[R] Reproducible research

[Rainer M Krug]

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On 09/09/10 07:47, David Scott wrote:
>  I am investigating some approaches to reproducible research. I need in
> the end to produce .html or .doc or .docx. I have used hwriter in the
> past but have had some problems with verbatim output from  R. Tables are
> also not particularly convenient.
> 
> I am interested in R2HTML and R2wd in particular, and possibly odfWeave.
> 
> Does anyone have sample documents using any of these approaches which
> they could let me have?

Hi David

I am using emacs + org-mode (http://orgmode.org/) for exactly this (see
http://orgmode.org/worg/org-contrib/babel/intro.php#reproducable-research for
an example for Reproducible research
andhttp://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php
about R in emacs + org-mode + ESS.

It is literate programming at its best.

Concerning reproducible research and report generating, org-babel has
one HUGE advantage: you an combine different programming languages
easily in the report - so e.g. you can do your analysis in R, do some
data preparation in python, and some final file manipulations in bash -
and everything is in one file and reproducible (see
http://orgmode.org/worg/org-contrib/babel/intro.php#meta-programming-language
and
http://orgmode.org/worg/org-contrib/babel/examples/data-collection-analysis.php).

I think that would be the best tool for the job (see
http://orgmode.org/worg/org-contrib/babel/uses.php for examples for what
it can be used - some will be relevant for your intended application).

Although emacs has a steep learning curve, it is definitely worth it
(and it works on Linux, Windows and Mac) - and the mailing list is also
really good.

Cheers,

Rainer



> 
> David Scott
> 
> _________________________________________________________________
> 
> David Scott    Department of Statistics
>         The University of Auckland, PB 92019
>         Auckland 1142,    NEW ZEALAND
> Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
> Email:    d.scott at auckland.ac.nz,  Fax: +64 9 373 7018
> 
> Director of Consulting, Department of Statistics
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
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