R devel - Apr 2013 - Non-vignette sweave file in package

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.

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

To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey

* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
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The views expressed in this message and any annex are purely those of the writer
and may not be regarded as stating an official position of INBO, as long as the
message is not confirmed by a duly signed document.

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
>
> To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say what
the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver
weer en binden het INBO onder geen enkel beding, zolang dit bericht niet
bevestigd is door een geldig ondertekend document.
> The views expressed in this message and any annex are purely those of the
writer and may not be regarded as stating an official position of INBO, as long
as the message is not confirmed by a duly signed document.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel