Writing a dissertation using org-mode

Writing a dissertation using org-mode

[Henri-Paul Indiogine]

I started writing my doctoral dissertation in history using org-mode. I
am also using git.el for my version control and gnus for my email. Of
course I export my org file to LaTeX which I compile to pdf.  My
bibliography is managed using BibTeX.

This all on a Ubuntu Karmic laptop with Emacs 23.1.1.

I may do some text mining using R-project + the tm package.

Any suggestion is welcome.

Thanks,


-- 
Henri-Paul Indiogine
Email: hindiogine@gmail.com
Skype: hindiogine
Website: http://www.coe.tamu.edu/~enrico

Re: Writing a dissertation using org-mode

[Torsten Wagner]

Dear Henri,

On 03/04/2010 01:45 PM, Henri-Paul Indiogine wrote:
> I started writing my doctoral dissertation in history using org-mode. I
> am also using git.el for my version control and gnus for my email. Of
> course I export my org file to LaTeX which I compile to pdf.  My
> bibliography is managed using BibTeX.

please consider that you might have to follow a very stricy layout style 
depening on your university, department, lab or supervisor. If your are 
lucky there will be a LaTeX template somewhere at your university. If 
you are unlucky there is nothing like that or even worse only a MS-word 
template.

I'm not sure how good org-mode might be usable in that case. org-mode is 
really great and I try to use it for many purposes. However, for a 
thesis I would use directly LaTeX which gives me a bit more control of 
what is going on.

Furthermore, try biber [1] and biblatex [2]... the somehow next 
generation of bibtex and bib-file compatible. For me they work very well 
already despite of the fact that they are still beta-versions. biblatex 
gives you much more freedom of formatting your citations and 
bibliography... I guess both highly needed in your scientific field.

Good luck

Torsten

[1] http://biblatex-biber.sourceforge.net/
[2] http://www.ctan.org/tex-archive/help/Catalogue/entries/biblatex.html

Re: Writing a dissertation using org-mode

[Scot Becker]

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Henri-Paul,

I'm doing the same, with basically the same setup, but using biblatex, and
Zotero, but planning to give Mendeley a serious test for PDF management.
(And yes there are still problems and repeated manual tweaking associated
with using Zotero + bibtex.  The export is just not bibtex-y enough).   It
remains to be seen whether I'll wish I had worked in pure LaTeX at the end.
It's true that I have run into occaisional problems with the latex
conversion.  Sometimes things like quotes (") and italics next to each other
can conflict.  (I haven't done recent tests to see if I still have these
problems). But the org-mode community has seemed pretty wiling to help
navigate, fix or work around these problems.

Still, I like the outlinability the oversee-ability of keeping all my work
in org-mode, as well as the ability to use comments and "inline" TODOs.
(they're not really inline, but they are independant of the outline
structure.)  And I figure when the thing is nearing its final form, I'll nix
org if I have to and just work in the exportd LaTeX.

My next small project is finding a way to make my thesis.org file keep a
standard header outline (where the '** Headlines" hold the text that will
eventually head the chapters, sections and subsections), and also an outline
of my argument, which won't be printed, but is more useful for the writing
process. I've tried a few things but have not settled on anything yet.

Keep well,

Scot


On Thu, Mar 4, 2010 at 5:33 AM, Torsten Wagner <torsten.wagner@gmail.com>wrote:

> Dear Henri,
>
>
> On 03/04/2010 01:45 PM, Henri-Paul Indiogine wrote:
>
>> I started writing my doctoral dissertation in history using org-mode. I
>> am also using git.el for my version control and gnus for my email. Of
>> course I export my org file to LaTeX which I compile to pdf.  My
>> bibliography is managed using BibTeX.
>>
>
> please consider that you might have to follow a very stricy layout style
> depening on your university, department, lab or supervisor. If your are
> lucky there will be a LaTeX template somewhere at your university. If you
> are unlucky there is nothing like that or even worse only a MS-word
> template.
>
> I'm not sure how good org-mode might be usable in that case. org-mode is
> really great and I try to use it for many purposes. However, for a thesis I
> would use directly LaTeX which gives me a bit more control of what is going
> on.
>
> Furthermore, try biber [1] and biblatex [2]... the somehow next generation
> of bibtex and bib-file compatible. For me they work very well already
> despite of the fact that they are still beta-versions. biblatex gives you
> much more freedom of formatting your citations and bibliography... I guess
> both highly needed in your scientific field.
>
> Good luck
>
> Torsten
>
> [1] http://biblatex-biber.sourceforge.net/
> [2] http://www.ctan.org/tex-archive/help/Catalogue/entries/biblatex.html
>
>
>
>
>
>
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>

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Re: Writing a dissertation using org-mode

[Henri-Paul Indiogine]

Torsten Wagner <torsten.wagner@gmail.com> writes:
> please consider that you might have to follow a very stricy layout
> style depening on your university, department, lab or supervisor. If
> your are lucky there will be a LaTeX template somewhere at your
> university. If you are unlucky there is nothing like that or even
> worse only a MS-word template.

That is true.  My university has a LaTeX template.  However, it is in
the previous version of LaTeX.  I find that inexcusable. They should
update it.  It is not happening.  I think I should make a formal complaint.



> I'm not sure how good org-mode might be usable in that case. org-mode
> is really great and I try to use it for many purposes. However, for a
> thesis I would use directly LaTeX which gives me a bit more control of
> what is going on.

True,  I probably will use org-mode as an intermediary step.  I will use
it to create my drafts and then at the end change to the university
LaTeX template.  That should not be too much work.

> Furthermore, try biber [1] and biblatex [2]... the somehow next
> generation of bibtex and bib-file compatible. For me they work very
> well already despite of the fact that they are still
> beta-versions. biblatex gives you much more freedom of formatting your
> citations and bibliography... I guess both highly needed in your
> scientific field.

Good point, I am just worried about learning too many things (Emacs,
LaTeX, git, org-mode, R, ESS, ...) to take on new technologies. Writing
a dissertation is quite a load already.  But I will into it.

Thanks,


-- 
Henri-Paul Indiogine
Email: hindiogine@gmail.com
Skype: hindiogine
Website: http://www.coe.tamu.edu/~enrico

Re: Writing a dissertation using org-mode

[Detlef Steuer]

On Thu, 04 Mar 2010 11:12:42 -0600
Henri-Paul Indiogine <hindiogine@gmail.com> wrote:

> Good point, I am just worried about learning too many things (Emacs,
> LaTeX, git, org-mode, R, ESS, ...) to take on new technologies. Writing
> a dissertation is quite a load already.  But I will into it.

Don't worry about that. All these really fine tools (exactly my set of
tools btw) share a common property: You'll improve your productivity
from, say, day three. Of i.e. git I know may be 1% of the features. But
I was going in no time. There will be the moments of 'oh, had I known
this four weeks before', but that happens whatever art you learn! So,
drop bibtex and choose one of the utf-ready alternatives and you have
a very capable set of tools to write your dissertation (and beyond)!

(Luckily mine was done a while ago, but org-mode would have made my self-organisation 
 so much easier! And org-babel ...)

Good luck
Detlef

Re: Writing a dissertation using org-mode

[Eric S Fraga]

On Thu, 04 Mar 2010 14:33:33 +0900, Torsten Wagner <torsten.wagner@gmail.com> wrote:
> On 03/04/2010 01:45 PM, Henri-Paul Indiogine wrote:
> > I started writing my doctoral dissertation in history using org-mode. I
> > am also using git.el for my version control and gnus for my email. Of
> > course I export my org file to LaTeX which I compile to pdf.  My
> > bibliography is managed using BibTeX.
> 
> please consider that you might have to follow a very stricy layout
> style depening on your university, department, lab or supervisor. If

[...]

> I'm not sure how good org-mode might be usable in that case. org-mode
> is really great and I try to use it for many purposes. However, for a
> thesis I would use directly LaTeX which gives me a bit more control of
> what is going on.

Torsten,

if I may (respectfully) disagree?  Having examined too many PhD theses
to count, I would prefer PhD candidates spent more of their time
worrying about the content and organisation of their thesis than the
actual layout.  Unlike the preparation of camera ready copy for
conferences, say, most of the defaults taken by LaTeX are usually fine
once you've set up the layout to meet the university's requirements
(which are usually only about page size, margins and font sizes).  The
great thing about using org-mode for writing is the outlining and the
ability to easily move sections around.

Being able to insert LaTeX code directly when required means that
there is seldom the need to edit the actual LaTeX code generated by
org-mode (bugs excepted, of course, but not only are these few and far
between but Carsten et al. usually fix bugs very quickly).

cheers,
eric

Re: Writing a dissertation using org-mode

[Sven Bretfeld]

Eric S Fraga <ucecesf@ucl.ac.uk> writes:

> if I may (respectfully) disagree?  Having examined too many PhD theses
> to count, I would prefer PhD candidates spent more of their time
> worrying about the content and organisation of their thesis than the
> actual layout.  Unlike the preparation of camera ready copy for
> conferences, say, most of the defaults taken by LaTeX are usually fine
> once you've set up the layout to meet the university's requirements
> (which are usually only about page size, margins and font sizes).  The
> great thing about using org-mode for writing is the outlining and the
> ability to easily move sections around.

I fully agree and would add some other advantages:

- Orgmode can help to plan a paper or thesis right from the first second
  onwards. If you plan your texts in the canonical bottom-up way,
  orgmode helps you through all the stages: 

  1. Brainstorming
  2. Selecting
  3. Mindmapping
  4. Visualizing (org-mindmap)
  5. Structuring
  6. Writing

- Orgmode has the fantastic (and AFAIK unique) feature that you can
  integrate your text project directly into your time and todo
  management. Most people writing with MSWord etc. use to use
  marginnotes or something similar to make notes like "Check the
  pagenumber of this citation again". They are lucky if they actually
  remember this task when they are in a library. Writing in orgmode you
  can just add:

  * TODO Check the pagenumber of this citation again   :@LIBRARY:

  And you automatically have that todo in your daily agenda.

Greetings,

Sven

Re: Writing a dissertation using org-mode

[Markus Heller]

On 3/5/2010 2:14 AM, Sven Bretfeld wrote:
> Eric S Fraga<ucecesf@ucl.ac.uk>  writes:
>
>> if I may (respectfully) disagree?  Having examined too many PhD theses
>> to count, I would prefer PhD candidates spent more of their time
>> worrying about the content and organisation of their thesis than the
>> actual layout.  Unlike the preparation of camera ready copy for
>> conferences, say, most of the defaults taken by LaTeX are usually fine
>> once you've set up the layout to meet the university's requirements
>> (which are usually only about page size, margins and font sizes).  The
>> great thing about using org-mode for writing is the outlining and the
>> ability to easily move sections around.
>
> I fully agree and would add some other advantages:
>
> - Orgmode can help to plan a paper or thesis right from the first second
>    onwards. If you plan your texts in the canonical bottom-up way,
>    orgmode helps you through all the stages:
>
>    1. Brainstorming
>    2. Selecting
>    3. Mindmapping
>    4. Visualizing (org-mindmap)
>    5. Structuring
>    6. Writing
>
> - Orgmode has the fantastic (and AFAIK unique) feature that you can
>    integrate your text project directly into your time and todo
>    management. Most people writing with MSWord etc. use to use
>    marginnotes or something similar to make notes like "Check the
>    pagenumber of this citation again". They are lucky if they actually
>    remember this task when they are in a library. Writing in orgmode you
>    can just add:
>
>    * TODO Check the pagenumber of this citation again   :@LIBRARY:
>
>    And you automatically have that todo in your daily agenda.

I have to agree with Torsten: I'd write the thesis directly in LaTeX, 
only because of the power of AUCTeX and RefTeX (and preview, if you have 
lots of plots and math).

I do see the advantages of orgmode in terms of brainstorming etc. as 
outlined by Sven, and I'd use orgmode for 1.--5. for sure.

Just one remark on Sven's last point: Having the TODO item in your 
agenda when you're in the library only helps if you have access to your 
org-files ...

Just my 2 cents
Markus

Re: Re: Writing a dissertation using org-mode

[Eric S Fraga]

> I have to agree with Torsten: I'd write the thesis directly in LaTeX,
> only because of the power of AUCTeX and RefTeX (and preview, if you
> have lots of plots and math).

For me, org-mode's power overwhelms what auctex brings to the show.
Not having to worry about any \begins etc not only keeps the text
cleaner, it helps me in my continuing battle against RSI!

However, I do agree that reftex is particularly useful and I do miss
some aspects of it.

The preview aspects will of course depend on the topic of the thesis!

> Just one remark on Sven's last point: Having the TODO item in your
> agenda when you're in the library only helps if you have access to
> your org-files ...

What??  You sometimes don't have access to your org-files?  I could
not function in this way any more!  ;-)

Re: Re: Writing a dissertation using org-mode

[Thomas S. Dye]

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On Mar 6, 2010, at 1:54 PM, Eric S Fraga wrote:

>> I have to agree with Torsten: I'd write the thesis directly in LaTeX,
>> only because of the power of AUCTeX and RefTeX (and preview, if you
>> have lots of plots and math).
>
> For me, org-mode's power overwhelms what auctex brings to the show.
> Not having to worry about any \begins etc not only keeps the text
> cleaner, it helps me in my continuing battle against RSI!
>
> However, I do agree that reftex is particularly useful and I do miss
> some aspects of it.
>
> The preview aspects will of course depend on the topic of the thesis!

Aloha Eric,

I have this in my emacs starter-kit and it gives me access to reftex  
in latex code blocks in org-babel.  I've changed a few things from the  
code I found on the link provided, which has two methods of  
integrating reftex with org-mode.  The link also provides suggestions  
for key-bindings within org-mode.  Perhaps you don't have to miss  
reftex anymore.

*** ON Org-mode RefTeX setup
     - Kevin Brubeck Unhammer, [[http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/ 
][Reftex Setup]]
#+begin_src emacs-lisp :tangle yes
   (defun org-mode-article-modes ()
     (reftex-mode t)
     (and (buffer-file-name)
          (file-exists-p (buffer-file-name))
          (reftex-parse-all)))

   (add-hook 'org-mode-hook
              (lambda ()
                (if (member "REFTEX" org-todo-keywords-1)
                    (org-mode-article-modes))))
#+end_src

I was struggling without reftex!

All the best,
Tom

Thomas S. Dye, Ph.D.
T. S. Dye & Colleagues, Archaeologists, Inc.
Phone: (808) 529-0866 Fax: (808) 529-0884
http://www.tsdye.com



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Re: Re: Writing a dissertation using org-mode

[Eric S Fraga]

On Sat, 6 Mar 2010 17:10:38 -1000, "Thomas S. Dye" <tsd@tsdye.com> wrote:

[...]

> 
> Aloha Eric,
> 
> I have this in my emacs starter-kit and it gives me access to reftex
> in latex code blocks in org-babel.  I've changed a few things from the
> code I found on the link provided, which has two methods of
> integrating reftex with org-mode.  The link also provides suggestions
> for key-bindings within org-mode.  Perhaps you don't have to miss
> reftex anymore.

> http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/

[...]

> 
> I was struggling without reftex!
> 
> All the best,
> Tom

Thanks for these pointers Tom!  I actually already had the key
bindings suggested set up but had simply forgotten about them (one of
the problems with such a powerful system is that it's impossible to
keep everything in mind at all times...).  However, the comments on
that web site are quite useful as well!

Thanks again,
eric

Re: Re: Writing a dissertation using org-mode

[Carsten Dominik]

Hi Thomas,

I think this explanation would be good to have (a bit longer, maybe)  
in the FAQ.

- Carsten

On Mar 7, 2010, at 4:10 AM, Thomas S. Dye wrote:

>
> On Mar 6, 2010, at 1:54 PM, Eric S Fraga wrote:
>
>>> I have to agree with Torsten: I'd write the thesis directly in  
>>> LaTeX,
>>> only because of the power of AUCTeX and RefTeX (and preview, if you
>>> have lots of plots and math).
>>
>> For me, org-mode's power overwhelms what auctex brings to the show.
>> Not having to worry about any \begins etc not only keeps the text
>> cleaner, it helps me in my continuing battle against RSI!
>>
>> However, I do agree that reftex is particularly useful and I do miss
>> some aspects of it.
>>
>> The preview aspects will of course depend on the topic of the thesis!
>
> Aloha Eric,
>
> I have this in my emacs starter-kit and it gives me access to reftex  
> in latex code blocks in org-babel.  I've changed a few things from  
> the code I found on the link provided, which has two methods of  
> integrating reftex with org-mode.  The link also provides  
> suggestions for key-bindings within org-mode.  Perhaps you don't  
> have to miss reftex anymore.
>
> *** ON Org-mode RefTeX setup
>     - Kevin Brubeck Unhammer, [[http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/ 
> ][Reftex Setup]]
> #+begin_src emacs-lisp :tangle yes
>   (defun org-mode-article-modes ()
>     (reftex-mode t)
>     (and (buffer-file-name)
>          (file-exists-p (buffer-file-name))
>          (reftex-parse-all)))
>
>   (add-hook 'org-mode-hook
>              (lambda ()
>                (if (member "REFTEX" org-todo-keywords-1)
>                    (org-mode-article-modes))))
> #+end_src
>
> I was struggling without reftex!
>
> All the best,
> Tom
>
> Thomas S. Dye, Ph.D.
> T. S. Dye & Colleagues, Archaeologists, Inc.
> Phone: (808) 529-0866 Fax: (808) 529-0884
> http://www.tsdye.com
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

- Carsten

Re: Re: Writing a dissertation using org-mode

[Thomas S. Dye]

Hi Carsten,

I added an entry to the Export section of the FAQ.

All the best,
Tom

On Mar 9, 2010, at 6:27 AM, Carsten Dominik wrote:

> Hi Thomas,
>
> I think this explanation would be good to have (a bit longer, maybe)  
> in the FAQ.
>
> - Carsten
>
> On Mar 7, 2010, at 4:10 AM, Thomas S. Dye wrote:
>
>>
>> On Mar 6, 2010, at 1:54 PM, Eric S Fraga wrote:
>>
>>>> I have to agree with Torsten: I'd write the thesis directly in  
>>>> LaTeX,
>>>> only because of the power of AUCTeX and RefTeX (and preview, if you
>>>> have lots of plots and math).
>>>
>>> For me, org-mode's power overwhelms what auctex brings to the show.
>>> Not having to worry about any \begins etc not only keeps the text
>>> cleaner, it helps me in my continuing battle against RSI!
>>>
>>> However, I do agree that reftex is particularly useful and I do miss
>>> some aspects of it.
>>>
>>> The preview aspects will of course depend on the topic of the  
>>> thesis!
>>
>> Aloha Eric,
>>
>> I have this in my emacs starter-kit and it gives me access to  
>> reftex in latex code blocks in org-babel.  I've changed a few  
>> things from the code I found on the link provided, which has two  
>> methods of integrating reftex with org-mode.  The link also  
>> provides suggestions for key-bindings within org-mode.  Perhaps you  
>> don't have to miss reftex anymore.
>>
>> *** ON Org-mode RefTeX setup
>>    - Kevin Brubeck Unhammer, [[http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/ 
>> ][Reftex Setup]]
>> #+begin_src emacs-lisp :tangle yes
>>  (defun org-mode-article-modes ()
>>    (reftex-mode t)
>>    (and (buffer-file-name)
>>         (file-exists-p (buffer-file-name))
>>         (reftex-parse-all)))
>>
>>  (add-hook 'org-mode-hook
>>             (lambda ()
>>               (if (member "REFTEX" org-todo-keywords-1)
>>                   (org-mode-article-modes))))
>> #+end_src
>>
>> I was struggling without reftex!
>>
>> All the best,
>> Tom
>>
>> Thomas S. Dye, Ph.D.
>> T. S. Dye & Colleagues, Archaeologists, Inc.
>> Phone: (808) 529-0866 Fax: (808) 529-0884
>> http://www.tsdye.com
>>
>>
>> _______________________________________________
>> Emacs-orgmode mailing list
>> Please use `Reply All' to send replies to the list.
>> Emacs-orgmode@gnu.org
>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>
> - Carsten
>
>
>

Re: Re: Writing a dissertation using org-mode

[Carsten Dominik]

On Mar 21, 2010, at 8:19 PM, Thomas S. Dye wrote:

> Hi Carsten,
>
> I added an entry to the Export section of the FAQ.

Thanks Tom!

- Carsten


>
> All the best,
> Tom
>
> On Mar 9, 2010, at 6:27 AM, Carsten Dominik wrote:
>
>> Hi Thomas,
>>
>> I think this explanation would be good to have (a bit longer,  
>> maybe) in the FAQ.
>>
>> - Carsten
>>
>> On Mar 7, 2010, at 4:10 AM, Thomas S. Dye wrote:
>>
>>>
>>> On Mar 6, 2010, at 1:54 PM, Eric S Fraga wrote:
>>>
>>>>> I have to agree with Torsten: I'd write the thesis directly in  
>>>>> LaTeX,
>>>>> only because of the power of AUCTeX and RefTeX (and preview, if  
>>>>> you
>>>>> have lots of plots and math).
>>>>
>>>> For me, org-mode's power overwhelms what auctex brings to the show.
>>>> Not having to worry about any \begins etc not only keeps the text
>>>> cleaner, it helps me in my continuing battle against RSI!
>>>>
>>>> However, I do agree that reftex is particularly useful and I do  
>>>> miss
>>>> some aspects of it.
>>>>
>>>> The preview aspects will of course depend on the topic of the  
>>>> thesis!
>>>
>>> Aloha Eric,
>>>
>>> I have this in my emacs starter-kit and it gives me access to  
>>> reftex in latex code blocks in org-babel.  I've changed a few  
>>> things from the code I found on the link provided, which has two  
>>> methods of integrating reftex with org-mode.  The link also  
>>> provides suggestions for key-bindings within org-mode.  Perhaps  
>>> you don't have to miss reftex anymore.
>>>
>>> *** ON Org-mode RefTeX setup
>>>   - Kevin Brubeck Unhammer, [[http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/ 
>>> ][Reftex Setup]]
>>> #+begin_src emacs-lisp :tangle yes
>>> (defun org-mode-article-modes ()
>>>   (reftex-mode t)
>>>   (and (buffer-file-name)
>>>        (file-exists-p (buffer-file-name))
>>>        (reftex-parse-all)))
>>>
>>> (add-hook 'org-mode-hook
>>>            (lambda ()
>>>              (if (member "REFTEX" org-todo-keywords-1)
>>>                  (org-mode-article-modes))))
>>> #+end_src
>>>
>>> I was struggling without reftex!
>>>
>>> All the best,
>>> Tom
>>>
>>> Thomas S. Dye, Ph.D.
>>> T. S. Dye & Colleagues, Archaeologists, Inc.
>>> Phone: (808) 529-0866 Fax: (808) 529-0884
>>> http://www.tsdye.com
>>>
>>>
>>> _______________________________________________
>>> Emacs-orgmode mailing list
>>> Please use `Reply All' to send replies to the list.
>>> Emacs-orgmode@gnu.org
>>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>>
>> - Carsten
>>
>>
>>
>

- Carsten

Re: Writing a dissertation using org-mode

[Maurizio Vitale]

I'd recommend you use auctex for writing your thesis: it knows about
many LaTeX packages (and you can teach it more), so you get
autocompletion and highlighting. It does quasi-wysiwyg for fonts and
math. It can render fragments for quick checking and interface with
external viewers. And it has some folding support, albeit not as nice as
org-mode's.

Org-mode would basically give you three things:
  - sectioning/folding
  - todo lists
  - simple tables
Org-mode is wonderful for quickly taking notes and generate LaTeX/pdf
out of them. But for a book/thesis you cannot beat auctex.

Best regards,

     Maurizio

Re: Re: Writing a dissertation using org-mode

[Thomas S. Dye]

On Mar 4, 2010, at 4:02 AM, Maurizio Vitale wrote:

>
> I'd recommend you use auctex for writing your thesis: it knows about
> many LaTeX packages (and you can teach it more), so you get
> autocompletion and highlighting. It does quasi-wysiwyg for fonts and
> math. It can render fragments for quick checking and interface with
> external viewers. And it has some folding support, albeit not as  
> nice as
> org-mode's.
>
> Org-mode would basically give you three things:
>  - sectioning/folding
>  - todo lists
>  - simple tables
> Org-mode is wonderful for quickly taking notes and generate LaTeX/pdf
> out of them. But for a book/thesis you cannot beat auctex.
>
> Best regards,
>
>     Maurizio


Aloha Henri-Paul,

I think this is good advice for a thesis writer.  auctex, with the  
reftex plug-in, is a huge help.

The model I'm working with now for writing a book (still evolving as I  
learn org-mode and org-babel and try different things) has 3 parts:

1) The main body of the book, held in several tex files, typically one  
file per chapter.  A master tex file contains the memoir header, the  
includes, and the glossary, bibliography, and index paraphernalia.  I  
do almost all my writing in these files.

2) An org-mode file with a level one heading for each chapter,  
underneath which is a place for notes, todo items, random thoughts,  
and outline fragments.  Immediately beneath the level one heading is a  
link to the chapter tex file.  I use the org-mode file to keep track  
of what I've finished and what still needs work.  This is a tremendous  
help when I have to put the work down for a while and then pick it up  
again.  I'm back up to speed in short order.

3) Several org-babel LaTeX code blocks and noweb references to the  
output from statistical analyses mostly in R and carried out in org- 
babel.  These are mostly descriptive sections and the benefit of  
writing them this way is that they track changes in the database as I  
augment observations or spot data entry errors while writing.  These  
are exported to tex files that are referenced in the master tex file.

4) Compiling my book is a three-step process (ignoring for the moment  
the bibliography, glossary, and index).  First, re-run the statistical  
analyses in org-babel.  Second, run org-babel-tangle on the org-mode  
file to refresh the output of the org-babel LaTeX code blocks.  Lastly  
compile to pdf with auctex.

I'll be interested to learn how you end up writing your thesis with  
LaTeX and org-mode.

HTH,
Tom

Re: Re: Writing a dissertation using org-mode

[Henri-Paul Indiogine]

"Thomas S. Dye" <tsd@tsdye.com> writes:
> The model I'm working with now for writing a book (still evolving as I
> learn org-mode and org-babel and try different things) has 3 parts:

I am very impressed by your setup and it closely matches my
requirements.  I will most likely implement it once my proposal has been
accepted.

I am in your debt :-)    I am very glad to be able to use org-mode and
be part of its wonderful user and developer community.



-- 
Henri-Paul Indiogine
Email: hindiogine@gmail.com
Skype: hindiogine
Website: http://www.coe.tamu.edu/~enrico