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<!DOCTYPE html>
<html>
<head>
<title>Reproducible research</title>
<meta charset="utf-8">
<meta name="description" content="Reproducible research">
<meta name="author" content="Joona Lehtomäki">
<meta name="generator" content="slidify" />
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<script data-main="libraries/frameworks/io2012/js/slides"
src="libraries/frameworks/io2012/js/require-1.0.8.min.js">
</script>
<link rel="stylesheet" href = "assets/css/repro.css">
<link rel="stylesheet" href = "assets/css/ribbons.css">
</head>
<body style="opacity: 0">
<slides class="layout-widescreen">
<!-- LOGO SLIDE -->
<!-- END LOGO SLIDE -->
<!-- TITLE SLIDE -->
<!-- Should I move this to a Local Layout File? -->
<slide class="title-slide segue nobackground">
<hgroup class="auto-fadein">
<h1>Reproducible research</h1>
<h2>Few concepts and a couple of tools, v0.1</h2>
<p>Joona Lehtomäki<br/></p>
</hgroup>
</slide>
<!-- SLIDES -->
<slide class="" id="license" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>CC-BY</h2>
</hgroup>
<article>
<p><img src="assets/img/ccby_badge.png" class="centered-img" title="Dan McGlin, CC-BY 3.0"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="attribution" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Attribution</h2>
</hgroup>
<article>
<ul>
<li><a href="https://github.com/johnmcdonnell/Git-Tutorial">Git tutorial</a> by John McDonnel</li>
<li><a href="https://github.com/ethanwhite/USU-SWC-Bootcamp/blob/master/version_control_slides.pdf">Introduction to Version Control with a focus on Git</a> by Dan McGlinn</li>
<li><a href="https://github.com/karthikram/smb_git">Reproducible research in computational science</a> by Karthik Ram</li>
<li><a href="https://github.com/yihui/yihui.github.com/blob/master/slides/2012-knitr-RStudio.html">knitr and RStudio</a> by Yihui Xie</li>
</ul>
<h3>Sources for this presentationa available at</h3>
<ul>
<li><a href="https://github.com/jlehtoma/reproScience">Reproducible research: Concepts and tools</a></li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="content">
<hgroup>
<h2>Content</h2>
</hgroup>
<article class = 'flexbox vcenter'>
<ol>
<li>Background</li>
<li>Concepts</li>
<li>Tools: RStudio and Git</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="motivation1" style="background:url(assets/img/motivation_composite.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
<h2>My own PhD</h2>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="open-science" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Open science</h2>
</hgroup>
<article>
<p>"Opening up access to the data and software, not just the final publication, is one of goals of the open science movement" <br />(Ram, 2013)</p>
<div style='float:left;width:48%;' class='centered'>
<ul>
<li>Open access</li>
<li>Open data</li>
<li>Open notebook science</li>
<li>Open source software</li>
</ul>
</div>
<div style='float:right;width:48%;'>
<p><img src="http://upload.wikimedia.org/wikipedia/commons/b/bb/Open_Science_Logo.jpg" class="centered-img" style="max-height:50%;" title="By G.emmerich (Own work) CC-BY-SA-3.0, via Wikimedia Commons"></img></p>
</div>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="slide-6" style="background:black;">
<article>
<p><img src="http://bit.ly/10FmaGf" class="centered-img"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="concepts" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Reproducibility</h2>
</hgroup>
<article>
<ul class = "build">
<li>With replication, independent investigators address a scientific hypothesis and build up evidence for or against it (Peng, 2011)</li>
<li>Allows others to build upon existing work and use it to test new ideas and develop methods (Ram, 2013)</li>
<li>While currently there is unilateral emphasis on "first" discoveries, there should be as much emphasis on replication of discoveries (<a href="http://www.telegraph.co.uk/technology/3342867/Is-the-spirit-of-Piltdown-man-alive-and-well.html">Ioannidis, 2005</a>)</li>
</ul>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="problems1" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<p><img src="assets/img/wolkowich_et_al_data_sharing.png" class="centered-img" title="Wolkowich et al. 2012"></img></p>
<p>Wolkovich et al. 2012</p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="problems2" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<p><img src="assets/img/peng_comp_repro.png" class="centered-img" title="Peng 2011"></img></p>
<p>Peng 2011</p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="problems3" style="background:url(assets/img/reproducibility_initiative.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="problems4" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<p><img src="assets/img/sirkia_et_al_workflow.png" class="centered-img" style="margin-left: 0; float: left;" title="Sirkiä et al. 2012"></img></p>
<p>Sirkiä et al. 2012</p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="problems5" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<iframe src="http://bit.ly/10FnSHI"></iframe>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio1" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Tools for reproducible research</h2>
</hgroup>
<article>
<p><br /></p>
<p><img src="http://bit.ly/Z2DkiR" class="centered-img" style="max-height:50%;" title="RStudio, GPLv3"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio2" style="background:url(assets/img/rstudio_analysis.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio3" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Reproducible?</h2>
</hgroup>
<article>
<ul class = "build">
<li>Automatically regenerate documents when code, data, or assumptions change</li>
<li>Eliminate transposition errors that occur when copying results into documents</li>
<li>Preserve contextual narrative about why analysis was performed in a certain fashion</li>
<li>Documentation for the analytic and computational processes from which conclusions are drawn</li>
</ul>
<p><a href="https://github.com/yihui/yihui.github.com">Xie, 2012</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio4" style="background:;">
<article>
<p><br />
<br /></p>
<p><img src="assets/img/tech_logos.png" class="centered-img" style="max-height:100%;" title="RStudio, GPLv3"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio5" style="background:url(assets/img/rstudio_knitr_input.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio6" style="background:url(assets/img/rstudio_knitr_output.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio7" style="background:url(assets/img/knitr_workflow.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
<p><span style="position: fixed; bottom: 75px;">
Adapted from <a href="http://markuskainu.fi/r-tutorial/repro/suomeksi.html">Markus Kainu</a>
</span></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio8" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>More R-code</h2>
</hgroup>
<article>
<pre><code class="r"># Quick summary
library(ggplot2)
summary(cars)
</code></pre>
<pre><code>## speed dist
## Min. : 4.0 Min. : 2
## 1st Qu.:12.0 1st Qu.: 26
## Median :15.0 Median : 36
## Mean :15.4 Mean : 43
## 3rd Qu.:19.0 3rd Qu.: 56
## Max. :25.0 Max. :120
</code></pre>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio8" style="background:;">
<article>
<pre><code class="r"># Quick plot of the data
qplot(speed, dist, data = cars) + geom_smooth()
</code></pre>
<p><img src="figure/unnamed-chunk-2.png" alt="plot of chunk unnamed-chunk-2"> </p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="rstudio9">
<hgroup>
</hgroup>
<article class = 'flexbox vcenter'>
<p><a href="http://bit.ly/Y8y8uO"><strong>source</strong></a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git1" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Tools for reproducible research</h2>
</hgroup>
<article>
<p><br /></p>
<p><img src="http://bit.ly/Z2DNBq" class="centered-img" style="max-height:50%;" title="Jason Long, CC-BY 3.0, via Wikimedia Commons"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git2" style="background:url(assets/img/github_linux.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git3" style="background:url(assets/img/github_landing_page.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git4" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>What is git?</h2>
</hgroup>
<article>
<p><br /></p>
<p><img src="assets/img/threecommits.png" alt="threecommits"></p>
<ul>
<li>It stores snapshots of your projects</li>
<li>...It also stores the relationships between those snapshots</li>
</ul>
<p><a href="https://github.com/johnmcdonnell/Git-Tutorial">McDonnel, 2012</a></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git5" style="background:;">
<article>
<p><img src="http://www.phdcomics.com/comics/archive/phd101212s.gif" class="centered-img"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git6" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Why use git in science?</h2>
</hgroup>
<article>
<ol class = "build">
<li>Lab notebook</li>
<li>Facilitating collaboration</li>
<li>Backup and failsafe against data loss</li>
<li>Freedom to explore new ideas and methods</li>
<li>Mechanism to solicit feedback and reviews</li>
<li>Increase transparency and verifiability</li>
<li>Managing large data</li>
<li>Lowering barriers to reuse</li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git7" style="background:;">
<article>
<p><br />
<br /></p>
<p><img src="assets/img/smb_karihikram_git_workflow.png" class="centered-img"></img></p>
<p><br /></p>
<p>Ram, 2013</p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git8" style="background:; background-repeat:; background-position:;">
<hgroup>
<h2>Git: steep learning curve?</h2>
</hgroup>
<article>
<p><img src="http://d22zlbw5ff7yk5.cloudfront.net/images/cm-27811-1508860c9c2366.gif" class="centered-img" style="margin-top: 150px;"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git9" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<p><img src="assets/img/git_cli.png" class="centered-img" title="Nathan de Vries, CC-BY-SA 3.0"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git10" style="background:; background-repeat:; background-position:;">
<hgroup>
</hgroup>
<article>
<p><img src="assets/img/rstudio_git_panel.png" class="centered-img"></img></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="git11" style="background:url(assets/img/rstudio_git_history.png); background-repeat:no-repeat; background-position:center;">
<hgroup>
</hgroup>
<article>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="" id="thanks">
<hgroup>
</hgroup>
<article class = 'flexbox vcenter'>
<p><strong>Thank you!</strong></p>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="reference" id="reference" style="background:; background-repeat:; background-position:;">
<hgroup>
<h3>References:</h3>
</hgroup>
<article>
<ol>
<li>Peng RD (2011): Reproducible research in computational science. Science. 334(6060):1226–7. Available from: <a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3383002&tool=pmcentrez&rendertype=abstract">http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3383002&tool=pmcentrez&rendertype=abstract</a><br></li>
<li>Ram K. (2013): Git can facilitate greater reproducibility and increased transparency in science. Source Code for Biology and Medicine. 8(1):7. Available from: <a href="http://www.scfbm.org/content/8/1/7">http://www.scfbm.org/content/8/1/7</a><br></li>
<li>Sirkiä S, Lehtomäki J, Lindén H, Tomppo E, Moilanen A (2012): Defining spatial priorities for capercaillie Tetrao urogallus lekking landscape conservation in south-central Finland. Wildlife Biology. 2012;18(4):337–53. </li>
<li>Wolkovich EM, Regetz J, O’Connor MI (2012): Advances in global change research require open science by individual researchers. Global Change Biology. 18(7):2102–10. Available from: <a href="http://doi.wiley.com/10.1111/j.1365-2486.2012.02693.x">http://doi.wiley.com/10.1111/j.1365-2486.2012.02693.x</a></li>
</ol>
</article>
<!-- Presenter Notes -->
</slide>
<slide class="backdrop"></slide>
</slides>
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