# -*- coding: utf-8 -*-
# -*- mode: org -*-

#+TITLE:       Org document examples
#+AUTHOR:      Arnaud Legrand
#+STARTUP: overview indent inlineimages logdrawer
#+LANGUAGE:    en

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. [[file: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. [[file:labbook_single.org][labbook_single.org]]: this is an excerpt from the laboratory notebook
   [[https://cornebize.net/][Tom Cornebize]] 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. [[file: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. [[file:labbook_several.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. [[file:technical_report.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.

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 [[https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.org][typical source]] and the
  [[https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.pdf][resulting PDF]]
- Lucas Schnorr, a colleague, maintains:
  - a set of templates for various computer science
    journals/conferences: [[https://github.com/schnorr/ieeeorg][IEEE]], [[https://github.com/schnorr/wileyorg][Wiley]], [[https://github.com/schnorr/acmorg][ACM]], [[https://github.com/schnorr/llncsorg][LNCS]]
  - his lecture on programming languages for undergrads:
    https://github.com/schnorr/mlp/tree/master/conteudo

