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‎_footer.html‎

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[R We Having Fun Yet‽](https://rfun.library.duke.edu/)
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[Center for Data & Visualization Sciences](https://library.duke.edu/data/).
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[Duke University Libraries](https://library.duke.edu/)

‎_site.yml‎

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name: "Git & RStudio"
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title: "RStudio & Version Control"
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favicon: libs-local/rfun_logo.png
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base_url: https://rfun.library.duke.edu
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repository_url: https://github.com/data-and-visualization/git-tutorial
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twitter:
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site: "@duke_data"
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description: |
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How to use RStudio with Git & GitHub
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# exclude:
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# - README.md
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# - license.md
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# favicon: logo.png
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creative_commons: CC BY-NC
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navbar:
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# title: "RStudio & Version Control"
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logo:
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image: libs-local/rfun_logo.png
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href: https://rfun.library.duke.edu
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left:
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right:
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- text: "Resources"
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href: "resources.html"
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# logo:
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# image: libs-local/rfun_logo.png
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# href: https://rfun.library.duke.edu
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right:
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# - text: "GitHub"
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href: https://github.com/data-and-visualization/git-tutorial/
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href: https://github.com/data-and-visualization/git-tutorial/
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# - icon: fa-home
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# # - text: "Home"
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# menu:
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output_dir: docs
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distill::distill_article:
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include:
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after_body: libs-local/footer.html
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css:
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# include:
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# after_body: libs-local/footer.html
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# css:
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# - libs-local/duke.css
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# libs-local/cc-fonts.css

‎docs/index.html‎

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<meta property="description" itemprop="description" content="Makin&#39; it work!!"/>
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<link rel="license" href="https://creativecommons.org/licenses/by-nc/4.0/"/>
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<link rel="icon" type="image/png" href="libs-local/rfun_logo.png"/>
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<meta property="twitter:card" content="summary"/>
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<meta property="twitter:title" content="RStudio &amp; Version Control: Git, GitHub &amp; RStudio"/>
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<meta property="twitter:description" content="Makin&#39; it work!!"/>
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<meta property="twitter:site" content="@duke_data"/>
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}
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</style>
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<!--/radix_placeholder_site_in_header-->
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</head>
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<img src="libs-local/rfun_logo.png" alt="Logo"/>
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</a>
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<a href="index.html" class="title">RStudio &amp; Version Control</a>
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<a href="resources.html">Resources</a>
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</div>
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<div class="nav-right">
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<a href="resources.html">Resources</a>
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<a href="https://github.com/data-and-visualization/git-tutorial/">
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<i class="fa fa-github" aria-hidden="true"></i>
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</a>
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<div class="d-article">
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<p>Using RStudio to manage version control got a lot easier with the version 2.x release of the <a href="https://usethis.r-lib.org/"><code>usethis</code></a> package. Therefore, this site now consists of links and tips.</p>
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<p>After <code>usethis</code> setup, take your reproducibility to the next level. <a href="https://guides.github.com/activities/citable-code/">Make your code citable</a> by connecting your GitHub repo and your <a href="https://orcid.org/register">ORCID</a> (unique author ID) to the <a href="https://zenodo.org/">Zenodo</a> archival repository. This way, every time you commit a milestone release, you can mint a new DOI. Then, put your repository into a binder.org container with the <code>holepunch</code> package.</p>
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<p>Use RStudio to manage version control. It’s easy with the <a href="https://usethis.r-lib.org/"><code>usethis</code></a> package (version 2.x or ^.)</p>
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<p>Take your reproducibility to the next level. <a href="https://guides.github.com/activities/citable-code/">Make your code citable</a> by connecting your GitHub repo and your <a href="https://orcid.org/register">ORCID</a> (unique author ID) through to the <a href="https://zenodo.org/">Zenodo</a> archival repository. Now, every time you commit a milestone release, you also mint a DOI.</p>
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<p>Containerize your repository with binder.org using the <a href="https://karthik.github.io/holepunch/"><code>holepunch</code> package</a>.</p>
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<h3 id="setup">Setup</h3>
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<p>To get started, get a free GitHub.com account. Make sure you have the latest versions of R, RStudio, (Rtools if you’re Windows), and usethis. Then, you need to setup your RStudio configuration. Two key documents will help: <a href="https://usethis.r-lib.org/articles/articles/usethis-setup.html">Setup</a>, and <a href="https://usethis.r-lib.org/articles/articles/git-credentials.html">Managing Git(Hub) Credentials</a></p>
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<p>To get started, make a free GitHub.com account. Make sure you have the latest versions of R, RStudio, (Rtools if you’re Windows), and usethis. Then, setup your RStudio configuration using two key documents: <a href="https://usethis.r-lib.org/articles/articles/usethis-setup.html">Setup</a>, and <a href="https://usethis.r-lib.org/articles/articles/git-credentials.html">Managing Git(Hub) Credentials</a>.</p>
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<h3 id="tips">Tips</h3>
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<h4 id="clone-or-fork-from-github">Clone or fork from GitHub</h4>
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<pre><code>usethis::create_from_github(&quot;https://github.com/data-and-visualization/git-tutorial&quot;)</code></pre>
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<div class="layout-chunk" data-layout="l-body">
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<div class="sourceCode">
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<pre><code><span class='fu'>usethis</span><span class='fu'>::</span><span class='fu'><a href='https://usethis.r-lib.org/reference/create_from_github.html'>create_from_github</a></span><span class='op'>(</span><span class='st'>"https://github.com/data-and-visualization/git-tutorial"</span><span class='op'>)</span>
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</code></pre>
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</div>
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</div>
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<h4 id="create-the-github-repo-from-local">Create the GitHub repo from local</h4>
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<pre><code>library(usethis)
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use_git() # initialize a git repo
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use_git_ignore()
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use_readme.Rmd()
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use_ccby_license()
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use_github() # Connect local repo to GitHub</code></pre>
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<div class="layout-chunk" data-layout="l-body">
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<div class="sourceCode">
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<pre><code><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://usethis.r-lib.org'>usethis</a></span><span class='op'>)</span>
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<span class='fu'><a href='https://usethis.r-lib.org/reference/use_git.html'>use_git</a></span><span class='op'>(</span><span class='op'>)</span> <span class='co'># initialize a git repo</span>
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<span class='fu'><a href='https://usethis.r-lib.org/reference/use_git_ignore.html'>use_git_ignore</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>use_readme.Rmd</span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://usethis.r-lib.org/reference/licenses.html'>use_ccby_license</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://usethis.r-lib.org/reference/use_github.html'>use_github</a></span><span class='op'>(</span><span class='op'>)</span> <span class='co'># Connect local repo to GitHub</span>
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</code></pre>
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</div>
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</div>
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<h4 id="set-up-git-and-manage-github-credentials">set-up git and manage GitHub credentials</h4>
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<pre><code># Sign-in to your GitHub account
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# Read: https://usethis.r-lib.org/articles/articles/git-credentials.html
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# Read: https://usethis.r-lib.org/articles/articles/usethis-setup.html
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usethis::create_github_token()
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gh::gh_whoami()
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gh::git_sitrep()</code></pre>
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<div class="layout-chunk" data-layout="l-body">
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<pre><code><span class='co'># Sign-in to your GitHub account</span>
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<span class='co'># Read: https://usethis.r-lib.org/articles/articles/git-credentials.html</span>
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<span class='co'># Read: https://usethis.r-lib.org/articles/articles/usethis-setup.html</span>
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<span class='fu'>usethis</span><span class='fu'>::</span><span class='fu'><a href='https://usethis.r-lib.org/reference/github-token.html'>create_github_token</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>gitcreds</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/gitcreds/man/gitcreds_get.html'>gitcreds_set</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>gh</span><span class='fu'>::</span><span class='fu'><a href='https://gh.r-lib.org/reference/gh_whoami.html'>gh_whoami</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>usethis</span><span class='fu'>::</span><span class='fu'><a href='https://usethis.r-lib.org/reference/git_sitrep.html'>git_sitrep</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'>usethis</span><span class='fu'>::</span><span class='fu'><a href='https://usethis.r-lib.org/reference/use_git_config.html'>use_git_config</a></span><span class='op'>(</span>user.name <span class='op'>=</span> <span class='st'>"Jane Doe"</span>, user.email <span class='op'>=</span> <span class='st'>"[email protected]"</span><span class='op'>)</span>
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<span class='fu'>gh</span><span class='fu'>::</span><span class='fu'>git_sitrep</span><span class='op'>(</span><span class='op'>)</span>
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</code></pre>
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<h4 id="publish-your-code-in-a-binder.org-container">Publish your code in a binder.org container</h4>
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<p>Use the <a href="https://karthik.github.io/holepunch/"><code>holepunch</code> package</a></p>
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<pre><code>library(holepunch)
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<pre><code><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://github.com/karthik/holepunch'>holepunch</a></span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/pkg/holepunch/man/write_compendium_description.html'>write_compendium_description</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/pkg/holepunch/man/write_dockerfile.html'>write_dockerfile</a></span><span class='op'>(</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/pkg/holepunch/man/build_binder.html'>build_binder</a></span><span class='op'>(</span><span class='op'>)</span>
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<p>The old documentation from this site can be found in the <a href="https://github.com/data-and-visualization/git-tutorial/releases/tag/v0.9.2019">v.0.2019 release</a> on GitHub.</p>
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<p><em>The old documentation from this site can be found in the <a href="https://github.com/data-and-visualization/git-tutorial/releases/tag/v0.9.2019">v.0.2019 release</a> on GitHub</em>.</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r distill-force-highlighting-css"><code class="sourceCode r"></code></pre></div>
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<a href="https://rfun.library.duke.edu/">R We Having Fun Yet‽</a> -- an R Learning Series<br>
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<a href="http://library.duke.edu/data/">Center for Data & Visualization Sciences</a><br>
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<a href="http://library.duke.edu/">Duke University Libraries</a>
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<!-- Key: a: SA, b: BY, c: CC Circle, d: ND, n: NC, m: Sampling, s: Share, r: Remix, C: CC Full Logo -->
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<h3 id="updates-and-corrections">Corrections</h3>
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<p>If you see mistakes or want to suggest changes, please <a href="https://github.com/data-and-visualization/git-tutorial/issues/new">create an issue</a> on the source repository.</p>
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<h3 id="reuse">Reuse</h3>
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<p>Text and figures are licensed under Creative Commons Attribution <a rel="license" href="https://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC 4.0</a>. Source code is available at <a href="https://github.com/data-and-visualization/git-tutorial">https://github.com/data-and-visualization/git-tutorial</a>, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".</p>
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<p><a href="https://rfun.library.duke.edu/">R We Having Fun Yet‽</a></p>
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<p><a href="https://library.duke.edu/data/">Center for Data &amp; Visualization Sciences</a>. <a href="https://library.duke.edu/">Duke University Libraries</a></p>
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</div>
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‎docs/resources.html‎

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<a href="resources.html">Resources</a>
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<a href="https://github.com/data-and-visualization/git-tutorial/">
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<li>GitKracken – <strong>Free</strong> if you have the <a href="https://education.github.com/pack">GitHub Student</a> Pack or the <a href="https://www.gitkraken.com/github-teacher-toolbox">GitHub Teacher toolbox</a></li>
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<li><a href="https://www.sourcetreeapp.com/">SourceTree</a> – Free. (defaults to use with <a href="https://bitbucket.org/">BitBucket</a>)</li>
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<h3 id="packages">Packages</h3>
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<ul>
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<li><a href="https://karthik.github.io/holepunch/"><code>holepunch</code></a> to make your reproducible code a container on binder.org</li>
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</ul>
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<h3 id="free-book">Free Book</h3>
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<ul>
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</div>
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<a href="https://rfun.library.duke.edu/">R We Having Fun Yet‽</a> -- an R Learning Series<br>
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<a href="http://library.duke.edu/data/">Center for Data & Visualization Sciences</a><br>
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<a href="http://library.duke.edu/">Duke University Libraries</a>
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Shareable via Creative Commons: CC <a href="https://creativecommons.org/licenses/by-nc/4.0/">By-NC</a>
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<div class="appendix-bottom"></div>
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<div class="appendix-bottom">
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<h3 id="updates-and-corrections">Corrections</h3>
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<p>If you see mistakes or want to suggest changes, please <a href="https://github.com/data-and-visualization/git-tutorial/issues/new">create an issue</a> on the source repository.</p>
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<h3 id="reuse">Reuse</h3>
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<p>Text and figures are licensed under Creative Commons Attribution <a rel="license" href="https://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC 4.0</a>. Source code is available at <a href="https://github.com/data-and-visualization/git-tutorial">https://github.com/data-and-visualization/git-tutorial</a>, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".</p>
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<p><a href="https://rfun.library.duke.edu/">R We Having Fun Yet‽</a></p>
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<p><a href="https://library.duke.edu/data/">Center for Data &amp; Visualization Sciences</a>. <a href="https://library.duke.edu/">Duke University Libraries</a></p>
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