Re: Using Org for a dissertation

[tsd@tsdye.com (Thomas S. Dye)]

Richard Lawrence <richard.lawrence@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 outdated knowledge of Org features.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
completely to move from one authoring environment to the other.

hth,
Tom
-- 
Thomas S. Dye
http://www.tsdye.com