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        <h1 itemprop="headline">R Notebook</h1>
        <meta itemprop="image"
          content="https://via.placeholder.com/1200x714/dbdbdb/4a4a4a.png?text=R%20Notebook"><span
          itemscope="" itemtype="http://schema.org/Organization" itemprop="publisher">
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        <h2 itemscope="" itemtype="http://schema.stenci.la/Heading" id="introduction">Introduction
        </h2>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">This document is primarily
          intended to be used as a syntax reference for authoring R Markdown files for sharing
          reproducible articles on Stencila. Please ensure you’re viewing the <a
            href="https://hub.stenci.la/stencila/reference-r-markdown/files/" itemscope=""
            itemtype="http://schema.stenci.la/Link">raw RMd file</a>, and not the converted HTML
          file.</p>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">If you’re looking for material
          on how to use R Markdown for reproducible research, we recommend starting with the
          following links:</p>
        <ul itemscope="" itemtype="http://schema.org/ItemList">
          <li itemscope="" itemtype="http://schema.org/ListItem" itemprop="itemListElement">
            <meta itemprop="position" content="1">
            <meta itemprop="url" content="#1">Chris Hartgerink (2017) <em itemscope=""
              itemtype="http://schema.stenci.la/Emphasis">Composing reproducible manuscripts using R
              Markdown</em> <a
              href="https://elifesciences.org/labs/cad57bcf/composing-reproducible-manuscripts-using-r-markdown"
              itemscope=""
              itemtype="http://schema.stenci.la/Link">https://elifesciences.org/labs/cad57bcf/composing-reproducible-manuscripts-using-r-markdown</a>
          </li>
          <li itemscope="" itemtype="http://schema.org/ListItem" itemprop="itemListElement">
            <meta itemprop="position" content="2">
            <meta itemprop="url" content="#2">Daniel Nüst, Vicky Steeves, Rémi Rampin, Markus
            Konkol, Edzer Pebesma (2018)<em itemscope=""
              itemtype="http://schema.stenci.la/Emphasis">Writing reprocible geoscience papers using
              R Markdown, Docker, and GitLab</em> <a
              href="https://vickysteeves.gitlab.io/repro-papers/index.html" itemscope=""
              itemtype="http://schema.stenci.la/Link">https://vickysteeves.gitlab.io/repro-papers/index.html</a>
          </li>
          <li itemscope="" itemtype="http://schema.org/ListItem" itemprop="itemListElement">
            <meta itemprop="position" content="3">
            <meta itemprop="url" content="#3">Paul Bauer (2018) <em itemscope=""
              itemtype="http://schema.stenci.la/Emphasis">Writing a Reproducible Paper in R
              Markdown</em> <a href="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3175518"
              itemscope=""
              itemtype="http://schema.stenci.la/Link">https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3175518</a>
          </li>
        </ul>
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="project-assets">Project
          Assets</h3>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">You can refer to any of you
          project files using relative paths, both as markdown assets such as the photo below, and
          as data sources inside your code blocks.</p>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph"><a
            href="https://unsplash.com/photos/loL9nnBK-fE" itemscope=""
            itemtype="http://schema.stenci.la/Link"><img src="index.html.media/redPandas.png"
              alt="Photo by Valentin Petkov" itemscope=""
              itemtype="http://schema.org/ImageObject"></a></p>
        <hr itemscope="" itemtype="http://schema.stenci.la/ThematicBreak">
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="code-chunks">Code chunks
        </h3>
        <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="the-basics">The basics</h4>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">At the heart of R Markdown are
          &quot;code chunks&quot;. Code chunks can produce outputs, or they can be used to execute
          arbitrary R code. For example, here we assign a variable called <code itemscope=""
            itemtype="http://schema.stenci.la/CodeFragment">randoms</code> which will be an array of
          1000 random numbers sampled from a normal distribution:</p>
        <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk"
          data-programminglanguage="r">
          <pre class="language-r" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"
            slot="text"><code>randoms &lt;- rnorm(1000)</code></pre>
        </stencila-code-chunk>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">When you assign a variable in a
          code chunk you can reuse it in another chunk, later in the document. For example, we can
          plot the frequency distribution of the random numbers we assigned to the <code
            itemscope="" itemtype="http://schema.stenci.la/CodeFragment">randoms</code> variable
          earlier:</p>
        <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk"
          data-programminglanguage="r">
          <pre class="language-r" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"
            slot="text"><code>hist(randoms, breaks=30, col=&quot;grey&quot;, main=&quot;&quot;)</code></pre>
        </stencila-code-chunk>
        <h4 itemscope="" itemtype="http://schema.stenci.la/Heading"
          id="adding-figure-and-table-captions">Adding figure and table captions</h4>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">R Markdown allows you to
          specify &quot;options&quot; for code chunks. One such option is <code itemscope=""
            itemtype="http://schema.stenci.la/CodeFragment">fig.cap</code> which allows you to
          specify a figure caption:</p>
        <figure itemscope="" itemtype="http://schema.stenci.la/Figure">
          <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk"
            data-programminglanguage="r">
            <pre class="language-r" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"
              slot="text"><code>plot(randoms)</code></pre>
          </stencila-code-chunk>
          <figcaption>
            <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">My figure</p>
          </figcaption>
        </figure>
        <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="longer-captions">Longer
          captions</h5>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">The above method is OK for
          short captions, but when you have longer captions you will probably want to use <a
            href="https://bookdown.org/home/" itemscope=""
            itemtype="http://schema.stenci.la/Link">Bookdown</a> style text references e.g.</p>
        <figure itemscope="" itemtype="http://schema.stenci.la/Figure">
          <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk"
            data-programminglanguage="r">
            <pre class="language-r" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"
              slot="text"><code>plot(randoms)</code></pre>
          </stencila-code-chunk>
          <figcaption>
            <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">This is a slightly longer
              caption for my figure including some <strong itemscope=""
                itemtype="http://schema.stenci.la/Strong">strong</strong> emphasis.</p>
          </figcaption>
        </figure>
        <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="complex-captions">Complex
          captions</h5>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Bookdown style text references
          are good for longer, single paragraph captions. However, for more structured captions
          having a title and paragraph as is often found in academic journals we suggest that you
          use a code chunk block extension. e.g.</p>
        <figure itemscope="" itemtype="http://schema.stenci.la/Figure" id="fig3" title="Figure 3">
          <label data-itemprop="label">Figure 3</label>
          <stencila-code-chunk itemscope="" itemtype="http://schema.stenci.la/CodeChunk"
            data-programminglanguage="r">
            <pre class="language-r" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"
              slot="text"><code>plot(randoms)</code></pre>
          </stencila-code-chunk>
          <figcaption>
            <h5 itemscope="" itemtype="http://schema.stenci.la/Heading" id="the-title-of-my-plot">
              The title of my plot</h5>
            <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">A paragraph for my figure
              including some <strong itemscope=""
                itemtype="http://schema.stenci.la/Strong">strong</strong> emphasis.</p>
          </figcaption>
        </figure>
        <hr itemscope="" itemtype="http://schema.stenci.la/ThematicBreak">
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="inline-code-chunks">Inline
          code chunks</h3>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In R Markdown you can also
          inline &quot;inline&quot; code chunks within paragraphs and other text content. For
          example, here is the mean of the <code itemscope=""
            itemtype="http://schema.stenci.la/CodeFragment">randoms</code> variable that we assigned
          earlier: <stencila-code-expression programming-language="r" itemscope=""
            itemtype="http://schema.stenci.la/CodeExpression"><code class="r"
              slot="text">mean(randoms)</code><output slot="output"></output>
          </stencila-code-expression>.</p>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">In Stencila, we call these
          <code itemscope="" itemtype="http://schema.stenci.la/CodeFragment">CodeExpression</code>s,
          because they are intended to display a calculated value, and shouldn&#39;t be used for
          statements, such as assigning a variable.</p>
        <hr itemscope="" itemtype="http://schema.stenci.la/ThematicBreak">
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="references">References</h3>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">When creating Code Chunks, you
          can assign them an identifier which can be used as a reference from other places. For
          example <a href="#fig3" itemscope="" itemtype="http://schema.stenci.la/Link">this links to
            the code chunk above</a>.</p>
        <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="syntax">Syntax</h4>
        <pre class="language-md" itemscope="" itemtype="http://schema.stenci.la/CodeBlock"><code>chunk: Figure Title here
:::

#### This is the caption title

Some descriptive paragraph.

```r
# code goes here
```

:::
{#unique-identifier} # &lt;-- ID to use when referring to this figure</code></pre>
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="citations">Citations</h3>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">Stencila automatically parses a
          <a href="http://www.bibtex.org" itemscope=""
            itemtype="http://schema.stenci.la/Link">BibTeX</a> file if one is set under the <code
            itemscope="" itemtype="http://schema.stenci.la/CodeFragment">bibliography</code> key in
          the file&#39;s front-matter. The references will be automatically parsed and appended at
          the end of the document under a <em itemscope=""
            itemtype="http://schema.stenci.la/Emphasis">References</em> heading.</p>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">You can refer to items in the
          bibliography file be prefixing the item&#39;s identifier with an <code itemscope=""
            itemtype="http://schema.stenci.la/CodeFragment">@</code> symbol. This will automatically
          create a formatted citation. The citation style can vary depending on the output file
          format, as well as your <a
            href="http://help.stenci.la/en/articles/4330629-project-settings#theme" itemscope=""
            itemtype="http://schema.stenci.la/Link">chosen theme</a>.</p>
        <h4 itemscope="" itemtype="http://schema.stenci.la/Heading" id="example">Example</h4>
        <blockquote itemscope="" itemtype="http://schema.stenci.la/QuoteBlock">
          <p itemscope="" itemtype="http://schema.stenci.la/Paragraph"><em itemscope=""
              itemtype="http://schema.stenci.la/Emphasis">Twenty Thousand Leagues Under the
              Seas</em> (<cite itemscope="" itemtype="http://schema.stenci.la/Cite"><a
                href="#julesverne1870">Verne, 1870</a></cite>) is a great read.</p>
        </blockquote>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">However if you don’t want to
          create a formal inline citation, and simply link to the References section at the end of
          the document, you can use the same reference identifier but use a <code itemscope=""
            itemtype="http://schema.stenci.la/CodeFragment">#</code> symbol instead of a <code
            itemscope="" itemtype="http://schema.stenci.la/CodeFragment">@</code>.</p>
        <blockquote itemscope="" itemtype="http://schema.stenci.la/QuoteBlock">
          <p itemscope="" itemtype="http://schema.stenci.la/Paragraph"><a href="#julesverne1870"
              itemscope="" itemtype="http://schema.stenci.la/Link"><em itemscope=""
                itemtype="http://schema.stenci.la/Emphasis">Twenty Thousand Leagues Under the
                Seas</em> by Jules Verne</a> is a great read.</p>
        </blockquote>
        <hr itemscope="" itemtype="http://schema.stenci.la/ThematicBreak">
        <h3 itemscope="" itemtype="http://schema.stenci.la/Heading" id="feedback-welcome">Feedback
          welcome</h3>
        <p itemscope="" itemtype="http://schema.stenci.la/Paragraph">This document is continuously
          being refined based on your feedback, so please reach out to us at <a
            href="mailto:hello@stenci.la" itemscope=""
            itemtype="http://schema.stenci.la/Link">hello<cite itemscope=""
              itemtype="http://schema.stenci.la/Cite"><a href="#stenci">stenci</a></cite>.la</a> if
          you have questions or suggestions, would like to see a section added to this document, or
          if you find something unclear. We’d love to hear from you!</p>
        <section data-itemprop="references">
          <h2 data-itemtype="http://schema.stenci.la/Heading">References</h2>
          <ol>
            <li itemscope="" itemtype="http://schema.org/CreativeWork" itemprop="citation"
              id="RMD-Guide">
              <ol data-itemprop="authors">
                <li itemscope="" itemtype="http://schema.org/Person" itemprop="author">
                  <meta itemprop="name" content="Stencila"><span data-itemprop="familyNames"><span
                      itemprop="familyName">Stencila</span></span>
                </li>
              </ol><time itemprop="datePublished" datetime="2021">2021</time><a itemprop="url"
                href="http://help.stenci.la/en/"><span itemprop="headline">R Markdown: Authoring
                  executable documents with R Markdown</span></a><span itemscope=""
                itemtype="http://schema.org/Organization" itemprop="publisher">
                <meta itemprop="name" content="Unknown"><span itemscope=""
                  itemtype="http://schema.org/ImageObject" itemprop="logo">
                  <meta itemprop="url"
                    content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown">
                </span>
              </span>
            </li>
            <li itemscope="" itemtype="http://schema.org/CreativeWork" itemprop="citation"
              id="julesverne1870">
              <ol data-itemprop="authors">
                <li itemscope="" itemtype="http://schema.org/Person" itemprop="author">
                  <meta itemprop="name" content="Jules Verne"><span data-itemprop="givenNames"><span
                      itemprop="givenName">Jules</span></span><span
                    data-itemprop="familyNames"><span itemprop="familyName">Verne</span></span>
                </li>
              </ol><time itemprop="datePublished" datetime="1870">1870</time><span
                itemprop="headline">Twenty Thousand Leagues Under the Seas</span><span itemscope=""
                itemtype="http://schema.org/Organization" itemprop="publisher"><span
                  itemprop="name">Pierre-Jules Hetzel</span><span itemscope=""
                  itemtype="http://schema.org/ImageObject" itemprop="logo">
                  <meta itemprop="url"
                    content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Pierre-Jules%20Hetzel">
                </span></span>
            </li>
            <li itemscope="" itemtype="http://schema.org/CreativeWork" itemprop="citation"
              id="bibtex-editor">
              <ol data-itemprop="authors"></ol><a itemprop="url"
                href="https://truben.no/latex/bibtex/"><span itemprop="headline">BibTeX
                  Editor</span></a><span itemscope="" itemtype="http://schema.org/Organization"
                itemprop="publisher">
                <meta itemprop="name" content="Unknown"><span itemscope=""
                  itemtype="http://schema.org/ImageObject" itemprop="logo">
                  <meta itemprop="url"
                    content="https://via.placeholder.com/600x60/dbdbdb/4a4a4a.png?text=Unknown">
                </span>
              </span>
            </li>
          </ol>
        </section>
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