From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Christopher W. Ryan" Subject: Re: how do scientists use org mode? Date: Wed, 01 Feb 2012 23:25:27 -0500 Message-ID: <4F2A1037.4010108@binghamton.edu> References: <4F26D54C.8000608@binghamton.edu> <4F2847DC.3030503@gmx.de> Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([140.186.70.92]:46201) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RsoEo-0005aN-TH for emacs-orgmode@gnu.org; Wed, 01 Feb 2012 23:25:36 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1RsoEn-0007Vo-H2 for emacs-orgmode@gnu.org; Wed, 01 Feb 2012 23:25:34 -0500 Received: from hrndva-omtalb.mail.rr.com ([71.74.56.124]:46477) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1RsoEn-0007VM-DC for emacs-orgmode@gnu.org; Wed, 01 Feb 2012 23:25:33 -0500 In-Reply-To: <4F2847DC.3030503@gmx.de> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org 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 wrote: >>>> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph >>>> 13 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 >>> >> >> >