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Re: [O] how do scientists use org mode?


From: Christopher W. Ryan
Subject: Re: [O] how do scientists use org mode?
Date: Wed, 01 Feb 2012 23:25:27 -0500
User-agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1.16) Gecko/20101206 SeaMonkey/2.0.11

Thanks everyone for the advice and ideas. I see lots of potential, and also lots to learn.

I made my first attempt at an R code block in an Org file. I'm running Ubuntu 10.04 LTS. Synaptic tells me that I have emacs 23.1+1-4ubuntu7.2, and Org 6.34c-1.

I added this to my .emacs:

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   ))

Here is the source block:

#+begin_src R
getwd()
dd <- read.csv("cars.csv", sep=",", header=TRUE)
head(dd)
str(dd)
dd$date <- as.Date(as.character(dd$Date), format="%d-%b-%y")
names(dd)[4] <- "city"
table(is.na(dd$date))
min(dd$date, na.rm=TRUE); max(dd$date, na.rm=TRUE)
#+end_src

emacs seems to do the syntax highlighting properly, so I guess it is recognizing this as a code block.

When I put point inside the block and type C-c C-c, emacs gives me this message:

C-c C-c can do nothing useful at this location.

I wonder if I have Babel? Is it "built in" to the emacs or Org versions that I have?

Thanks.

--Chris Ryan

Simon Thum wrote:
Hi Christopher,

to add my 2c: I'm using org-mode to track our participation in a
mid-sized project (9 Partners, ~30 People, 3 Years). I'm not
coordinating, in which case I'd probably look for more project
management centric tools, and thus found org-mode to be very useful.

I use it to track the project state, not hard data (which is typically
massive), our commitments and other's compliance with their commitments,
and all the rest that comes up and needs project context: Ideas, tasks,
deadlines, project reports & what not. The outline of this file reflects
the project structure. I have tags for partners and people in that file,
so e.g. when I speak someone I can easily check for further things to
discuss.

Big projects get their own file, for smaller projects and commitments I
have a few more files. I'm not using the attachments as it's
unfortunately a very microsoft-wordey project where git won't help much,
but plan to use them privately. Ah yes, I use org-mode for private stuff
too. It's the first tool that I use for more than a month.

I use export (tags) to inform my supervisor and other people on the
project about certain aspects, which usually works OK. I also found the
custom links to be helpful, as we have multiple web frontends for
project-specific matters whose contents I can link in easily this way.

The whole thing synced to a server using git, which saved my shiny a few
times. This is something I wouldn't recommend anyone to put off, even if
your backup schedule is in minutes.

HTH,

Simon


On 01/30/2012 06:37 PM, Christopher W. Ryan wrote:
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?

Thanks very much.

--Chris
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY 13904
cryanatbinghamtondotedu

"Observation is a more powerful force than you could possibly reckon.
The invisible, the overlooked, and the unobserved are the most in danger
of reaching the end of the spectrum. They lose the last of their light.
From there, anything can happen . . ." [God, in "Joan of Arcadia,"
episode entitled, "The Uncertainty Principle."]

Tomas Grigera wrote:
Hi Cristoph

On Fri, Jan 27, 2012 at 15:27, John Hendy<address@hidden> wrote:
On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph
13<address@hidden> wrote:
Hi
this is my first post here and although I am evaluating org mode
with great interest, I am also asking myself in which way other
scientists are making use of org mode. It will take a while to get
my head around how to accomplish certain things in org mode but for
the moment I am intrigued by *why* one would want to approach the
problem of organizing one's research with org mode and in which way.

[...]

Thomas, Eric and John gave very useful answers, I just want to add my
$0.02 as a physicist who recently (about a year ago) started using Org
mode. I started mainly looking for a workflow organization system,
but slowly discovered it has many other possibilities. For research, I
find org-babel is a great tool. It allows you to have a document
collecting together thoughts and discussion along with data, data
analysis, scripts for data manipulations and plots (Org tables are
actually more like a spreadsheet since Org supports quite complex
formulas and even plotting directly from the table). The many export
possibilities mean that you can share your notes with colleagues not
using Org (or even Emacs).

I have also discovered it is a great tool for drafting presentations
and then actually producing your slides via Latex- Beamer export.

HTH,

Tomas







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