Re: Using Org for a dissertation

Re: Using Org for a dissertation

[Eric Schulte]

Hi Richard,

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 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 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.
>

This always feels hacky, but I just place this command at the end of the
document in whatever section (usually "conclusion") that may be.

>
> 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!
>

When preparing a JSS paper for publication [4] we found that to satisfy
some of the Journal's specific formatting rules we had to add a new
document class, add a new link type, and post-process the generated
LaTeX.  The entirety of this customization may be found here [5] -- the
Makefile in that directory may also be helpful.

In summary, I have very much enjoyed writing longer documents in
Org-mode (on those few occasions when all authors are Org-mode users).
With the ability to write in-line latex it is possible to meet any
stringent output requirements.

I hope this helps,

>
> Thanks,
> Richard
>
>


Footnotes: 
[1]  http://cs.unm.edu/~eschulte/dissertation/refs/force.html

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

[3]  http://gitweb.adaptive.cs.unm.edu/dissertation.git/blob_plain/HEAD:/Makefile

[4]  http://www.jstatsoft.org/v46/i03

[5]  https://github.com/eschulte/org-mode-jss/blob/master/init.el

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

Using Org for a dissertation

[Richard Lawrence]

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

Re: Using Org for a dissertation

[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

Re: Using Org for a dissertation

[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

Re: Using Org for a dissertation

[Richard Lawrence]

Hi Eric,

Eric Schulte <eric.schulte@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: Using Org for a dissertation

[Richard Lawrence]

Thomas S. Dye <tsd@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: Using Org for a dissertation

[suvayu ali]

[-- Attachment #1: Type: text/plain, Size: 1265 bytes --]

Hi Richard,

On Sat, May 12, 2012 at 8:23 PM, Richard Lawrence
<richard.lawrence@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_11110.pdf>
[2] <https://github.com/suvayu/.emacs.d/blob/master/org-mode-config.el>

-- 
Suvayu

Open source is the future. It sets us free.

[-- Attachment #2: shortthesis.txt --]
[-- Type: text/plain, Size: 12741 bytes --]

# -*- 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.Ali@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 diagrams[fn:1]
    responsible for the production of $W'$ bosons at a hadron
    collider are known as charged current (CC) processes. These are
    flavour changing interactions occurring between up-like and
    down-like quarks (or anti-quarks) where the weak current involved
    is charged as the gauge bosons involved are charged.
    \Figref{fig:LO-Wprime} shows a diagram responsible for $W'$
    production at the LHC.

    The production of a heavy $W'$ boson from a pp collision depends
    strongly on the momenta of the initial state particles. Since
    protons are composite particles made of (anti-)quarks and gluons,
    knowledge about the momentum fraction carried by the initial
    state particles is important. This is achieved by a /Parton
    Distribution Function/ (PDF) determined from deep inelastic
    scattering experiments with hadrons and leptons. In 1968--69,
    Bjorken proposed a dimensionless quantity /x/ which is
    independent of the momentum transfer during a hard scattering
    event. They exhibit a scaling behaviour in the asymptotic limit
    of very high energy collisions, known as /Bjorken scaling/. The
    discovery of scaling behaviour as predicted by Bjorken led to the
    modern formulation of the strong force as an asymptotically free
    quantum field theory \cite{Tung:2009}. The scaling was later
    shown to be only approximately true at low energies due to higher
    order QCD corrections (scaling violations).

    In 1969 Feynman proposed the /parton model/. It describes hadrons
    as composite particles made of its constituent quarks,
    anti-quarks and gluons \cite{PhysRevLett.23.1415}. The
    constituent quarks can be either valence or sea quarks. If the
    quark is one of the three quarks forming the hadron bound state
    and responsible for the quantum number, then it is called the
    /valence quark/. On the other hand if it is a virtual quark
    formed by splitting of gluons, it is called a /sea quark/.
    Modern QCD explains the interaction of hadrons in hard scattering
    experiments using this parton model.

    #+begin_src latex
      \begin{equation}
      \label{eq:partondistribfn}
      \frac{d\sigma}{dm_T} = \sum\limits_{a,b} \int dx_A f_{a/A}(x_A,\mu) \int dx_B f_{b/B}(x_B,\mu) \frac{d\hat{\sigma}}{dm_T}
      \end{equation}
    #+end_src

    The differential production cross section ($d\sigma/dm_T$) for
    observing certain events in a channel in a hadron collider is
    given by \Eqref{eq:partondistribfn}. $f_{a/A}$ and $f_{b/B}$ are
    the parton distribution functions mentioned earlier. They are the
    probability distributions of finding a parton of type /a/ (/b/)
    originating from a hadron of type /A/ (/B/) with the momentum
    fraction $x_A$ ($x_B$). $d\hat{\sigma}/dm_T$ is the parton level
    cross section given by perturbative QCD. The Bjorken scaling
    violations observed earlier could be incorporated into this
    picture by including corrections to the PDFs from perturbative
    QCD. These corrections introduce the dependence on the parameter
    \mu in the PDFs. The parameter \mu is related to the
    renormalisation of the strong coupling in the cross section
    calculation and the QCD corrections to the PDFs. They are often
    referred to separately as /renormalisation scale/ and
    /factorisation scale/ \cite{Soper:1996sn}.

    #+begin_src latex
      \begin{figure}[p]
      \centering
      \begin{tabular}{c}
      \includegraphics[width=0.7\textwidth,trim=0 150 0 150]{plots/PDF-upv.pdf} \\
      \includegraphics[width=0.7\textwidth,trim=0 150 0 150]{plots/PDF-downv.pdf}
      \end{tabular}

      \caption[PDF for the proton at $Q^2 = 1$ TeV/c$^2$]{Proton PDFs
      showing the probability distributions for up (top) and down
      (bottom) quarks at $Q^2 = 1$ TeV/c$^2$. The valence quark PDF
      (black) is compared with the sea quark (red) and gluon (green)
      PDFs. A common choice for the factorisation scale when
      calculating a PDF set is to set it to $Q^2$ of the process
      \cite{website:HepData}.}

      \label{fig:PDF}
      \end{figure}
    #+end_src


* Appendices 						      :ignoreheading:
  :PROPERTIES:
  :VISIBILITY: folded
  :END:

#+LaTeX: \newpage
#+LaTeX: \appendix
# Needs \usepackage{appendix}
#+LaTeX: \addappheadtotoc
#+LaTeX: \appendixpage

** Particle track parametrisation in ATLAS				:trk:

   \label{app:trackparam}

   A particle track in ATLAS is represented by the perigee[fn:2] of the
   track. The perigee is specified by the five parameters:

   + d_0 - transverse impact parameter, the distance of the closest
     approach of helix to beam pipe,
   + z_0 - longitudinal impact parameter, the z value at the point of
     closest approach,
   + \phi_0 - azimuth angle of the momentum at point of closest
     approach, measured in the range $[-\pi,\pi)$,
   + \theta - polar angle in the range $[0,\pi]$,
   + q/p - charge over momentum magnitude.


   In ATLAS the /z/-axis is parallel to the magnetic field (which is
   parallel to the beam axis). \Figref{fig:trkperigee} shows the five
   parameters split into transverse and longitudinal planes.

   #+CAPTION: [Schematic showing all 5 track parameters]{The diagram shows the five parameters, the three longitudinal parameters in the x-y plane and two longitudinal parameters in the r-z plane.}
   #+LABEL: fig:trkperigee
   #+ATTR_LaTeX: width=0.6\textwidth placement=[p]
   [[file:figs/Perigee.png]]


** Limit formalism						     :limits:

   \label{app:limits}

   The limits are set with the observed events in a bin with $m_T$ >
   $m_{Tmin}$, where the lower bin threshold is determined by taking
   the half of the $W'$ mass. The expected number of events are given
   by \Eqref{eq:expevts}, where $\nbg$ is the expected number of
   events from our background model and $N_{sig}$ is the predicted
   number of signal events from \Eqref{eq:sigevts}. $L_{int}$ is the
   integrated luminosity of the recorded data and $\epsilon_{sig}$ is
   the event selection efficiency.

   #+begin_src latex
     \begin{align}
     \label{eq:expevts}
     N_{exp} &= N_{sig} + \nbg \\
     \label{eq:sigevts}
     N_{sig} &= L_{int} \epsilon_{sig} \SB
     \end{align}
   #+end_src

   The likelihood function in \Eqref{eq:likelihood} is obtained from
   Poisson statistics for $N_{obs}$ observed events. Uncertainties are
   included as nuisance parameters in the analysis. They are assumed
   to follow a Gaussian probability distribution. In this analysis we
   consider uncertainties on $L_{int}$, $\epsilon_{sig}$ and $\nbg$ in
   our calculations. Taking the above into consideration we get the
   likelihood function shown in \Eqref{eq:llnuissance}.

   #+begin_src latex
     \begin{align}
     \label{eq:likelihood}
     \mathcal{L}(\SB) &= \frac{(L_{int}\SB + \nbg)^{N_{obs}}e^{-(L_{int}\epsilon_{sig}\SB+\nbg)}}{N_{obs}!} \\
     \label{eq:llnuissance}
     \mathcal{L}(\SB,\theta_1,\dotsc\theta_N) &= \frac{(L_{int}\SB + \nbg)^{N_{obs}}e^{-(L_{int}\epsilon_{sig}\SB+\nbg)}}{N_{obs}!} \prod g_i(\theta_i) \\
     g_i(\theta_i) &= \frac{1}{\sqrt{2\pi}\sigma_i}e^{-\frac{(\theta -\bar{\theta}_i)^2}{2\sigma_i^2}} \nonumber
     \end{align}
   #+end_src

   This likelihood function is used to calculate the log-likelihood
   ratio (LLR) test statistic shown in \Eqref{eq:LLR}
   \cite{Junk:1999kv}. The LLR is used to calculate /p/-values which
   correspond to confidence levels for the signal + background
   (CL_{s+b}) and background (CL_b) only hypotheses. These are
   evaluated by conducting pseudo-experiments and integrating over the
   corresponding LLR distributions.

   #+begin_src latex
     \begin{equation}
     \label{eq:LLR}
     LLR = -2 \ln \frac{\mathcal{L}(data\lvert s+b)}{\mathcal{L}(data\lvert b)}
     \end{equation}
   #+end_src

   The CL_s method finally uses the ratio of the /p/-values to
   determine the exclusion limits (\eqref[name=eq.~]{eq:CLs}). To set
   the limits at 95% confidence level, the signal cross section is
   increased until CL_s = 1 - \alpha where \alpha is 0.95. For a more
   complete discussion of the limit setting procedure see the
   referenced ATLAS internal note \cite{Adams:1317922}.

   #+begin_src latex
     \begin{equation}
     \label{eq:CLs}
     CL_s = \frac{CL_{s+b}}{CL_b}
     \end{equation}
   #+end_src


* Bibliography						      :ignoreheading:

#+LaTeX: \backmatter
#+LaTeX: \newpage
#+LaTeX: \addcontentsline{toc}{chapter}{\bibname}
#+LaTeX: \bibliographystyle{ieeetr}
#+LaTeX: \bibliography{master}


* Footnotes

[fn:1] Here and in the rest of this thesis /diagram/ refers to Feynman
diagrams unless otherwise specified.

[fn:2] The point where the track comes closest to the geometrical
centre of the detector is called the perigee of the track.


* COMMENT local setup

# Local Variables:
# org-export-allow-BIND: t
# org-latex-to-pdf-process: ("pdflatex -interaction nonstopmode %b" "/usr/bin/bibtex %b" "pdflatex -interaction nonstopmode %b" "pdflatex -interaction nonstopmode %b")
# End:

Re: Using Org for a dissertation

[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: Using Org for a dissertation

[Nicolas Goaziou]

Hello,

Richard Lawrence <richard.lawrence@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: Using Org for a dissertation

[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: Using Org for a dissertation

[Richard Lawrence]

Hi Suvayu,

suvayu ali <fatkasuvayu+linux@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: Using Org for a dissertation

[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 <post@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: Using Org for a dissertation

[Matt Lundin]

Richard Lawrence <richard.lawrence@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: Using Org for a dissertation

[Rasmus]

Eric Schulte <eric.schulte@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: Using Org for a dissertation

[Eric S Fraga]

[-- Attachment #1: Type: text/plain, Size: 977 bytes --]

Rasmus <rasmus@gmx.us> writes:

> Eric Schulte <eric.schulte@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.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: t.org --]
[-- Type: text/org, Size: 134 bytes --]

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

[-- Attachment #3: Type: text/plain, Size: 102 bytes --]


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