add org example

2022-03-replication/org/eg.org

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+#+title: Example research paper written with org mode
+#+author: James Brusey
+#+options: toc:nil
+#+property: header-args:ipython :session eg-sess :results output raw drawer :exports results
+#+latex_class: IEEEtran
+#+latex_header: \input{header}
+#+begin_abstract
+Every abstract should have 4 parts: motive, method, results, conclusions.
+Use no more than 3 sentences for each.
+Aim for about 100 words.
+#+end_abstract
+* Introduction
+The introduction should not just repeat the abstract but should properly introduce the topic.
+
+Towards the end of the introduction, there should be a statement about what the contribution of the paper.
+In computer science these days, it is common to use a bullet pointed list with forward references to sections where that contribution can be found.
+* Related work
+When it comes to citing references, org-ref is pretty cool. For example, I can cite a work [[cite:&kitchinExamplesEffectiveData2015]], and this will then show up in the references [[cite:&wilkinsModellingUncontrolledSolar2018]]. 
+* Methods and materials
+In the method section, you might have a diagram.
+
+#+caption: By putting a caption on the diagram, org-mode automatically changes it to a floating figure.
+#+attr_latex: :width 0.3\columnwidth
+[[file:heartbeat-0.pdf]]
+
+* Results
+While you can manually enter tables in org-mode, such as in autoref:table1.
+#+latex: \sisetup{round-mode=places}
+
+#+caption: Tables also can be floats. This example shows the power of using siunitx. label:table1
+#+attr_latex: :align lSS
+| Class | \protect{Mean} | \protect{Std} |
+|-------+----------------+---------------|
+| a     |            0.2 |      1.203030 |
+| b     |       1.234e-1 |        3.8e-3 |
+|       |                |               |
+
+A similar table can be produced using code, as in autoref:table2.
+
+#+BEGIN_SRC ipython
+import pandas as pd
+import numpy as np
+import tabulate
+
+df = pd.read_csv("../all.csv")
+result = pd.melt(df).groupby("variable").agg(["mean", "std"])
+print("""
+#+caption: This table was produced from the all.csv data-set. label:table2
+#+attr_latex: :align lSS""")
+
+print(
+    tabulate.tabulate(result, tablefmt="orgtbl", headers=["Class", "\protect{mean}", "\protect{std}"]),
+)
+#+END_SRC
+
+#+RESULTS:
+:results:
+
+#+caption: This table was produced from the all.csv data-set. label:table2
+#+attr_latex: :align lSS
+| Class   |   \protect{mean} |   \protect{std} |
+|---------+------------------+-----------------|
+| a       |         4.3      |         3.16394 |
+| b       |        -0.114247 |         1.00812 |
+| c       |         4.72661  |         3.85745 |
+:end:
+
+#+BEGIN_SRC ipython
+%matplotlib inline
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+df = pd.read_csv("../all.csv")
+plt.figure()
+plt.plot(df['a'], df['b'], '.')
+plt.show()
+
+#+END_SRC
+
+#+RESULTS:
+:results:
+# Out [2]: 
+# text/plain
+: <Figure size 432x288 with 1 Axes>
+
+# image/png
+[[file:obipy-resources/2abc833ac46639e8c3c3db1b162ed52c45494cc7/2b10c27d7fec897b3ebf8364b6da6e8b674ac4e0.png]]
+:end:
+
+
+* Conclusions
+In conclusion, there are many interesting tools for helping with increasing automation and thus reducing errors.
+
+bibliography:~/Documents/zotero-export.bib
+bibliographystyle:plain
+* Needed for adding IEEEtran class                                 :noexport:
+
+#+BEGIN_SRC emacs-lisp
+(add-to-list 'org-latex-classes
+             '("IEEEtran"
+               "\\documentclass\[10pt\]\{IEEEtran\}"
+               ("\\section\{%s\}" . "\\section*\{%s\}")
+               ("\\subsection\{%s\}" . "\\subsection*\{%s\}")
+               ("\\subsubsection\{%s\}" . "\\subsubsection*\{%s\}")
+               ("\\paragraph\{%s\}" . "\\paragraph*\{%s\}")
+	       ))
+
+#+END_SRC
+
+#+RESULTS:
+| IEEEtran            | \documentclass[10pt]{IEEEtran}        | (\section{%s} . \section*{%s}) | (\subsection{%s} . \subsection*{%s}) | (\subsubsection{%s} . \subsubsection*{%s}) | (\paragraph{%s} . \paragraph*{%s})         |                                            |
+| scrartcl            | \documentclass[10pt]{scrartcl}        | (\section{%s} . \section*{%s}) | (\subsection{%s} . \subsection*{%s}) | (\subsubsection{%s} . \subsubsection*{%s}) | (\paragraph{%s} . \paragraph*{%s})         |                                            |
+| scrreprt            | \documentclass[10pt,DIV=11]{scrreprt} | (\chapter{%s} . \chapter*{%s}) | (\section{%s} . \section*{%s})       | (\subsection{%s} . \subsection*{%s})       | (\subsubsection{%s} . \subsubsection*{%s}) | (\paragraph{%s} . \paragraph*{%s})         |
+| beamer              | \documentclass[presentation]{beamer}  | (\section{%s} . \section*{%s}) | (\subsection{%s} . \subsection*{%s}) | (\subsubsection{%s} . \subsubsection*{%s}) |                                            |                                            |
+| default-koma-letter | \documentclass[11pt]{scrlttr2}        |                                |                                      |                                            |                                            |                                            |
+| article             | \documentclass[11pt]{article}         | (\section{%s} . \section*{%s}) | (\subsection{%s} . \subsection*{%s}) | (\subsubsection{%s} . \subsubsection*{%s}) | (\paragraph{%s} . \paragraph*{%s})         | (\subparagraph{%s} . \subparagraph*{%s})   |
+| report              | \documentclass[11pt]{report}          | (\part{%s} . \part*{%s})       | (\chapter{%s} . \chapter*{%s})       | (\section{%s} . \section*{%s})             | (\subsection{%s} . \subsection*{%s})       | (\subsubsection{%s} . \subsubsection*{%s}) |
+| book                | \documentclass[11pt]{book}            | (\part{%s} . \part*{%s})       | (\chapter{%s} . \chapter*{%s})       | (\section{%s} . \section*{%s})             | (\subsection{%s} . \subsection*{%s})       | (\subsubsection{%s} . \subsubsection*{%s}) |
+
+[[elisp:(org-latex-export-to-pdf)]]

2022-03-replication/org/header.tex

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+\usepackage{xcolor}
+
+\usepackage{tikz}
+
+\definecolor{Blues1}{HTML}{eff3ff}
+\definecolor{Blues2}{HTML}{bdd7e7}
+\definecolor{Blues3}{HTML}{6baed6}
+\definecolor{Blues4}{HTML}{2171b5}
+
+\usepackage{siunitx}