Re: how do scientists use org mode?

["Christopher W. Ryan" <cryan@binghamton.edu>]

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<jw.hendy@gmail.com> wrote:
>>>> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph
>>>> 13<christoph-13@gmx.net> 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
>>>
>>
>>
>