---
title:       Document Examples
author:      Arnaud Legrand
date:   Wed Mar 20 13:03:17 2019 
---

# Table of Contents <span class="tag" data-tag-name="TOC"><span class="smallcaps">TOC</span></span>

  - [Examples from the Video](#examples-from-the-video)
  - [Other examples](#other-examples)

# Examples from the Video

In the MOOC video, I quickly demo how org-mode can be used in various
contexts. Here are the (sometimes trimmed) corresponding org-files.
These documents depend on many other external data files and are not
meant to lead to reproducible documents but it will give you an idea of
how it can be organized:

1.  [journal.org](journal.org): an excerpt (I've only left a few code
    samples and links to some resources on R, Stats, …) from my own
    journal. This is a personal document where everything (meeting
    notes, hacking, random thoughts, …) goes by default. Entries are
    created with the `C-c c` shortcut.
2.  [labbook<sub>single</sub>.org](labbook_single.org): this is an
    excerpt from the laboratory notebook [Tom
    Cornebize](https://cornebize.net/) wrote during his Master thesis
    internship under my supervision. This a personal labbook. I consider
    this notebook to be excellent and was the ideal level of details for
    us to communicate without any ambiguity and for him to move forward
    with confidence.
3.  [paper.org](paper.org): this is an ongoing paper based on the
    previous labbook of Tom Cornebize. As such it is not reproducible as
    there are hardcoded paths and uncleaned dependencies but writing it
    from the labbook was super easy as we just had to cut and paste the
    parts we needed. What may be interesting is the organization and the
    org tricks to export to the right LaTeX style. As you may notice, in
    the end of the document, there is a commented section with emacs
    commands that are automatically executed when opening the file. It
    is an effective way to depend less on the `.emacs/init.el` which is
    generally customized by everyone.
4.  [labbook<sub>several</sub>.org](labbook_several.org): this is a
    labbook for a specific project shared by several persons. As a
    consequence it starts with information about installation, common
    scripts, has section with notes about all our meetings, a section
    with information about experiments and an other one about analysis.
    Entries could have been labeled by who wrote them but there were
    only a few of us and this information was available in git so we did
    not bother. In such labbook, it is common to find annotations
    indicating that such experiment was `:FLAWED:` as it had some
    issues.
5.  [technical<sub>report</sub>.org](technical_report.org): this is a
    short technical document I wrote after a colleague sent me a PDF
    describing an experiment he was conducting and asked me about how
    reproducible I felt it was. It turned out I had to cut and paste the
    C code from the PDF, then remove all the line numbers and fix
    syntax, etc. Obviously I got quite different performance results but
    writing everything in org-mode made it very easy to generate both
    HTML and PDF and to explicitly explain how the measurements were
    done.

# Other examples

Here are a few links to other kind of examples:

  - Slides: all my slides for a series of lectures is available here:
    <https://github.com/alegrand/SMPE>. Here is a [typical
    source](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.org)
    and the [resulting
    PDF](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.pdf)
  - Lucas Schnorr, a colleague, maintains:
      - a set of templates for various computer science
        journals/conferences:
        [IEEE](https://github.com/schnorr/ieeeorg),
        [Wiley](https://github.com/schnorr/wileyorg),
        [ACM](https://github.com/schnorr/acmorg),
        [LNCS](https://github.com/schnorr/llncsorg)
      - his lecture on programming languages for undergrads:
        <https://github.com/schnorr/mlp/tree/master/conteudo>
  - John Kitchin is an expert org-mode user and he maintains a very
    interesting [blog with many interesting
    tips](http://kitchingroup.cheme.cmu.edu/blog/). You may want to
    check this [seminar he gave at
    SciPy](https://www.youtube.com/watch?v=IsSMs-4GlT8&list=FLQp2VLAOlvq142YN3JO3y8w&app=desktop).