From murdoch.duncan at gmail.com  Thu Apr  4 19:04:04 2013
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Thu, 04 Apr 2013 13:04:04 -0400
Subject: [Rd] Non-vignette sweave file in package
In-Reply-To: <AA818EAD2576BC488B4F623941DA7427C28B09B5@inbomail.inbo.be>
References: <AA818EAD2576BC488B4F623941DA7427C28B09B5@inbomail.inbo.be>
Message-ID: <515DB284.8030000@gmail.com>

On 04/04/2013 10:55 AM, ONKELINX, Thierry wrote:
> Dear all,
>
> I'm documenting an elaborate analysis as a private package. The package writes all required output to a database. I use a Sweave file to transform all the results from the database into a report.
>
> Now I would like to add this Sweave to my package. I'm a bit puzzled on how to do that. It is not a vignette: the data is not available when the package is build and I need to recompile the Sweave file on demand (after the analysis was run).
>
> So I have two questions.
> 1) Where to put a non-vignette Sweave file in a package.
> 2) How do I compile that Sweave file.

1) You can put it anywhere you like in the inst directory, but "doc" 
might make sense (if it doesn't trigger warnings about a badly formed 
vignette, I haven't checked).  When installed, it moves up one level.  
So ".../inst/doc/mydoc.Rnw"
will be retrievable as system.file("doc/mydoc.Rnw", package="mypkg").

2) Use Sweave() and tools::texi2pdf().  You might want to write your own 
function that calls those, after saving the data in the appropriate place.

Duncan Murdoch

>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
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> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
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> ~ John Tukey
>
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[Rd] Non-vignette sweave file in package
Duncan Murdoch