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

[Christopher W. Ryan]

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