Re: [O] Using Org for a dissertation

2012-06-14 Thread Rasmus
Eric Schulte eric.schu...@gmx.com writes:

 1) Section labels and other in-document references.  It's nice that
 Org
 generates these on export, but I need to be able to assign and use
 labels that will not change if the document is reordered.  I know I
 can
 simply add such labels via a \label command, but I am worried that
 using
 them in addition to Org's autogenerated labels might cause numbering
 problems in LaTeX.


 I've not run into any such problems.  I tend to construct all of my
 labels through Org-mode (which works well for export to both HTML and
 LaTeX).

Could you describe how to do section links and references from within
Org.  I have tried to figure this out for a while now.  The only
solution I can find (on Worg) depends on precise section names, which is
not so stable.  I use the new latex export engine 

 [2] http://gitweb.adaptive.cs.unm.edu/dissertation.git/tree

This link is unfortunately dead.

–Rasmus

-- 
Send from my Emacs







Re: [O] Using Org for a dissertation

2012-06-14 Thread Eric S Fraga
Rasmus ras...@gmx.us writes:

 Eric Schulte eric.schu...@gmx.com writes:

 1) Section labels and other in-document references.  It's nice that
 Org
 generates these on export, but I need to be able to assign and use
 labels that will not change if the document is reordered.  I know I
 can
 simply add such labels via a \label command, but I am worried that
 using
 them in addition to Org's autogenerated labels might cause numbering
 problems in LaTeX.


 I've not run into any such problems.  I tend to construct all of my
 labels through Org-mode (which works well for export to both HTML and
 LaTeX).

 Could you describe how to do section links and references from within
 Org.  I have tried to figure this out for a while now.  The only
 solution I can find (on Worg) depends on precise section names, which is
 not so stable.  I use the new latex export engine 

The attached is a simple example which works for latex.

* Introduction
# intro
  This is some introductory text.
* Background
  In section [[latex:ref][intro]], we introduced the topic.

-- 
: Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
: in Emacs 24.1.50.1 and Org release_7.8.11-69-ga2fd96


Re: [O] Using Org for a dissertation - appendices

2012-05-23 Thread Bastien
Hi Suvayu,

suvayu ali fatkasuvayu+li...@gmail.com writes:

 On Mon, May 21, 2012 at 9:08 AM, Henri-Paul Indiogine
 hindiog...@gmail.com wrote:
 The LaTeX export of course does not know the that last chapter should
 contain the appendices.  I have tried to insert several LaTeX commands
 in the orgmode file, but I could not make it work.

 This might help:

 http://stackoverflow.com/questions/10295177/is-there-an-equivalent-of-org-modes-b-ignoreheading-for-non-beamer-documents/10305270#10305270

If there is anything useful from the link above that should
be added to Worg, please let us know.

Thanks!

-- 
 Bastien



Re: [O] Using Org for a dissertation - appendices

2012-05-23 Thread suvayu ali
Hi Bastien,

On Wed, May 23, 2012 at 12:19 PM, Bastien b...@gnu.org wrote:

 http://stackoverflow.com/questions/10295177/is-there-an-equivalent-of-org-modes-b-ignoreheading-for-non-beamer-documents/10305270#10305270

 If there is anything useful from the link above that should
 be added to Worg, please let us know.

Well its just my customisation that lets me include Appendices and a
Bibliography in the regular org document tree for latex export. However
I have not ported my customisation to the new export engine.

For the last few months (and the coming month or two) I have been
extremely busy. When I have time I can write-up nicely for Worg and put
it in org-hacks (under LaTeX export). However if someone else could do
it earlier, you are welcome to give it a shot. :) I think the SO answer
is complete enough and can be included almost as is (except for the
missing new exporter changes). In any case, once there is an entry it
can be refined endlessly. :)

Thanks,

-- 
Suvayu

Open source is the future. It sets us free.



Re: [O] Using Org for a dissertation - appendices

2012-05-21 Thread Henri-Paul Indiogine
Hi!

2012/5/12 Richard Lawrence richard.lawre...@berkeley.edu:
 (Henri-Paul, do you still read this list?)

Yes, I do.  Still using orgmode each day.

I do not have anything fancy going on and actually would like to know
how to set up appendices for LaTeX export.

I have the following outline:

* Review of Literature
* Methodology
* Findings
* Discussion
* Conclusion
* Footnotes
* References
* Appendices
** Appendix A
** Appendix B
** Appendix C

The LaTeX export of course does not know the that last chapter should
contain the appendices.  I have tried to insert several LaTeX commands
in the orgmode file, but I could not make it work.

Does anyone have a suggestion?

Thanks,
Henri-Paul


-- 
Henri-Paul Indiogine

Curriculum  Instruction
Texas AM University
TutorFind Learning Centre
http://www.tutorfind.ca

Email: hindiog...@gmail.com
Skype: hindiogine



Re: [O] Using Org for a dissertation - appendices

2012-05-21 Thread Tim Burt
Henri-Paul Indiogine hindiog...@gmail.com writes:

 Hi!

 2012/5/12 Richard Lawrence richard.lawre...@berkeley.edu:
 (Henri-Paul, do you still read this list?)

 Yes, I do.  Still using orgmode each day.

 I do not have anything fancy going on and actually would like to know
 how to set up appendices for LaTeX export.

 I have the following outline:

 * Review of Literature
 * Methodology
 * Findings
 * Discussion
 * Conclusion
 * Footnotes
 * References
 * Appendices
 ** Appendix A
 ** Appendix B
 ** Appendix C

 The LaTeX export of course does not know the that last chapter should
 contain the appendices.  I have tried to insert several LaTeX commands
 in the orgmode file, but I could not make it work.

Use the \appendix command to turn on alphabetic numbering.

 Does anyone have a suggestion?

If you want the last three headlines to each have a different letter,
then you make them top-level headlines instead of children: 

* References
\appendix
* Appendix A
* Appendix B
* Appendix C



 Thanks,
 Henri-Paul

-- 
Tim Burt
www.rketburt.org
It is healthful to every sane man to utter the art within him; -- GK 
Chesterton



Re: [O] Using Org for a dissertation

2012-05-21 Thread Matt Lundin
Richard Lawrence richard.lawre...@berkeley.edu writes:

 I am a graduate student in philosophy, and I am about to begin writing
 my dissertation.  I am wondering about whether I should write it in Org,
 or stick to plain LaTeX.

I would recommend LaTeX. In my experience, writing long documents (or
Beamer slides) in org-mode creates additional work, insofar as I have to
think through two layers of translation: 1) how to get org-mode to
translate nicely into LaTeX; and 2) how to get LaTeX to output the final
document I desire. In larger documents, leaky abstractions can quickly
become a problem. I tried writing in org-mode but ended up with a
document encrusted with all sorts of hacks (#+LaTeX: lines and the
like). IMO, writing in LaTeX/AUCTeX affords greater control over the
final document. (Note: the new export engine will give the user greater
ability to reduce the number of leaks.)

I would recommend using org-mode if the following apply:

1. You will rely heavily on org-babel.
2. You anticipate having to output to multiple formats (e.g., your
   dissertation advisor requires you to submit .doc files).
3. Your document structure will be straightforward.

I would recommend using LaTeX if the following apply:

1. You have numerous footnotes. (Fontification and export of footnotes
   in org-mode can be painfully slow when a document contains hundreds
   of footnotes.)
2. You are using biblatex. (If you are relying heavily on biblatex for
   citations, then you will need to export to LaTeX to output your final
   document, thus precluding the possibility of outputting to other
   formats. Furthermore, AUCTeX offers very helpful syntax highlighting
   and folding of citations and footnotes, along with excellent reftex
   integration.)
3. You will be using a many cross-references.

My workflow is as follows. I rely on my org-mode files for drafting
small segments of a project. I then export the segments to the kill ring
with the following function and yank them into the relevant LaTeX file.

--8---cut here---start-8---
(defun my-org-export-latex-to-kill-ring ()
  (interactive)
  (kill-new (org-export-region-as-latex (point) (mark) t 'string)))
--8---cut here---end---8---

Best,
Matt



Re: [O] Using Org for a dissertation - appendices

2012-05-21 Thread suvayu ali
On Mon, May 21, 2012 at 9:08 AM, Henri-Paul Indiogine
hindiog...@gmail.com wrote:
 The LaTeX export of course does not know the that last chapter should
 contain the appendices.  I have tried to insert several LaTeX commands
 in the orgmode file, but I could not make it work.

This might help:

http://stackoverflow.com/questions/10295177/is-there-an-equivalent-of-org-modes-b-ignoreheading-for-non-beamer-documents/10305270#10305270

-- 
Suvayu

Open source is the future. It sets us free.




Re: [O] Using Org for a dissertation

2012-05-15 Thread suvayu ali
Hi Richard,

On Sat, May 12, 2012 at 8:23 PM, Richard Lawrence
richard.lawre...@berkeley.edu wrote:
 I am a graduate student in philosophy, and I am about to begin writing
 my dissertation.  I am wondering about whether I should write it in Org,
 or stick to plain LaTeX.

Since others have added their bits, I'll just say I wrote my Master's
thesis in Physics last year with the then org-mode HEAD. I rather liked
the process and the end result[1]. Although I have to admit, I had to
hack around a bit because of buggy mandatory templates from my
university. Apart from that, everything was very smooth. If you are
interested, my org-mode setup is in a public repo[2]. However I haven't
had the time to make the org source for the thesis publicly available.
In case you are interested, I'm attaching some relevant bits. It has
examples on how to put in tables (with short and long captions),
figures, latex snippets and finally how I included a bibliography and
appendices.

Hope this will help.

Footnotes:

[1] 
https://theses.lib.sfu.ca/sites/all/files/public_copies/etd6682_sali_pdf_0.pdf
[2] https://github.com/suvayu/.emacs.d/blob/master/org-mode-config.el

-- 
Suvayu

Open source is the future. It sets us free.
# -*- mode: org; -*-
#+TITLE: Estimation and modelling of Standard Model backgrounds in the 
search for \(W'\) gauge bosons with ATLAS (\mu channel)
#+AUTHOR:Suvayu Ali
#+EMAIL: suvayu@cern.ch
#+DATE:  \today
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE:  en
#+OPTIONS:   H:4 num:4 toc:nil ::t |:t ^:t -:t f:t *:t :nil
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:nil pri:nil tags:nil

#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport

#+STARTUP: content
#+BIND: org-confirm-babel-evaluate nil
#+BIND: org-export-latex-title-command 

#+LaTeX_CLASS: book
#+LaTeX_CLASS_OPTIONS: [12pt,letterpaper,oneside]
#+LaTeX_HEADER: \usepackage{amsfonts}
#+LaTeX_HEADER: \usepackage{amsmath}
#+LaTeX_HEADER: \usepackage{appendix}
#+LaTeX_HEADER: \usepackage{varioref}
#+LaTeX_HEADER: \usepackage[nokeyprefix]{refstyle}
# more Physics specific packages

# LaTeX Macros
#+LaTeX_HEADER: \newcommand{\p}[1]{\phantom{#1}}
#+LaTeX_HEADER: \newcommand{\modulus}[1]{\ensuremath{\lvert #1 \rvert}}
# some more Physics specific macros

# University stuff
##+LaTeX_HEADER: \usepackage[headings]{thesisstyle}
# ...
# #+LaTeX_HEADER: \include{abstract}
# \include{preamble}

* Introduction

** The Standard Model:SM:

   \label{chap:SMintro}

   The Standard Model is a quantum field theoretical approach to
   describe interactions in nature. The theory is primarily built upon
   symmetry arguments supported by experimental data. It describes the
   interactions between all fermions mediated by vector gauge bosons.
   These include the electromagnetic, weak and strong interactions.
   The formulation of the SM does not include gravity. There are
   various approaches to include gravity in BSM theories which are
   discussed elsewhere \cite{ArkaniHamed:1998rs,Randall:1999ee}.

   #+CAPTION: [Interactions and particles described by the SM.]{The 
interactions and the participating particles described by the Standard Model 
are tabulated below. Although the $Z^0$ is listed both as force carrier and a 
particle interacting by the weak force, it should be noted it does not couple 
with another $Z^0$.}
   #+LABEL: tbl:interactions
   
|--+-++-|
   | Charge   | Force   | Force carrier  | Interacting particles
   |
   
|--+-++-|
   | Electric | Electromagnetic | \gamma | all charged fermions, 
\(W^\pm\) |
   | Weak | Weak| \(W^\pm, Z^0\) | all fermions, \(W^\pm, Z^0\) 
   |
   | Colour   | Strong  | \(g\)  | all quarks, anti-quarks, 
\(g\)  |
   
|--+-++-|

   In the SM all particles carry various charges which describe all
   the interactions they undergo: the electric charge is responsible
   for all electromagnetic interactions, the weak charge for all weak
   interactions and the colour charge for all strong interactions.
   Since any quantum fields have bosonic exchange particles, all the
   interactions discussed earlier are associated with different spin-1
   bosons as force carriers. This has been summarised in
   \Tabref{tbl:interactions}.

*** Production and Decay of the \(W'\) Boson:pdf:

\label{subsec:Wprod}

#+CAPTION: A representative diagram for \(W'\) production at the LHC.
#+LABEL: fig:LO-Wprime
#+ATTR_LaTeX: width=0.6\textwidth
[[file:figs/Wprime-s-channel.eps]]

\noindent *Production:* The $W'$ boson is assumed to have a
coupling constant that is the same as its lighter SM counterpart.
This is known as the sequential SM $W'$ boson. The 

Re: [O] Using Org for a dissertation

2012-05-15 Thread Markus Grebenstein

Hi Richard,

I recently have written my dissertation in orgmode.

I switched to latex for the final 4 weeks between the correction version 
(completely written in orgmode) and the final version.


What I liked about org:
- Outlining functionality
- Synopsis drawers and view
- Markup
- Compiling subtrees
- noexport tag
- tagging

What I disliked/ preferred in auctex:
- missing footnote folding in stable version
- footnotes frequently lead to trouble with overlapping latex groups.
- missing/spare syntax highlighting
- reference handling in especial w.r.t headings (if you change the 
heading you use the reference)

- debugging
- missing subfigure abilities
- compile time i.e. if you have much babel-snippets
- whitespace handling i.e. after e.g. \si{someunit} (you cannot place a 
footnote at the place where it should be.


The main reasons to switch to auctex in the end for me has been the 
much  better debugging possibilities and the better reftex integration 
(you have to fix quite a bit of wrong references in the final stage of 
your work. Furthermore, I had to do some additional time consuming 
debugging of the orgmode markup several times (most frequently related 
to org-babel).


I would do it again but I'd switch to latex as soon as the basic 
structure of the text is fixed.


Just my 2 cents.

Best Markus



Re: [O] Using Org for a dissertation

2012-05-15 Thread Nicolas Goaziou
Hello,

Richard Lawrence richard.lawre...@berkeley.edu writes:

 I have seen mention of the new exporter on this list a bit, but I don't
 read the list enough to know where to find it.  How can I try it, if I
 want to see how it compares to the current exporter?  Is it in a public
 branch somewhere?  

Assuming contrib directory is in your load-path, just evaluate

  (require 'org-export)

Then, you can call the dispatcher with M-x org-export-dispatch.

 Would feedback from me be helpful?

Certainly.


Regards,

-- 
Nicolas Goaziou



Re: [O] Using Org for a dissertation

2012-05-15 Thread Richard Lawrence
Tom and Nicolas,

Thanks!  I will give the new exporter a shot when I have a chance and
let you know how it goes.

Best,
Richard




Re: [O] Using Org for a dissertation

2012-05-15 Thread Richard Lawrence
Hi Suvayu,

suvayu ali fatkasuvayu+li...@gmail.com wrote:

 In case you are interested, I'm attaching some relevant bits. It has
 examples on how to put in tables (with short and long captions),
 figures, latex snippets and finally how I included a bibliography and
 appendices.
 
 Hope this will help.

Thanks!  This is definitely helpful.  The ignoreheading tag is a nice
hack -- fixes one of those niggling issues I've had with LaTeX export.

Best,
Richard



Re: [O] Using Org for a dissertation

2012-05-15 Thread Richard Lawrence
Hi Markus,

Thanks for your advice.  I figure that, like you, I may eventually need
to switch to LaTeX, but will stick with Org for now, at least until my
document structure is quite settled.

Can you elaborate a bit on the following?

Markus Grebenstein p...@mgrebenstein.de wrote:

 What I disliked/ preferred in auctex:
 - missing footnote folding in stable version

Stable version of Org, or Auctex?  What exactly is missing?

 - footnotes frequently lead to trouble with overlapping latex groups.

What is a Latex group? How they could overlap?  (I would especially like
to be aware of potential footnote problems ahead of time.)

 - reference handling in especial w.r.t headings (if you change the
 heading you use the reference)

Do you mean you prefer \label and \ref in Latex over Org's abstraction?

Thanks!

Best,
Richard







Re: [O] Using Org for a dissertation

2012-05-14 Thread Richard Lawrence
Hi Eric,

Eric Schulte eric.schu...@gmx.com wrote:

 I am currently writing my dissertation (proposal) in Org-mode.  So far
 it is working very well for me, I can export to both PDF for more formal
 submissions to my adviser and to HTML for less formal posting to a web
 page.  I keep *all* of my reading notes as Org-bibtex headlines in a
 single large reading.org file.  I have a (somewhat complex) system
 whereby I am able to reference these bibtex entries from the
 dissertation and automatically generate the required .bib file as part
 of my document export process.  One nice side effect of this setup has
 been the ability to do a fun graphical export of my references [1].
 
 My entire dissertation directory is in a public git repository [2], you
 may find my Makefile [3] useful (although again I should warn you that
 my particular setup may be needlessly complex).

Thanks for your helpful advice!  Your org-bibtex setup in particular
looks like exactly what I need.  (Your dissertation proposal looks very
interesting, too!)

I think what I will do is stick with Org for now, and try to be smarter
about a few things (like the #+LABEL command...which I must have read
about at some point but forgotten) so that, if I ever need to drop down
to straight LaTeX, it will be easy to make the switch.  You've given me
a helpful example to follow.

Best,
Richard




Re: [O] Using Org for a dissertation

2012-05-14 Thread Richard Lawrence
Thomas S. Dye t...@tsdye.com wrote:

 The current Org-mode LaTeX exporter is nifty, but it was designed to
 export notes and not dissertations.  It can be configured to do that,
 but the extra translation step adds some complexity and potentially
 introduces problems.  In my work this potential downside is more than
 made up for by the reproducible research facilities of Org-mode.  When I
 don't need these, I typically write in LaTeX.  The AucTeX environment is
 a terrific help to the author of a LaTeX document and in many ways it is
 ideal for a dissertation writer.

Thanks for your advice.  This has been my experience so far as well.

 That said, the new LaTeX exporter in Org-mode is being designed to
 overcome some of the limitations of the old exporter, so it will
 probably be the case that the translation step from Org-mode to LaTeX
 will get easier.  It would be good to have someone write a dissertation
 using the new exporter because it might stretch the exporter in ways
 that smaller, simpler documents do not.  But I doubt if this will be the
 path of least resistance to the finished dissertation.  

I have seen mention of the new exporter on this list a bit, but I don't
read the list enough to know where to find it.  How can I try it, if I
want to see how it compares to the current exporter?  Is it in a public
branch somewhere?  Would feedback from me be helpful?

 I'm using ebib to manage BibTeX data now and I really like it.  It works
 well with both LaTeX and Org-mode, so I don't have to switch gears
 completely to move from one authoring environment to the other.

Hmm, I hadn't heard of ebib, but I will have a look at it.  Thanks for
the tip!

Best,
Richard




Re: [O] Using Org for a dissertation

2012-05-12 Thread Eric Schulte
Hi Richard,

Richard Lawrence richard.lawre...@berkeley.edu writes:

 Hi all,

 I am a graduate student in philosophy, and I am about to begin writing
 my dissertation.  I am wondering about whether I should write it in Org,
 or stick to plain LaTeX.

 This question has been asked before:
 http://article.gmane.org/gmane.emacs.orgmode/22756

 But that was two years ago; Org has changed a fair bit, and I'm
 wondering if there are any updates to the advice given there.  Moreover,
 I'm wondering if anyone has written a dissertation or other long
 documents in Org in the meantime, and what their experiences have been.
 (Henri-Paul, do you still read this list?)


I am currently writing my dissertation (proposal) in Org-mode.  So far
it is working very well for me, I can export to both PDF for more formal
submissions to my adviser and to HTML for less formal posting to a web
page.  I keep *all* of my reading notes as Org-bibtex headlines in a
single large reading.org file.  I have a (somewhat complex) system
whereby I am able to reference these bibtex entries from the
dissertation and automatically generate the required .bib file as part
of my document export process.  One nice side effect of this setup has
been the ability to do a fun graphical export of my references [1].

My entire dissertation directory is in a public git repository [2], you
may find my Makefile [3] useful (although again I should warn you that
my particular setup may be needlessly complex).


 I have used Org to write most of the shorter papers I have so far
 written as a graduate student, and been very happy with the results.  I
 prefer most of Org's editing features and conventions to bare LaTeX.  I
 haven't previously had much of a need to mix TODO items and writing, but
 imagine I will with a dissertation.  I *have* been relying on Org's
 to-do list features for my reading: I enter new readings as TODO items
 via capture, and include the bibliographic fields that make them
 suitable to export via org-bibtex when it comes time to reference them.
 None of the writing I've done so far has had strict formatting
 requirements, however, and I have run into enough small formatting
 issues in the past that I want to avoid having them grow into large
 issues in the context of a dissertation.

 Since I am not in the sciences, I doubt that I will have many figures or
 complex tables, which I know can lead to headaches.  Here are a few of
 the things I *am* worried about.  I'm sure most of them can be dealt
 with; I am guessing that most of these issues reflect my ignorance or
 outdated knowledge of Org features.  I'd be grateful for pointers or
 workarounds for them:

 1) Section labels and other in-document references.  It's nice that Org
 generates these on export, but I need to be able to assign and use
 labels that will not change if the document is reordered.  I know I can
 simply add such labels via a \label command, but I am worried that using
 them in addition to Org's autogenerated labels might cause numbering
 problems in LaTeX.


I've not run into any such problems.  I tend to construct all of my
labels through Org-mode (which works well for export to both HTML and
LaTeX).


 2) Escaping/unrecognized commands.  I have occassionally run into
 annoyances where Org escapes characters or commands that I intend to be
 exported literally (~ and $ are perennial offenders).  Export also
 tends to break when fill-paragraph breaks a LaTeX command across a line,
 like:

 some preceding text up to the end of the line \cite{SomeAuthorReference,
 AnotherReference}.


I deal with the above by not placing spaces in such commands, so the
above becomes

\cite{SomeAuthorReference,AnotherReference}


 3) Indentation around #+BEGIN_*/#+END_* environments. (I most often
 use QUOTE.)  I usually have to explicitly control indentation in a way
 that I wouldn't have to in LaTeX, because Org inserts blank lines
 around them during export.

 4) Inline footnotes.  I usually prefer to use inline footnotes, but I
 think I have found in the past that Org's syntax for inline footnotes
 ([fn:: ...]) interacts badly with LaTeX commands, especially anything
 requiring a ] in the footnote text.


again, I haven't run into either of the above, but working in Philosophy
you likely have more stringent footnotes needs than I do in CS.


 5) Bibtex and bibliographies.  I love keeping my reading list as Org
 TODO entries, but would like a more automated way to export (just) the
 entries I need for a particular document to a .bib file.

My setup is to keep a tasks.org file with reading related tasks which
holds Org-mode links to all of my references.  As part of my document
export process I scan through that file, jumping to each link and
running `org-bibtex-export-to-kill-ring' at each reference.  I then dump
all of these bibtex entries into a .bib file.  By using a Makefile rule
the .bib file is only regenerated when I've changed my tasks.org file.

 I would also like to have 

Re: [O] Using Org for a dissertation

2012-05-12 Thread Thomas S. Dye
Richard Lawrence richard.lawre...@berkeley.edu writes:

 Hi all,

 I am a graduate student in philosophy, and I am about to begin writing
 my dissertation.  I am wondering about whether I should write it in Org,
 or stick to plain LaTeX.

 This question has been asked before:
 http://article.gmane.org/gmane.emacs.orgmode/22756

 But that was two years ago; Org has changed a fair bit, and I'm
 wondering if there are any updates to the advice given there.  Moreover,
 I'm wondering if anyone has written a dissertation or other long
 documents in Org in the meantime, and what their experiences have been.
 (Henri-Paul, do you still read this list?)

 I have used Org to write most of the shorter papers I have so far
 written as a graduate student, and been very happy with the results.  I
 prefer most of Org's editing features and conventions to bare LaTeX.  I
 haven't previously had much of a need to mix TODO items and writing, but
 imagine I will with a dissertation.  I *have* been relying on Org's
 to-do list features for my reading: I enter new readings as TODO items
 via capture, and include the bibliographic fields that make them
 suitable to export via org-bibtex when it comes time to reference them.
 None of the writing I've done so far has had strict formatting
 requirements, however, and I have run into enough small formatting
 issues in the past that I want to avoid having them grow into large
 issues in the context of a dissertation.

 Since I am not in the sciences, I doubt that I will have many figures or
 complex tables, which I know can lead to headaches.  Here are a few of
 the things I *am* worried about.  I'm sure most of them can be dealt
 with; I am guessing that most of these issues reflect my ignorance or
 outdated knowledge of Org features.  I'd be grateful for pointers or
 workarounds for them:

 1) Section labels and other in-document references.  It's nice that Org
 generates these on export, but I need to be able to assign and use
 labels that will not change if the document is reordered.  I know I can
 simply add such labels via a \label command, but I am worried that using
 them in addition to Org's autogenerated labels might cause numbering
 problems in LaTeX.

 2) Escaping/unrecognized commands.  I have occassionally run into
 annoyances where Org escapes characters or commands that I intend to be
 exported literally (~ and $ are perennial offenders).  Export also
 tends to break when fill-paragraph breaks a LaTeX command across a line,
 like:

 some preceding text up to the end of the line \cite{SomeAuthorReference,
 AnotherReference}.

 3) Indentation around #+BEGIN_*/#+END_* environments. (I most often use
 QUOTE.)  I usually have to explicitly control indentation in a way that
 I wouldn't have to in LaTeX, because Org inserts blank lines around them
 during export.

 4) Inline footnotes.  I usually prefer to use inline footnotes, but I
 think I have found in the past that Org's syntax for inline footnotes
 ([fn:: ...]) interacts badly with LaTeX commands, especially anything
 requiring a ] in the footnote text.

 5) Bibtex and bibliographies.  I love keeping my reading list as Org
 TODO entries, but would like a more automated way to export (just) the
 entries I need for a particular document to a .bib file.  I would also
 like to have more control over the bibliography as a section of my
 document.  The \bibliography command must live under some Org heading or
 other, and as far I as know it can't live under its own without
 generating an extraneous heading, so I have to be careful that it ends
 up at the end of the last section.

 Are there other issues that people have run into when using Org to write
 a longer document with strict formatting requirements?  Again, any and
 all advice is greatly appreciated!

 Thanks,
 Richard



Aloha Richard,

The current Org-mode LaTeX exporter is nifty, but it was designed to
export notes and not dissertations.  It can be configured to do that,
but the extra translation step adds some complexity and potentially
introduces problems.  In my work this potential downside is more than
made up for by the reproducible research facilities of Org-mode.  When I
don't need these, I typically write in LaTeX.  The AucTeX environment is
a terrific help to the author of a LaTeX document and in many ways it is
ideal for a dissertation writer.

That said, the new LaTeX exporter in Org-mode is being designed to
overcome some of the limitations of the old exporter, so it will
probably be the case that the translation step from Org-mode to LaTeX
will get easier.  It would be good to have someone write a dissertation
using the new exporter because it might stretch the exporter in ways
that smaller, simpler documents do not.  But I doubt if this will be the
path of least resistance to the finished dissertation.  

I'm using ebib to manage BibTeX data now and I really like it.  It works
well with both LaTeX and Org-mode, so I don't have to switch gears

Re: [O] Using Org for a dissertation

2012-05-12 Thread Peter Münster
On Sat, May 12 2012, Richard Lawrence wrote:

 I am a graduate student in philosophy, and I am about to begin writing
 my dissertation.  I am wondering about whether I should write it in Org,
 or stick to plain LaTeX.

Or in ConTeXt...

Sorry, I can't answer your questions about Org-mode. I just know, that
ConTeXt is a much better tool for writing dissertations than LaTeX is.

-- 
   Peter