Re: how do scientists use org mode?

[cberry@tajo.ucsd.edu]

"Christopher W. Ryan" <cryan@binghamton.edu> writes:

> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
> started to dabble in Org mode in the past couple of weeks. Just as
> Christoph is, I'm trying to decide whether/how Org-mode might be useful
> in organizing and carrying out research projects, presentations, etc. So
> this thread has been very useful and timely.
>
> I'm trying to envision what a small research project, managed via a
> single Org file, might look like. There would be notes from meetings,
> thoughts from brainstorming sessions, scheduled appointments, data, R
> code, R output, and manuscript/presentation prose. Some of this might be
> destined for a manuscript, some for a beamer presentation, and some only
> for "internal consumption." How are all these pieces differentiated in
> the Org file, so that Org knows what to put in the
> presentation/manuscript, and what not to? Could anyone share or point to
> a short, perhaps fictional, example?

Have you looked at 

     http://orgmode.org/worg/org-contrib/babel/uses.html
??

There are almost too many possibilities --- it is a bit overwhelming. 

Here are three things I find useful:

1) The ability to export a subtree allows you to have many documents
within the *.org file. Setting EXPORT_* properties for the subtree gives
you a lot of flexibility. And it is easy to do with TAB completion to
prompt you to fill in the needed pieces.

2) Internal hyperlinks are really useful in staying on course in a big,
complicated document.

3) Noweb syntax allows you to mix and match different parts of the
document. Below is a minimal example. The latex chunks can be used
anywhere I need them. Navigating to '* mini report' and typing 

         'C-c @ C-c C-e l'

produces mini.tex.


,----
| * COMMENT latex chunks
| 
| #+name: chunk1
| #+begin_src latex
|   \begin{displaymath}
|     y = r\sin\theta
|   \end{displaymath}
| #+end_src
| 
| #+name: chunk2
| #+begin_src latex
|   \begin{displaymath}
|     x = s\cos\theta
|   \end{displaymath}
| #+end_src
| 
| 
| * mini report
|   :PROPERTIES:
|   :EXPORT_FILE_NAME: mini.tex
|   :EXPORT_TITLE: Minimal Report
|   :EXPORT_AUTHOR: Mister CCB
|   :END:
| 
| #+begin_src latex :noweb yes
| <<chunk1>>
| <<chunk2>>
| #+end_src
`----

HTH,

Chuck

>
> Thanks very much.
>
> --Chris

[snip]

-- 
Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at ucsd edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901