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Academic writing using RMarkdown

Books, reports, blogs, slides, …

Sebastian Sauer

FOM
DGPs 2018

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What is RMarkdown?

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Markdown is not HTML

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<main class="content" role="main">
  <article class="article">
    <span class="article-duration">40 min read</span>
    <h1 class="article-title">Bayesian modeling of populist party success in German federal elections - A notebook from the lab</h1>
    <span class="article-date">2018/08/25</span>
    <div class="article-content">
      <p>Following up on an <a href="https://data-se.netlify.com/2017/10/10/afd-map/">earlier post</a>, we will model the voting success of the (most prominent) populist party, AfD, in the recent federal elections. This time, Bayesian modeling techniques will be used, drawing on the <a href="https://xcelab.net/rm/statistical-rethinking/">excellent textbook</a> my McElreath.</p>
<p>Note that this post is rather a notebook of my thinking, doing, and erring. I’ve made no efforts to hide scaffolding. I think it will be confusing to the uniniate and the initiate as well …</p>
<hr />
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Markdown is not Latex

\makeatletter
\newenvironment{kframe}{%
\medskip{}
\setlength{\fboxsep}{.8em}
 \def\at@end@of@kframe{}%
 \ifinner\ifhmode%
  \def\at@end@of@kframe{\end{minipage}}%
  \begin{minipage}{\columnwidth}%
 \fi\fi%
 \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
 \colorbox{shadecolor}{##1}\hskip-\fboxsep
     % There is no \\@totalrightmargin, so:
     \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
 \MakeFramed {\advance\hsize-\width
   \@totalleftmargin\z@ \linewidth\hsize
   \@setminipage}}%
 {\par\unskip\endMakeFramed%
 \at@end@of@kframe}
\makeatother
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Last time I tried to tweak some details in my Latex document

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Markdown is simple markup

# This is a title
This is a sentence.
Now a list begins:
- no importance
- again
- repeat
A numbered list:
1. first
2. second
3. third
__bold__, _italic_, ~~strike through~~

This is a title

This is a sentence.

Now a list begins:

  • no importance
  • again
  • repeat


A numbered list:

  1. first
  2. second
  3. third

bold, italic, strike through

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Want some more?

# Title level 1
## Title level 2
Link:  [my blog](https://data-se.netlify.com/)
Citation: [@Xie2018]
Image: ![my image](imgs/R-logo_small.png)

Title level 1

Title level 2

Link: my blog.

Citation: (Xie & Allaire, 2018)

Image:

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I know you love your formulas

$$e^{\ln{e}} = e$$
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I know you love your formulas

$$e^{\ln{e}} = e$$

eln⁡e=e

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I know you love your formulas

$$e^{\ln{e}} = e$$

eln⁡e=e

$$\frac{\sum (\bar{x} - x_i)^2}{n-1}$$
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I know you love your formulas

$$e^{\ln{e}} = e$$

eln⁡e=e

$$\frac{\sum (\bar{x} - x_i)^2}{n-1}$$

∑(x¯−xi)2n−1

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I know you love your formulas

$$e^{\ln{e}} = e$$

eln⁡e=e

$$\frac{\sum (\bar{x} - x_i)^2}{n-1}$$

∑(x¯−xi)2n−1

ad nauseam

Enter LATEX code in the same way.

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Quickstart with Markdown

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Markdown's Philosophy

Keep. it. Simple.

  • No formating/styling. Content only

  • Pleasant to the eye

  • Portable

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That's R Markdown (.Rmd)

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Simple R Markdown code

```
Admire this curve:
curve(dnorm(x), from = -2, to = 2)
```
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Simple R Markdown code

```
Admire this curve:
curve(dnorm(x), from = -2, to = 2)
```

Admire this curve:

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Metadata is referenced in a separate container called YAML

---
author: Sebastian Sauer
date: 2018-09-20
title: Some title
output_format: pdf_document
bibliography: cited_papers.bib
csl: apa.csl
---
Now normal text.
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What's RMarkdown good for?

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Websites/ Blogs

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Reports

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Books

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Slides






👌

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Papaja: a template for APA papers

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yart: a template for research reports

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Why should I use it?

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RMarkdown has more power

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But I love MS Word...

Start writing with Word. Keep on writing. Sooner or later ...

Markdown does not choke at big documents.

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Put code and text in the same document

The median reaction time was `r rt_md` sec.
It was incredibly significant (p < `r. very_low_p`).
We made science great again.
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Put code and text in the same document

The median reaction time was `r rt_md` sec.
It was incredibly significant (p < `r. very_low_p`).
We made science great again.

The median reaction time was 0.420 sec.

It was incredibly significant (p < .001).

We made science great again.

💖 no more copy-paste-errors. More reproducible

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Word's typography is so 80ies

Word :

Latex (Markdown):

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Do cool stuff

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Interactive diagrams

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Sample project

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Book "Moderne Datenanalyse mit R"

  • 500 pages
  • ~200 figures
  • ~200 R listings

Big thing.

No choking, but long compilation.

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Chapter file

rmd_files: 
[
  "index.Rmd",
  "01_Statistik_heute.Rmd",
  "02_Hallo_R.Rmd",
  "03_R_starten.Rmd",
  "04_Erstkontakt.Rmd",
  # "05_Datenstrukturen.Rmd",
  "06_Datenimport_und_export.Rmd",
  ...
]
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Config file

title: "Moderne Datenanalyse mit R"
subtitle: "Entwurf"
author: "Sebastian Sauer"
lang: de-De
documentclass: book
classoption: a4paper
fontsize: 11pt
fontfamily: mathpazo
...
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Sample page

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Now what?

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Get going with this book

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Or with this one

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Disclaimer: There may be issues at times

StackOverflow is your friend

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Thank you

Sebastian Sauer

sebastiansauer

https://data-se.netlify.com/

ssauer@posteo.de

Sebastian Sauer

Get slides here:

http://data-se.netlify.com/slides/rmd-writing/rmd-writing_dgps2018.html#1

CC-BY

Built using R, RMarkdown, Xaringan. Inspiration from and thanks to Yihui Xie and Antoine Bichat, among others

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What is RMarkdown?

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