[R] Authoring a book

[Ramon Diaz-Uriarte]

Dear Tom,

To add a few things to explore:

- I'd definitely go with LaTeX. Depending on how much formatting control you 
want, though, and if your coworkers are reluctant to jump into LaTeX, you 
might start with reStructuredText (http://docutils.sourceforge.net/rst.html) 
or text2tags (http://txt2tags.sourceforge.net/). With both, you can produce 
LaTeX, but innitially at least it allows you to write text with structure 
using markup that is a lot simpler than latex.


- I'd definitely use a version control system. Instead of CVS or SVN, though, 
I'd suggest you take a look at some of the distributed ones, in particular 
Bazaar-NG (http://bazaar-vcs.org), Mercurial 
(http://www.selenic.com/mercurial/wiki/index.cgi) or Darcs 
(http://abridgegame.org/darcs/). 

These three are probably among the most mature ones (though oppinions will 
vary, of course; I have some notes and links at: 
http://www.ligarto.org/rdiaz/VersionControl.html). 

What I like about any of these is that I think they provide you essentially 
all SVN can provide (except for the user-base and years of existence of SVN) 
plus a lot more. For instance, if you often work without access to the remote 
repository, with any of these three systems you can enjoy all the benifits of 
version control. Cherry-picking is easier with any of these than with 
CVS/SVN, and Darcs in particular excels at it.


- For bibliography, I find CiteULike (http://www.citeulike.org/) fabulous. 
Needs internet access, and might not work with the journals/data bases that 
you use, though. It can export as bibtex.


- If you find outliners useful (or absolutely essential) then you might want 
to look at Leo (http://webpages.charter.net/edreamleo/front.html). Leo is 
agnostic regarding whether you write LaTeX, plain text, or R code (though it 
has great support for some languages such as Python or rst), and you can use 
Leo and still edit files in your editor of choice (I use Leo for working with 
fairly large latex files that I edit under Emacs). However, for this to work, 
all of you should agree to use Leo (or at least not disturb the "sentinel 
lines" that leo uses).


Hope this helps (or at least provides entertaining links :-).

R.


On Thursday 24 August 2006 21:10, Tom Backer Johnsen wrote:
> Stefan Grosse wrote:
> > I think Peter Dalgaard is right.
> >
> > Since you are able to use R I believe you will be very fast in learning
> > LaTeX.
> >
> > I think it needs less then a week to learn the most common LaTeX
> > commands. And setting up a wiki and trying then to convert this into a
> > printable document format plus learning the wiki syntax is probably more
> > time consuming. Beside this R is able to work perfectly together with
> > LaTeX, it creates LaTeX output and is doing excellent graphics in the
> > EPS/PS format.
> >
> > The best introduction for LaTeX is the not so short introduction:
> > http://people.ee.ethz.ch/~oetiker/lshort/lshort.pdf
>
> It really was a "not too short" intro.  I'll have a look at it.
>
> > If you still are not convinced have a look at UniWakkaWiki:
> > http://uniwakka.sourceforge.net/HomePage
> >
> > It is a Wiki for Science and University purposes and claims to be able
> > to export to Openoffice as well as to LaTeX.
>
> Looks interesting and I really like the concept, but how stable is it?
>   It looks rather fresh from the web page, but I may be wrong.  A
> bibliography function is really a big advantage, so ... perhaps.
>
> Tom
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics 
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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