmate at lists.macromates.com>
>> Cc: bapt_4510 at yahoo.fr
>> Date: Lundi 28 Avril 2008, 3h53
>> In principal it won't be such a big deal to write such a
>> parser. But
>> the problems will appear in the details. One has to create
>> a kind of
>> meta syntax - processing statements - for all these R
>> chunks. E.g.
>> @RCODE quiet@
>> a <- matrix(c(1,2,3,4,5,6), nrow=2 byrow=T)
>> @/RCODE@
>> foo foo
>> @RCODE insertAsTable noCommandLine@
>> print(a*2)
>> @/RCODE@
>> etc.
>> But this would be mean to reinvent the wheel twice in some
>> sense.
>> Markdown to LaText and Sweave for LaTeX works fine.
>> On the other hand I use quite often the R bundle command
>> 'Execute
>> Selection/Document in R and' > 'Insert
>> Result' for such things.
>> Of course, to have such a pre-parser for expanding R code
>> chunks and
>> insert the result depending on the current language (HTML,
>> LaTeX,
>> Markdown, Plain Text) would be nice.
>> --Hans

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