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<body class="fullcontent">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<section id="code-and-data-lab-management-guidelines-r-and-github-starter-kit-for-new-team-members" class="level1">
<h1>Code and Data Lab Management Guidelines: <img src="img/logo.png" align="right" height="150"> R and GitHub Starter Kit for New Team Members</h1>
<p><a href="https://creativecommons.org/licenses/by-nc/4.0/"><img src="https://img.shields.io/badge/License-CC_BY--NC_4.0-lightgrey.svg" class="img-fluid" alt="License: CC BY-NC 4.0"></a> <a href="https://doi.org/10.5281/zenodo.14510774"><img src="https://zenodo.org/badge/896263653.svg" class="img-fluid" alt="DOI"></a> <a href="https://github.com/StringhiniLab/GitHubProceduresLab/actions/workflows/pages/pages-build-deployment"><img src="https://github.com/StringhiniLab/GitHubProceduresLab/actions/workflows/pages/pages-build-deployment/badge.svg" class="img-fluid" alt="pages-build-deployment"></a></p>
<section id="description" class="level2">
<h2 class="anchored" data-anchor-id="description">Description</h2>
<p>This book aims to provide a <strong>basic usage guide</strong> for new lab members regarding the <strong>handling of data and code</strong> with <strong>R</strong> and <strong>GitHub</strong> platform.</p>
<p>It provides: - A series of steps for <strong>onboarding</strong>. - Instructions on <strong>programs to install</strong>. - A guide to <strong>starting a project</strong>. - Recommendations on <strong>best practices</strong>. - Instructions on how to <strong>push</strong> locally created code to GitHub using <strong>RStudio</strong>.</p>
</section>
<section id="installation-and-setup" class="level2">
<h2 class="anchored" data-anchor-id="installation-and-setup">Installation and Setup</h2>
<p>Follow these steps only in case you want to edit the book:</p>
<ol type="1">
<li><strong>Clone the repository</strong>:</li>
</ol>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone git@github.com:StringhiniLab/GitHubProceduresLab.git</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<ol start="2" type="1">
<li><strong>Install dependencies</strong> using <code>renv</code>:</li>
</ol>
<div class="sourceCode" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"renv"</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">::</span><span class="fu">restore</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<ol start="3" type="1">
<li>Open the project in <strong>RStudio</strong> and compile the book running:</li>
</ol>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> render</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="contact" class="level2">
<h2 class="anchored" data-anchor-id="contact">Contact</h2>
<p>If you have any questions or suggestions, please contact open a <a href="https://github.com/StringhiniLab/GitHubProceduresLab/issues">GitHub issue</a>.</p>
</section>
<section id="code-of-conduct" class="level2">
<h2 class="anchored" data-anchor-id="code-of-conduct">Code of Conduct</h2>
<p>Please note that the github_procedures project is released with a <a href="https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html">Contributor Code of Conduct</a>. By contributing to this project, you agree to abide by its terms.</p>
</section>
<section id="inspired-cite-us" class="level2">
<h2 class="anchored" data-anchor-id="inspired-cite-us">Inspired? Cite Us!</h2>
<p>If you use this book, please cite it as follows:</p>
<p><strong>D’Andrea, F., & Stringhini, S. GitHub Lab Procedures: Onboarding Guide for New Lab Members [Computer software]. https://github.com/StringhiniLab/GitHubProceduresLab. <em>https://doi.org/10.5281/zenodo.14510774</em></strong></p>
</section>
<section id="session-info" class="level2">
<h2 class="anchored" data-anchor-id="session-info">Session Info</h2>
<p>The current environment setup is managed using <code>renv</code> to ensure reproducibility. The session info is as follows:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>R version <span class="dv">4</span>.<span class="fl">2.1</span> (<span class="dv">2022-06-23</span>)</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>Platform<span class="sc">:</span> aarch64<span class="sc">-</span>apple<span class="sc">-</span><span class="fu">darwin20</span> (<span class="dv">64</span><span class="sc">-</span>bit)</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>Running under<span class="sc">:</span> macOS Monterey <span class="fl">12.5</span></span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>Matrix products<span class="sc">:</span> default</span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>LAPACK<span class="sc">:</span> <span class="er">/</span>Library<span class="sc">/</span>Frameworks<span class="sc">/</span>R.framework<span class="sc">/</span>Versions<span class="sc">/</span><span class="fl">4.2</span><span class="sc">-</span>arm64<span class="sc">/</span>Resources<span class="sc">/</span>lib<span class="sc">/</span>libRlapack.dylib</span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a>locale<span class="sc">:</span></span>
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] en_US.UTF<span class="dv">-8</span><span class="sc">/</span>en_US.UTF<span class="dv">-8</span><span class="sc">/</span>en_US.UTF<span class="dv">-8</span><span class="sc">/</span>C<span class="sc">/</span>en_US.UTF<span class="dv">-8</span><span class="sc">/</span>en_US.UTF<span class="dv">-8</span></span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a>attached base packages<span class="sc">:</span></span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] stats graphics grDevices datasets utils methods base </span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a>other attached packages<span class="sc">:</span></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a>[<span class="dv">1</span>] usethis_3.<span class="fl">1.0</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a>loaded via a <span class="fu">namespace</span> (and not attached)<span class="sc">:</span></span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a> [<span class="dv">1</span>] fansi_1.<span class="fl">0.6</span> withr_3.<span class="fl">0.2</span> rprojroot_2.<span class="fl">0.4</span> utf8_1.<span class="fl">2.4</span> </span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a> [<span class="dv">5</span>] lifecycle_1.<span class="fl">0.4</span> magrittr_2.<span class="fl">0.3</span> pillar_1.<span class="fl">9.0</span> rlang_1.<span class="fl">1.4</span> </span>
<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a> [<span class="dv">9</span>] cli_3.<span class="fl">6.3</span> renv_1.<span class="fl">0.3</span> rstudioapi_0.<span class="fl">17.1</span> fs_1.<span class="fl">6.5</span> </span>
<span id="cb4-21"><a href="#cb4-21" aria-hidden="true" tabindex="-1"></a>[<span class="dv">13</span>] whisker_0.<span class="fl">4.1</span> vctrs_0.<span class="fl">6.5</span> tools_4.<span class="fl">2.1</span> glue_1.<span class="fl">8.0</span> </span>
<span id="cb4-22"><a href="#cb4-22" aria-hidden="true" tabindex="-1"></a>[<span class="dv">17</span>] purrr_1.<span class="fl">0.2</span> compiler_4.<span class="fl">2.1</span> pkgconfig_2.<span class="fl">0.3</span> clipr_0.<span class="fl">8.0</span> </span>
<span id="cb4-23"><a href="#cb4-23" aria-hidden="true" tabindex="-1"></a>[<span class="dv">21</span>] tibble_3.<span class="fl">2.1</span> </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
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