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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Tips for reproducibility in R</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
RUM-UMC
</div>
</div>
</div>
<p class="date">September 25, 2024</p>
</section>
<section id="what-is-reproducibility" class="slide level2">
<h2>What is reproducibility?</h2>
<blockquote>
<p>“We define reproducible research as work that can be independently recreated from the same data and the same code that the original team used.”</p>
</blockquote>
<center>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://book.the-turing-way.org/_images/reproducible-matrix.jpg" width="500"></p>
<figcaption>Source: <a href="https://book.the-turing-way.org/reproducible-research/overview/overview-definitions">The Turing Way</a></figcaption>
</figure>
</div>
</center>
</section>
<section id="section" class="slide level2">
<h2></h2>
<center>
<img data-src="img/drake.png" width="800">
</center>
</section>
<section id="focus-your-energy" class="slide level2">
<h2>Focus your energy</h2>
<ol type="1">
<li>Script <em>everything</em> (<a href="https://www.dropbox.com/s/vn7rn9m5ht2miol/reproducibility.pdf?e=1&dl=0">De Graaff., 2021</a>)</li>
<li>Project folders</li>
<li>Options in RStudio</li>
<li><code>renv</code></li>
<li>Quarto</li>
</ol>
</section>
<section id="script-everything" class="slide level2">
<h2>Script <em>everything</em></h2>
<p><br></p>
<p>“R is a statistics software” 😠 Well, partly… but it can (probably) be used for your <a href="https://wec.wur.nl/dse/images/11/tidyverse%20workflow.png">entire computational workflow</a>.</p>
<p><br></p>
<p>If you <strong>can</strong> script it, then <strong>script it</strong>.</p>
<p><br></p>
<p>RStudio can also support other languages (e.g., <a href="https://posit.co/blog/three-ways-to-program-in-python-with-rstudio/">Python</a>)</p>
</section>
<section id="project-folders" class="slide level2">
<h2>Project folders</h2>
<p><br> <br></p>
<center>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/setwd.png" width="700"></p>
<figcaption>Source: <a href="https://www.tidyverse.org/blog/2017/12/workflow-vs-script/">Jenny Bryan</a></figcaption>
</figure>
</div>
</center>
</section>
<section id="project-folders-1" class="slide level2">
<h2>Project folders</h2>
<p><br></p>
<center>
<p><img data-src="img/project_screenshot.png" width="700"></p>
<p><br></p>
<p><img data-src="img/folder_screenshot.png" width="800"></p>
</center>
</section>
<section id="project-folders-2" class="slide level2">
<h2>Project folders</h2>
<p>Avoids this:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">setwd</span>(<span class="st">"C:/SamL/my_projects/ridiculous_folder_name/data"</span>)</span>
<span id="cb1-2"><a href="#cb1-2"></a></span>
<span id="cb1-3"><a href="#cb1-3"></a>raw_data_df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"raw_records.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br> And this:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>raw_data_df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"C:/SamL/my_projects/ridiculous_folder_name/data/raw_records.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br></p>
<p>But instead:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>raw_data_df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"data/raw_records.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<!-- ## Options in RStudio -->
<!-- <br> -->
<!-- <br> -->
<!-- <center> -->
<!-- `Ctrl + shift + F10` -->
<!-- <br> -->
<!-- `Ctrl + A` -->
<!-- <br> -->
<!-- `Ctrl + Enter` -->
<!-- </center> -->
</section>
<section id="options-in-rstudio" class="slide level2">
<h2>Options in RStudio</h2>
<p><br></p>
<center>
<p><img data-src="img/global_options.png" width="700"></p>
<p><em>Workspaces are pure evil. Turn them off.</em></p>
<!-- ## `here` package -->
<!-- Bad: -->
<!-- ```{r, eval = FALSE, echo = TRUE} -->
<!-- raw_data_df <- read_csv("C:/SamL/my_projects/ridiculous_folder_name/data/raw_records.csv") -->
<!-- ``` -->
<!-- <br> -->
<!-- Good: -->
<!-- ```{r, eval = FALSE, echo = TRUE} -->
<!-- raw_data_df <- read_csv("data/raw_records.csv") -->
<!-- ``` -->
<!-- <br> -->
<!-- Even better: -->
<!-- ```{r, eval = FALSE, echo = TRUE} -->
<!-- raw_data_df <- read_csv( -->
<!-- here("data", "raw_records.csv") -->
<!-- ) -->
<!-- ``` -->
</center></section>
<section id="renv" class="slide level2">
<h2><code>renv</code></h2>
<center>
<p><img data-src="img/renv.png" width="400"></p>
<p><a href="https://rstudio.github.io/renv/">Read this</a>.</p>
</center>
</section>
<section id="renv-demonstration" class="slide level2">
<h2><code>renv</code> demonstration</h2>
</section>
<section id="renv-demonstration-1" class="slide level2">
<h2><code>renv</code> demonstration</h2>
<ol type="1">
<li>Create a project file</li>
<li><code>renv::init()</code></li>
<li>Do some stuff</li>
<li><code>renv::snapshot()</code></li>
<li>Share with someone</li>
<li><code>renv::restore()</code></li>
<li>Do some other stuff</li>
<li>Go to point 4…</li>
</ol>
</section>
<section id="renv-within-oneview" class="slide level2">
<h2><code>renv</code> within OneView</h2>
<p><br></p>
<center>
<strong>Activating the virtual environment causes RStudio to crash.</strong>
</center>
<p><br></p>
<p>But a low-effort alternative:</p>
<ol type="1">
<li>Create a project file</li>
<li>Do some stuff</li>
<li>When you’re done: <code>renv::snapshot()</code></li>
</ol>
</section>
<section id="renv-within-oneview-1" class="slide level2">
<h2><code>renv</code> within OneView</h2>
<p><br></p>
<center>
<strong>Activating the virtual environment causes RStudio to crash.</strong>
</center>
<p><br></p>
<p>Similar alternative: save your session info.</p>
<p><br></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="fu">writeLines</span>(<span class="fu">capture.output</span>(<span class="fu">sessionInfo</span>()), <span class="st">"sessionInfo.txt"</span>)<span class="st">`</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="quarto" class="slide level2">
<h2>Quarto</h2>
<p><br></p>
<p>Using Quarto allows you to make cool documents (and slideshows) while automating your results, making you approximately 200% more efficient.</p>
</section>
<section id="quarto-1" class="slide level2">
<h2>Quarto</h2>
<p><br></p>
<p>Using Quarto allows you to make cool documents (and slideshows) while automating your results, making you approximately 200% more efficient.</p>
<p><img data-src="img/quarto.png" width="1000"></p>
</section>
<section id="quarto-2" class="slide level2">
<h2>Quarto</h2>
<p><br></p>
<p>Using Quarto allows you to make cool documents (and slideshows) while automating your results, making you approximately 200% more efficient.</p>
<p><img data-src="img/quarto.png" width="1000"></p>
<p>It also makes everything <a href="https://github.com/danieltomasz/hikmah-academic-quarto?tab=readme-ov-file">look better</a>.</p>
</section>
<section id="summary" class="slide level2">
<h2>Summary</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p>DOs</p>
<ul>
<li>Script <strong>everything</strong><br>
</li>
<li>Use project files</li>
<li>Use <code>renv</code> to manage package versions</li>
<li>Use Quarto</li>
</ul>
</div><div class="column" style="width:50%;">
<p>DON’Ts</p>
<ul>
<li>Use <code>setwd()</code></li>
<li>Save workspaces</li>
<li>Manually copy results</li>
</ul>
</div>
</div>
</section>
<section id="advertisement-codecheck" class="slide level2">
<h2>Advertisement: CODECHECK</h2>
<center>
<p><br></p>
<p>Want a ‘second pair of eyes’ on your R workflow?</p>
<p>And a ‘bonus point’ for a journal submission?</p>
<p><br></p>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="img/codecheck_logo.svg" width="300"></p>
</figure>
</div>
<p>Then <a href="mailto:s.h.langton@amsterdamumc.nl">email me</a> or ping us via ServiceNow (‘Research Software Management’)</p>
</center>
</section>
<section id="extras" class="slide level2">
<h2>Extras</h2>
<h3 id="assumed">Assumed:</h3>
<ul>
<li>Documentation (including comments)</li>
<li>Linear scripts</li>
<li>Function conflicts</li>
</ul>
<h3 id="bonus-points">Bonus points:</h3>
<ul>
<li><code>here</code> package</li>
<li>Modular scripts</li>
<li>Version control (e.g., GitHub)</li>
</ul>
<div class="footer footer-default">
</div>
</section>
</div>
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