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? 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
FYI: If you use LaTex, you can work out on something between R and LaTex. -- View this message in context: http://r.789695.n4.nabble.com/Reproducible-research-tp2532353p2532361.html Sent from the R help mailing list archive at Nabble.com.
Hello David, You could also have a look to the ascii package : http://eusebe.github.com/ascii/ With asciidoc (http://www.methods.co.nz/asciidoc/), or one of other markup languages supported (restructuredtext, txt2tags, or textile), you can obtain good results. For example, vignettes of the book "Analysis and Interpretation of Freshwater Fisheries Data" (http://www.ncfaculty.net/dogle/fishR/bookex/AIFFD/AIFFD.html) are made with asciidoc and ascii package. If you are an emacs user, you might also be interested in org-mode and org-babel: http://orgmode.org/worg/org-contrib/babel/ Best, david 2010/9/9 David Scott <d.scott at auckland.ac.nz>:> ?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? > > 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. >
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel: +33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: Rainer at krugs.de Skype: RMkrug -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyIltUACgkQoYgNqgF2egpb/QCfW0zgFrNqC6/58sounMDwmsNm VgIAn3ZaDhcKGmo+Fwv+yz0UxXqiDaBC =vZV+ -----END PGP SIGNATURE-----
Dear David I have tried odfWeave and I find it quite useful for the purpose. I would recommend you give it a try. It comes with simple example files along with installation. You might have some difficulty in getting the zip files and path configurations set, which is a pre-requisite, but I am sure it is worth the efforts. Best of Luck. Regards Vijayan Padmanabhan -- View this message in context: http://r.789695.n4.nabble.com/Reproducible-research-tp2532353p2532458.html Sent from the R help mailing list archive at Nabble.com.
Another vote for org-mode here. In addition the advantages the other posts mentioned, you get multiple export engines (html, latex, ...) all built in. On 09/09/2010 12:47 AM, 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? > > 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.
I have a little package I've been using to write template blog posts (in HTML) with embedded R code. It's quite small but very flexible and extensible, and aims to do something similar to Sweave and brew. In fact, the package is heavily influenced by the brew package, though implemented quite differently. It depends on the evaluate package, available in the CRAN. The tentatively titled 'markup' package is attached. After it's installed, see ?markup and the few examples in the inst/ directory, or just example(markup). -Matt On Thu, 2010-09-09 at 01:47 -0400, 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? > > 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.-- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina