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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
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<title>Tools for reproducible research</title>
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<section>
<h1 class="title">Tools for reproducible research</h1>
</section>
<section><section id="why" class="titleslide slide level1"><h1>Why?</h1></section><section id="selfish-reasons-from-f.-markowetz-1" class="slide level2">
<h1>5 selfish reasons from <a href="http://www.markowetzlab.org/florian/">F. Markowetz</a> <sup><a href="#fn1" id="ref1">1</a></sup></h1>
<ol type="1">
<li><p>… helps to avoid disaster</p></li>
<li><p>… makes it easier to write papers</p></li>
<li><p>… helps reviewers see it your way</p></li>
<li><p>… enables continuity of your work</p></li>
<li><p>… helps to build your reputation</p></li>
</ol>
<aside class="notes">
<ul>
<li>
no dark tone here
</li>
<li>
you will profit in the end!
</li>
<li>
</li>
</ul>
</aside>
<hr>
</hr>
<p><sup id="fn1">1. <a href="https://dx.doi.org/10.1186/s13059-015-0850-7">Markowetz – Five selfish reasons to work reproducibly – 2015, Genome Biology</a> <a href="#ref1" title="Jump back to footnote 1 in the text."></a></sup></p>
</section></section>
<section><section id="the-tools-rmarkdown" class="titleslide slide level1"><h1>The tools: RMarkdown</h1></section><section id="markdown" class="slide level2">
<h1>Markdown</h1>
<ul>
<li>Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents: <a href="http://rmarkdown.rstudio.com" class="uri">http://rmarkdown.rstudio.com</a></li>
</ul>
</section><section id="text-formatting" class="slide level2">
<h1>Text formatting</h1>
<pre><code>*italic* or _italic_
**bold** __bold__</code></pre>
<h3 id="headings">Headings</h3>
<pre><code># 1st Level Header
## 2nd Level Header</code></pre>
<h3 id="lists">Lists</h3>
<pre><code>* Bulleted list item 1
* Item 2
1. Numbered list item 1
1. Item 2. The numbers are incremented automatically in the output.</code></pre>
</section><section id="links-and-images" class="slide level2">
<h1>Links and images</h1>
<pre><code><http://example.com>
[linked phrase](http://example.com)
![optional caption text](path/to/img.png)</code></pre>
<h3 id="tables">Tables</h3>
<pre><code>First Header | Second Header
------------- | -------------
Content Cell | Content Cell
Content Cell | Content Cell
</code></pre>
</section><section id="r-markdown" class="slide level2">
<h1>R Markdown</h1>
<ul>
<li><p><strong>R Markdown is a mix of R code and markdown comments</strong></p></li>
<li><p>In R Studio, R markdown can be run in a <strong>notebook mode</strong> or classic <strong>document mode</strong></p></li>
<li><p>… better than simple text based “scripts”</p></li>
</ul>
</section></section>
<section><section id="case-study-turning-the-wheels-of-time" class="titleslide slide level1"><h1>Case study: Turning the wheels of time</h1></section><section id="turning-the-wheels-of-time" class="slide level2">
<h1>Turning the wheels of time</h1>
<ul>
<li><p><a href="http://dx.doi.org/10.1177/1948550611419266">Topolinski and Sparenberg</a> : self–reported experiential openness is influenced by rotational movements</p></li>
<li><p>In 2015 <a href="http://dx.doi.org/10.3389/fpsyg.2015.00494">Wagenmakers et. al.</a><br />
could not confirm the results</p></li>
</ul>
</section><section id="section" class="slide level2">
<h1></h1>
<p><img src="kitchen_rolls.jpg" width="50%" height="50%" alt="kitchen rolls experiment"/></p>
</section><section id="section-1" class="slide level2">
<h1></h1>
<ul>
<li><p>The Wagenmakers et. al. data is available at <a href="https://osf.io/uszvx/" class="uri">https://osf.io/uszvx/</a>, and as part of the JASP program with the name <code>Kitchen_Rolls.csv</code>.</p></li>
<li><p>The authors use the “Openness to Experience” subscale from the (<a href="https://en.wikipedia.org/wiki/Revised_NEO_Personality_Inventory#Personality_dimensions">NEO</a>) inventory</p></li>
<li><p>They compare the mean response score between two groups with clockwise and counterclockwise turning of kitchen rolls</p></li>
</ul>
</section><section id="hands-on-rmarkdown" class="slide level2">
<h1>… hands on Rmarkdown …</h1>
</section></section>
<section><section id="jupyter-notebooks" class="titleslide slide level1"><h1>Jupyter Notebooks</h1></section><section id="jupyter-notebooks-1" class="slide level2">
<h1>Jupyter Notebooks</h1>
<ul>
<li><p>formely known as IPython Notebooks</p></li>
<li><p>Composed of “cells” where you enter either markdown or Python code</p></li>
<li><p>Other languages are supported as well</p></li>
</ul>
</section><section id="hands-on-in-jupyter" class="slide level2">
<h1>… hands on in Jupyter …</h1>
</section></section>
<section><section id="version-control" class="titleslide slide level1"><h1>Version control</h1></section><section id="why-version-control" class="slide level2">
<h1>Why version control?</h1>
<p><img src="version_control.png" width="50%" height="50%" alt="version control"/></p>
<p>from <a href="http://phdcomics.com/comics/archive_print.php?comicid=1531" class="uri">http://phdcomics.com/comics/archive_print.php?comicid=1531</a></p>
</section><section id="git-and-github" class="slide level2">
<h1>Git and github</h1>
<ul>
<li><p>Git = the modern version control tool</p></li>
<li><p>Github = company hosting git repositories</p></li>
<li><p>Intro in the pdf in your materials or</p></li>
<li><p><a href="http://happygitwithr.com/" class="uri">http://happygitwithr.com/</a></p></li>
</ul>
</section></section>
<section><section id="markdown-html-based-slides" class="titleslide slide level1"><h1>Markdown / html based slides</h1></section><section id="reproducible-slides" class="slide level2">
<h1>Reproducible slides</h1>
<ul>
<li><p>I recommend <a href="lab.hakim.se/reveal-js/">reveal.js</a></p></li>
<li><p>see <a href="http://rmarkdown.rstudio.com/revealjs_presentation_format.html" class="uri">http://rmarkdown.rstudio.com/revealjs_presentation_format.html</a></p></li>
<li><p>OR <a href="https://slides.com" class="uri">https://slides.com</a>/</p></li>
</ul>
</section></section>
</div>
</div>
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