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<meta name="author" content="Dhrumil Mehta">
<title>quickstart</title>
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<div class="quarto-title">
<h1 class="title">quickstart</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Dhrumil Mehta </p>
</div>
</div>
</div>
</header>
<section id="python-r" class="level2">
<h2 class="anchored" data-anchor-id="python-r">Python + R</h2>
<p>A workflow for using Python and R in the same quarto notebook!</p>
<p>GitHub Repo: <a href="https://github.com/dmil/quarto-quickstart" class="uri">https://github.com/dmil/quarto-quickstart</a></p>
<blockquote class="blockquote">
<p>Prefer to work in Jupyter notebooks? Check out this <a href="https://github.com/dmil/jupyter-quickstart">alternate setup</a> that allows you to use Python and R together in a Jupyter notebook.</p>
</blockquote>
</section>
<section id="installation" class="level2">
<h2 class="anchored" data-anchor-id="installation">Installation</h2>
<p>When you run this notebook, it should ask to install the <code>reticulate</code> package. Once that is installed correctly, you should be able to run both R and Python cells.</p>
<p>⚠️ <strong>Caveat:</strong> to make this work, you may need to re-install Python.</p>
<p>This setup only works if Python was installed with the <code>--enable-shared</code> option. I had to first uninstall python and then re-install it with the <code>--enable-shared</code> option. Since I use pyenv, I installed it as follows:</p>
<pre><code>env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.11.2</code></pre>
</section>
<section id="setup" class="level2">
<h2 class="anchored" data-anchor-id="setup">Setup</h2>
<p><strong>Note</strong>: The following cell creates a python virtualenv, installs some packages (like <code>pandas</code> and <code>scikit-learn</code>).</p>
<p><a href="https://rstudio.github.io/reticulate/articles/versions.html" class="uri">https://rstudio.github.io/reticulate/articles/versions.html</a></p>
<div class="cell">
<div class="sourceCode cell-code" 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">library</span>(reticulate)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>venv_path <span class="ot"><-</span> <span class="fu">paste0</span>(<span class="fu">getwd</span>(), <span class="st">'/.venv'</span>)</span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="co"># create virtualenv and install python libraries</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>python_libraries <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"pandas"</span>, <span class="st">"scikit-learn"</span>)</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="fu">virtualenv_create</span>(venv_path, <span class="at">packages=</span>python_libraries)</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># use virtualenv</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a><span class="fu">use_virtualenv</span>(venv_path, <span class="at">required=</span><span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="running-code" class="level2">
<h2 class="anchored" data-anchor-id="running-code">Running Code</h2>
<p>When you click the <strong>Render</strong> button a document will be generated that includes both content and the output of embedded code.</p>
<p>You can embed R code like this:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Imports in R</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">require</span>(<span class="st">'tidyverse'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>And python code like this:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Imports in Python</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="sharing-variables-between-python-and-r" class="level2">
<h2 class="anchored" data-anchor-id="sharing-variables-between-python-and-r">Sharing variables between Python and R</h2>
<p>The following code defines a dataframe <code>df</code> in Python with random data points.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># create a dataframe of random numbers with two columns, A and B</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>df <span class="op">=</span> pd.DataFrame(</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> np.random.randint(<span class="dv">0</span>,<span class="dv">100</span>,size<span class="op">=</span>(<span class="dv">100</span>, <span class="dv">2</span>)), columns<span class="op">=</span><span class="bu">list</span>(<span class="st">'AB'</span>))</span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="co"># display first 5 rows</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>df.head(<span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> A B
0 55 88
1 42 0
2 81 86
3 9 26
4 99 12</code></pre>
</div>
</div>
<p>The following is an R cell. The <code>df</code> variable defined above is available as <code>py$df</code>. Python variables should be accessible in R prefixed with <code>py$</code> .</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>title <span class="ot"><-</span> <span class="st">"Random points plotted"</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(py<span class="sc">$</span>df) <span class="sc">+</span></span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">x=</span>A, <span class="at">y=</span>B) <span class="sc">+</span></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggtitle</span>(title)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="quickstart_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<p>R variables should be accessible in Python prefixed with <code>r.</code></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>r.title</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>'Random points plotted'</code></pre>
</div>
</div>
<p>See the <a href="https://ugoproto.github.io/ugo_r_doc/pdf/reticulate.pdf">reticulate cheat sheet</a> for more details on how to use Python and R together.</p>
</section>
<section id="why-i-like-this-setup" class="level2">
<h2 class="anchored" data-anchor-id="why-i-like-this-setup">Why I like this setup</h2>
<ul>
<li><p>It lets me do some things in Python (hitting APIs, scraping, etc)</p></li>
<li><p>It lets do other things in R (statistical calculations, visualization, etc)</p></li>
<li><p>I have found it useful to learn R (or Python) while on deadline. When I was learning R it allowed me to switch back to Python if I was stuck on a step and the deadline was approaching, and then switch back to R to finish up.</p></li>
<li><p>I have also found it helpful for teaching R to students who are already familiar with Python. I’m sure it can also be used well for the reverse.</p></li>
<li><p>If your code starts to get complicated, you can move Python functions into <code>.py</code> files in the repo and then call those functions from the notebook. You can also define functions in R and save them into a <code>.R</code> file which you can call from this notebook. Storing code away in functions in separate files let me keep the notebooks very clean and readable and proved to be a good way to annotate my process for the quantitative edit.</p></li>
</ul>
</section>
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