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<meta name="author" content=" Jadey Ryan Molly McIlquham, Kwabena Sarpong, Leslie Michel, Teal Potter, Deirdre Griffin LaHue, Dani Gelardi posit::conf(2023) | September 20">
<title>Parameterized Quarto reports improve understanding of soil health</title>
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<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Parameterized Quarto reports improve understanding of soil health</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
<br><br><br><strong>Jadey Ryan</strong><br>Molly McIlquham, Kwabena Sarpong, Leslie Michel, <br>Teal Potter, Deirdre Griffin LaHue, Dani Gelardi<br><br>posit::conf(2023) | September 20
</div>
</div>
</div>
</section>
<section id="dont-care-about-soils" class="slide level2">
<h2>Don’t care about soils?</h2>
<p>Parameterized reporting is for everyone!</p>
<div class="columns">
<div class="column" style="width:33%;">
<p><img data-src="images/ocean_floor.png" alt="RStudio RMarkdown parameterized report project for mapping ocean floors."></p>
<p><a href="https://rmarkdown.rstudio.com/lesson-6.html">Ocean floor maps</a></p>
</div><div class="column" style="width:33%;">
<p><img data-src="images/urban_institute.png" alt="Report for Alabama spending with text and plots generated from parameterized RMarkdown."></p>
<p><a href="https://book.rwithoutstatistics.com/parameterized-reports-chapter.html">Fiscal briefs</a></p>
</div><div class="column" style="width:33%;">
<p><img data-src="images/driver_quality.png" alt="Report for Alaska driver quality with text, plot, and table generated from parameterized RMarkdown."></p>
<p><a href="https://urban-institute.medium.com/iterated-fact-sheets-with-r-markdown-d685eb4eafce">Bad drivers</a></p>
</div>
</div>
<aside class="notes">
<p>My point is the data don’t make a difference. The people do. So it’s our responsibility to make the data and results understandable and interpretable for the people who have the power to make a difference. Parameterized reports are one way to democratize data and reward people for data collection efforts.</p>
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<section id="why-should-you-listen-to-me" class="slide level2">
<h2>Why should you listen to me?</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p>Hired as an environmental technician.</p>
<p><img data-src="images/sampling.jpg" alt="Jadey in waders setting up a transect with a measuring tape to measure flow in a small stream."></p>
</div><div class="column" style="width:50%;">
<div class="fragment">
<p>Then transitioned to data scientist.</p>
<p><img data-src="images/mai.jpg" alt="Jadey's cat, Mai, sitting on her laptop that has RStudio open. The monitor next to the laptop and cat has the R Packages book by Hadley Wickham and Jenny Bryan open."></p>
</div>
</div>
</div>
<div class="fragment">
<p>I went from picking leeches off my boots to picking cats off my keyboard!</p>
<aside class="notes">
<p>No CS or coding background. Went from picking leeches off my boots to picking my cat off my keyboard.</p>
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<section id="how-did-i-go-from-a-non-coder-to-a-data-scientist" class="slide level2">
<h2>How did I go from a ‘non-coder’ to a data scientist?</h2>
<div class="columns">
<div class="column" style="width:55%;">
<div class="fragment">
<p><em>With a skills test!</em> <br><br></p>
</div>
<div class="fragment">
<p><strong>Task:</strong> generate custom Soil Health Reports for each individual farmer</p>
<p><br></p>
</div>
<div class="fragment">
<p><strong>Timeframe:</strong> one week</p>
<p><br></p>
</div>
<div class="fragment">
<p><strong>Challenge:</strong> how do I automate custom reports???</p>
</div>
</div><div class="column" style="width:45%;">
<p><img data-src="images/confused_tai.jpg" class="fragment" style="max-height:500px" alt="Cat with an expression of existential dread"></p>
<p><span class="fragment">YouTube and blog rabbit holes & tutorial hell…</span></p>
</div>
</div>
</section>
<section id="the-reports-that-got-me-my-job" class="slide level2">
<h2>2021: the reports that got me my job</h2>
<div class="quarto-layout-panel">
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<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: center;">
<p><img data-src="images/2021_pg4.png" style="max-height:700px" alt="Example 2021 report with box plots"></p>
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</div>
<aside class="notes">
<p>MS Word much easier and faster to get started with beautiful styling compared to LaTex.</p>
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<section id="new-html-reports-with-quarto" class="slide level2">
<h2>2023: new HTML reports with Quarto!</h2>
<img data-src="images/report_html.png" alt="Beginning of 2023 example HTML report" class="r-stretch"></section>
<section id="and-ms-word-to-pdf" class="slide level2">
<h2>and MS Word to PDF</h2>
<div class="fragment">
<p>…because LaTeX <span class="emoji" data-emoji="confounded">😖</span> <span class="emoji" data-emoji="shrug">🤷</span></p>
<div class="quarto-layout-panel">
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<p><img data-src="images/2023_pg1.png" style="max-height:625px" alt="First page of 2023 example MS Word report"></p>
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<p><img data-src="images/2023_pg11.png" style="max-height:625px" alt="Page from example MS Word report showing soil texture triangle"></p>
</div>
</div>
</div>
<aside class="notes">
<p>Still haven’t learned LaTex, and not sure I’m going to?</p>
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<section id="code-snippets-and-7-pages-of-resources" class="slide level2">
<h2>Code snippets and 7 pages of resources</h2>
<p>We’re end-of-conference tired <span class="emoji" data-emoji="yawning_face">🥱</span> and our brains are full <span class="emoji" data-emoji="dizzy_face">😵</span>.</p>
<p>Don’t worry about taking notes or copying code.</p>
<div class="quarto-figure quarto-figure-left">
<figure>
<p><a href="https://jadeynryan.github.io/2023_posit-parameterized-quarto/"><img data-src="images/qr.png" alt="QR code to slides." height="400"></a></p>
<figcaption>Slides at tinyurl.com/quarto-params</figcaption>
</figure>
</div>
</section>
<section id="workflow" class="slide level2">
<h2>Workflow</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><img data-src="images/mermaid.svg" style="max-height:750px" alt="Flow chart of workflow: Learn about parameterized reports, prepare subsettable data, create content for easy consumption, design for accessibility."></p>
</div><div class="column fragment" style="width:50%;">
<p>Parameterized Quarto reports work with both <code>Knitr</code> and <code>Jupyter</code> engines.</p>
<p><img data-src="images/typing_tai.jpg" style="max-height:600px" alt="Cat typing on laptop."></p>
</div>
</div>
</section>
<section>
<section id="step-1-learn-about-parameterized-reports" class="title-slide slide level1 center" data-background-color="#023B2C">
<h1>— Step 1 — <br> Learn about parameterized reports</h1>
</section>
<section id="what-are-parameterized-reports" class="slide level2">
<h2>What are parameterized reports?</h2>
<div class="r-stack">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/template1.png" class="fragment" alt="File with the word '.qmd' inside and the word 'Function' above." width="1300"></p>
</figure>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/template2.png" class="fragment" alt="An arrow points from 'Input' with 'params$year' to the previous image with 'Function' and '.qmd' file." width="1300"></p>
</figure>
</div>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/template3.png" class="fragment" alt="In addition to the previous two images, arrows point to five reports with years 2019 through 2023 on them in a flow chart." width="1300"></p>
</figure>
</div>
</div>
</section>
<section id="yaml-header-yet-another-markdown-language" class="slide level2">
<h2>YAML Header: Yet Another Markdown Language</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb1" data-code-line-numbers="2|3-5|6-8|11"><pre class="sourceCode numberSource yaml number-lines code-with-copy"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1"></a><span class="pp">---</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="fu">title</span><span class="kw">:</span><span class="at"> </span><span class="st">"Soil Health Report"</span><span class="co"> # Metadata</span></span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="fu">format</span><span class="kw">:</span><span class="co"> # Set format types</span></span>
<span id="cb1-4"><a href="#cb1-4"></a><span class="at"> </span><span class="fu">html</span><span class="kw">:</span><span class="at"> </span></span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="at"> </span><span class="fu">docx</span><span class="kw">:</span><span class="at"> </span></span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="fu">params</span><span class="kw">:</span><span class="co"> # Set default parameter key-value pairs</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="at"> </span><span class="fu">farmer</span><span class="kw">:</span><span class="at"> Sammy Sunflower </span></span>
<span id="cb1-8"><a href="#cb1-8"></a><span class="at"> </span><span class="fu">year</span><span class="kw">:</span><span class="at"> </span><span class="dv">2023</span><span class="at"> </span></span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="pp">---</span></span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="at"> </span></span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="at">Report content goes here.</span><span class="co"> # Write content</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="access-your-parameters" class="slide level2">
<h2>Access your parameters</h2>
<p>Run any line or chunk to add <code>params</code> to your environment.</p>
<div class="fragment">
<p><code>params</code> object is a list.</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><span class="fu">str</span>(params)</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>List of 2
$ farmer: chr "Sammy Sunflower"
$ year : num 2023</code></pre>
</div>
</div>
</div>
<div class="fragment">
<p>Access with <code>$</code> notation.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>params<span class="sc">$</span>farmer</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>[1] "Sammy Sunflower"</code></pre>
</div>
</div>
</div>
<div class="fragment">
<p>For inline code, enclose the expression in <code>`r `</code>.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode numberSource markdown number-lines code-with-copy"><code class="sourceCode markdown"><span id="cb6-1"><a href="#cb6-1"></a>These are results for <span class="in">`r params$farmer`</span>.</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>These are results for Sammy Sunflower.</p>
</div>
</section>
<section id="render-with-the-rstudio-ide" class="slide level2">
<h2>Render with the RStudio IDE</h2>
<img data-src="images/render.png" alt="RStudio Quarto Render button with a dropdown for HTML and MS Word with Render on Save option checked" class="r-stretch"><p><strong>Render Button</strong>, keyboard shortcut <code>Ctrl + Shift + K</code>, or by saving.</p>
<div class="fragment">
<p>Uses default parameters in the YAML.</p>
</div>
<div class="fragment">
<p>Output file has same name and location as input file.</p>
</div>
</section>
<section id="render-with-quartoquarto_render" class="slide level2">
<h2>Render with <code>quarto::quarto_render()</code></h2>
<p>Use in <code>Console</code> or an <code>iterate.R</code> script.</p>
<p><br></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb7" data-code-line-numbers="|2|3|4|5-7"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>quarto<span class="sc">::</span><span class="fu">quarto_render</span>(</span>
<span id="cb7-2"><a href="#cb7-2"></a> <span class="at">input =</span> <span class="st">"template.qmd"</span>, <span class="co"># Input Quarto file</span></span>
<span id="cb7-3"><a href="#cb7-3"></a> <span class="at">output_format =</span> <span class="st">"html"</span>, <span class="co"># Output format</span></span>
<span id="cb7-4"><a href="#cb7-4"></a> <span class="at">output_file =</span> <span class="st">"2022_OscarOrchard_Report.html"</span>, <span class="co"># Output file name</span></span>
<span id="cb7-5"><a href="#cb7-5"></a> <span class="at">execute_params =</span> <span class="fu">list</span>( <span class="co"># Named list of parameters</span></span>
<span id="cb7-6"><a href="#cb7-6"></a> <span class="at">farmer =</span> <span class="st">"Oscar Orchard"</span>,</span>
<span id="cb7-7"><a href="#cb7-7"></a> <span class="at">year =</span> <span class="dv">2022</span></span>
<span id="cb7-8"><a href="#cb7-8"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="render-all-reports-at-once" class="slide level2">
<h2>Render all reports at once</h2>
<p>Create a data frame with two columns that match <code>quarto_render()</code> args:</p>
<div>
<ul>
<li class="fragment"><code>output_file</code>: filename.ext</li>
<li class="fragment"><code>execute_params</code>: named list of parameters</li>
</ul>
</div>
<div class="fragment">
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>reports <span class="ot"><-</span> data <span class="sc">|></span></span>
<span id="cb8-2"><a href="#cb8-2"></a> dplyr<span class="sc">::</span><span class="fu">distinct</span>(farmer, year) <span class="sc">|></span></span>
<span id="cb8-3"><a href="#cb8-3"></a> dplyr<span class="sc">::</span><span class="fu">mutate</span>(</span>
<span id="cb8-4"><a href="#cb8-4"></a> <span class="at">output_file =</span> <span class="fu">paste0</span>(</span>
<span id="cb8-5"><a href="#cb8-5"></a> year, <span class="st">"_"</span>, <span class="fu">gsub</span>(<span class="st">" "</span>, <span class="st">""</span>, farmer), <span class="st">"_Report.html"</span></span>
<span id="cb8-6"><a href="#cb8-6"></a> ),</span>
<span id="cb8-7"><a href="#cb8-7"></a> <span class="at">execute_params =</span> purrr<span class="sc">::</span><span class="fu">map2</span>(</span>
<span id="cb8-8"><a href="#cb8-8"></a> farmer, year,</span>
<span id="cb8-9"><a href="#cb8-9"></a> \(x, y) <span class="fu">list</span>(<span class="at">farmer =</span> x, <span class="at">year =</span> y)</span>
<span id="cb8-10"><a href="#cb8-10"></a> )</span>
<span id="cb8-11"><a href="#cb8-11"></a> ) <span class="sc">|></span> </span>
<span id="cb8-12"><a href="#cb8-12"></a> dplyr<span class="sc">::</span><span class="fu">select</span>(output_file, execute_params)</span>
<span id="cb8-13"><a href="#cb8-13"></a></span>
<span id="cb8-14"><a href="#cb8-14"></a><span class="fu">head</span>(reports, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<div class="kable-table">
<table>
<thead>
<tr class="header">
<th style="text-align: left;">output_file</th>
<th style="text-align: left;">execute_params</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">2023_SammySunflower_Report.html</td>
<td style="text-align: left;">Sammy Sunflower, 2023</td>
</tr>
<tr class="even">
<td style="text-align: left;">2022_OscarOrchard_Report.html</td>
<td style="text-align: left;">Oscar Orchard, 2022</td>
</tr>
<tr class="odd">
<td style="text-align: left;">2022_TinaTomato_Report.html</td>
<td style="text-align: left;">Tina Tomato, 2022</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</section>
<section id="render-all-reports-at-once-1" class="slide level2">
<h2>Render all reports at once</h2>
<p>Map over each row of the <code>reports</code> dataframe.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a>reports <span class="sc">|></span></span>
<span id="cb9-2"><a href="#cb9-2"></a> purrr<span class="sc">::</span><span class="fu">pwalk</span>(</span>
<span id="cb9-3"><a href="#cb9-3"></a> quarto<span class="sc">::</span>quarto_render,</span>
<span id="cb9-4"><a href="#cb9-4"></a> <span class="at">input =</span> <span class="st">"template.qmd"</span>,</span>
<span id="cb9-5"><a href="#cb9-5"></a> <span class="at">output_format =</span> <span class="st">"html"</span> </span>
<span id="cb9-6"><a href="#cb9-6"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="section" class="slide level2">
<h2></h2>
<iframe src="https://drive.google.com/file/d/1uMz7iQzi06JcuuhYidNjvQDrrjhBPMeg/preview" width="100%" height="100%" allow="autoplay">
</iframe>
</section>
<section id="section-1" class="slide level2">
<h2></h2>
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/surprise_mai.jpg" alt="Surprised cat next to the surprised Pikachu meme." height="750"></p>
</figure>
</div>
</section></section>
<section>
<section id="step-2-prepare-subsettable-data" class="title-slide slide level1 center" data-background-color="#023B2C">
<h1>— Step 2 — <br>Prepare subsettable data</h1>
</section>
<section id="our-simple-data" class="slide level2">
<h2>Our simple data</h2>
<div class="cell">
<div class="cell-output-display">
<table data-quarto-postprocess="true">
<thead>
<tr class="header">
<th style="text-align: right;" data-quarto-table-cell-role="th">year</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">sampleId</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">farmer</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">crop</th>
<th style="text-align: right;" data-quarto-table-cell-role="th">sand_%</th>
<th style="text-align: right;" data-quarto-table-cell-role="th">silt_%</th>
<th style="text-align: right;" data-quarto-table-cell-role="th">clay_%</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right; background-color: #FDCE86 !important;">2023</td>
<td style="text-align: left;">23-SUN-01</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Sammy Sunflower</td>
<td style="text-align: left;">Sunflower</td>
<td style="text-align: right;">44</td>
<td style="text-align: right;">23</td>
<td style="text-align: right;">3</td>
</tr>
<tr class="even">
<td style="text-align: right; background-color: #FDCE86 !important;">2022</td>
<td style="text-align: left;">22-ORC-02</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Oscar Orchard</td>
<td style="text-align: left;">Cherry</td>
<td style="text-align: right;">69</td>
<td style="text-align: right;">21</td>
<td style="text-align: right;">10</td>
</tr>
<tr class="odd">
<td style="text-align: right; background-color: #FDCE86 !important;">2022</td>
<td style="text-align: left;">22-TOM-02</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Tina Tomato</td>
<td style="text-align: left;">Vegetable</td>
<td style="text-align: right;">11</td>
<td style="text-align: right;">79</td>
<td style="text-align: right;">10</td>
</tr>
<tr class="even">
<td style="text-align: right; background-color: #FDCE86 !important;">2022</td>
<td style="text-align: left;">22-HAR-03</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Henry Harvest</td>
<td style="text-align: left;">Herb</td>
<td style="text-align: right;">36</td>
<td style="text-align: right;">51</td>
<td style="text-align: right;">13</td>
</tr>
<tr class="odd">
<td style="text-align: right; background-color: #FDCE86 !important;">2023</td>
<td style="text-align: left;">23-GAR-03</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Grace Gardener</td>
<td style="text-align: left;">Sunflower</td>
<td style="text-align: right;">64</td>
<td style="text-align: right;">33</td>
<td style="text-align: right;">3</td>
</tr>
<tr class="even">
<td style="text-align: right; background-color: #FDCE86 !important;">2022</td>
<td style="text-align: left;">22-QUI-02</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Quincy Quinoa</td>
<td style="text-align: left;">Quinoa</td>
<td style="text-align: right;">24</td>
<td style="text-align: right;">62</td>
<td style="text-align: right;">14</td>
</tr>
</tbody>
</table>
</div>
</div>
<p><br></p>
<div class="fragment">
<p>fake farmer names: ChatGPT 🙏🏻</p>
</div>
</section>
<section id="use-params-to-set-up-comparisons" class="slide level2">
<h2>Use <code>params</code> to set up comparisons</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb10" data-code-line-numbers="2|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>data <span class="sc">|></span> </span>
<span id="cb10-2"><a href="#cb10-2"></a> dplyr<span class="sc">::</span><span class="fu">filter</span>(farmer <span class="sc">==</span> params<span class="sc">$</span>farmer) <span class="sc">|></span> </span>
<span id="cb10-3"><a href="#cb10-3"></a> more data wrangling</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb11" data-code-line-numbers="3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a><span class="co"># Get the farmer's crops</span></span>
<span id="cb11-2"><a href="#cb11-2"></a>farmer_crop <span class="ot"><-</span> data <span class="sc">|></span></span>
<span id="cb11-3"><a href="#cb11-3"></a> dplyr<span class="sc">::</span><span class="fu">filter</span>(farmer <span class="sc">==</span> params<span class="sc">$</span>farmer) <span class="sc">|></span></span>
<span id="cb11-4"><a href="#cb11-4"></a> dplyr<span class="sc">::</span><span class="fu">pull</span>(crop) <span class="sc">|></span></span>
<span id="cb11-5"><a href="#cb11-5"></a> <span class="fu">unique</span>()</span>
<span id="cb11-6"><a href="#cb11-6"></a></span>
<span id="cb11-7"><a href="#cb11-7"></a>data_long <span class="ot"><-</span> data <span class="sc">|></span></span>
<span id="cb11-8"><a href="#cb11-8"></a> <span class="co"># Tidy data: one observation per row</span></span>
<span id="cb11-9"><a href="#cb11-9"></a> tidyr<span class="sc">::</span><span class="fu">pivot_longer</span>(<span class="at">cols =</span> <span class="fu">c</span>(<span class="st">"sand_%"</span><span class="sc">:</span><span class="st">"clay_%"</span>),</span>
<span id="cb11-10"><a href="#cb11-10"></a> <span class="at">names_to =</span> <span class="st">"measurement"</span>) <span class="sc">|></span> </span>
<span id="cb11-11"><a href="#cb11-11"></a> dplyr<span class="sc">::</span><span class="fu">mutate</span>(</span>
<span id="cb11-12"><a href="#cb11-12"></a> <span class="co"># Categorize samples based on if they are from the farmer of</span></span>
<span id="cb11-13"><a href="#cb11-13"></a> <span class="co"># interest or are of the same crop type</span></span>
<span id="cb11-14"><a href="#cb11-14"></a> <span class="at">category =</span> dplyr<span class="sc">::</span><span class="fu">case_when</span>(</span>
<span id="cb11-15"><a href="#cb11-15"></a> farmer <span class="sc">==</span> params<span class="sc">$</span>farmer <span class="sc">~</span> <span class="st">"Your fields"</span>,</span>
<span id="cb11-16"><a href="#cb11-16"></a> crop <span class="sc">%in%</span> farmer_crop <span class="sc">~</span> <span class="st">"Same crop"</span>,</span>
<span id="cb11-17"><a href="#cb11-17"></a> <span class="cn">TRUE</span> <span class="sc">~</span> <span class="st">"Other fields"</span></span>
<span id="cb11-18"><a href="#cb11-18"></a> )</span>
<span id="cb11-19"><a href="#cb11-19"></a> )</span>
<span id="cb11-20"><a href="#cb11-20"></a></span>
<span id="cb11-21"><a href="#cb11-21"></a><span class="co"># Set category factor levels</span></span>
<span id="cb11-22"><a href="#cb11-22"></a>data_long<span class="sc">$</span>category <span class="ot"><-</span> <span class="fu">factor</span>(</span>
<span id="cb11-23"><a href="#cb11-23"></a> data_long<span class="sc">$</span>category,</span>
<span id="cb11-24"><a href="#cb11-24"></a> <span class="at">levels =</span> <span class="fu">c</span>(<span class="st">"Other fields"</span>, <span class="st">"Same crop"</span>, <span class="st">"Your fields"</span>),</span>
<span id="cb11-25"><a href="#cb11-25"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Other fields"</span>, <span class="st">"Same crop"</span>, <span class="st">"Your fields"</span>)</span>
<span id="cb11-26"><a href="#cb11-26"></a>)</span>
<span id="cb11-27"><a href="#cb11-27"></a></span>
<span id="cb11-28"><a href="#cb11-28"></a>data_long <span class="sc">|></span> </span>
<span id="cb11-29"><a href="#cb11-29"></a> dplyr<span class="sc">::</span><span class="fu">select</span>(<span class="sc">-</span><span class="fu">c</span>(year, sampleId)) <span class="sc">|></span> </span>
<span id="cb11-30"><a href="#cb11-30"></a> dplyr<span class="sc">::</span><span class="fu">slice_head</span>(<span class="at">by =</span> category) <span class="sc">|></span> </span>
<span id="cb11-31"><a href="#cb11-31"></a> kableExtra<span class="sc">::</span><span class="fu">kable</span>() <span class="sc">|></span> </span>
<span id="cb11-32"><a href="#cb11-32"></a> kableExtra<span class="sc">::</span><span class="fu">column_spec</span>(<span class="dv">5</span>, <span class="at">background =</span> <span class="st">"#FDCE86"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<table data-quarto-postprocess="true">
<thead>
<tr class="header">
<th style="text-align: left;" data-quarto-table-cell-role="th">farmer</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">crop</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">measurement</th>
<th style="text-align: right;" data-quarto-table-cell-role="th">value</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">category</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">Sammy Sunflower</td>
<td style="text-align: left;">Sunflower</td>
<td style="text-align: left;">sand_%</td>
<td style="text-align: right;">44</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Your fields</td>
</tr>
<tr class="even">
<td style="text-align: left;">Oscar Orchard</td>
<td style="text-align: left;">Cherry</td>
<td style="text-align: left;">sand_%</td>
<td style="text-align: right;">69</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Other fields</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Grace Gardener</td>
<td style="text-align: left;">Sunflower</td>
<td style="text-align: left;">sand_%</td>
<td style="text-align: right;">64</td>
<td style="text-align: left; background-color: #FDCE86 !important;">Same crop</td>
</tr>
</tbody>
</table>
</div>
</div>
</section></section>
<section>
<section id="step-3-create-content-for-easy-consumption" class="title-slide slide level1 center" data-background-color="#023B2C">
<h1>— Step 3 — <br>Create content for easy consumption</h1>
</section>
<section id="interpretation-through-comparison" class="slide level2">
<h2>Interpretation through comparison</h2>
<p>Show how their results compare to other samples in similar contexts.</p>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb12"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb12-2"><a href="#cb12-2"></a><span class="fu">set.seed</span>(<span class="dv">123</span>)</span>
<span id="cb12-3"><a href="#cb12-3"></a>data_long <span class="sc">|></span></span>
<span id="cb12-4"><a href="#cb12-4"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(</span>
<span id="cb12-5"><a href="#cb12-5"></a> <span class="at">x =</span> measurement,</span>
<span id="cb12-6"><a href="#cb12-6"></a> <span class="at">y =</span> value,</span>
<span id="cb12-7"><a href="#cb12-7"></a> <span class="at">color =</span> category,</span>
<span id="cb12-8"><a href="#cb12-8"></a> <span class="at">shape =</span> category,</span>
<span id="cb12-9"><a href="#cb12-9"></a> <span class="at">size =</span> category,</span>
<span id="cb12-10"><a href="#cb12-10"></a> <span class="at">alpha =</span> category</span>
<span id="cb12-11"><a href="#cb12-11"></a> )) <span class="sc">+</span></span>
<span id="cb12-12"><a href="#cb12-12"></a> <span class="fu">geom_jitter</span>(<span class="at">width =</span> <span class="fl">0.2</span>) <span class="sc">+</span></span>
<span id="cb12-13"><a href="#cb12-13"></a> <span class="co"># Define styles for producer's samples versus all samples</span></span>
<span id="cb12-14"><a href="#cb12-14"></a> <span class="fu">scale_alpha_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(</span>
<span id="cb12-15"><a href="#cb12-15"></a> <span class="st">"Other fields"</span> <span class="ot">=</span> <span class="fl">0.5</span>,</span>
<span id="cb12-16"><a href="#cb12-16"></a> <span class="st">"Same crop"</span> <span class="ot">=</span> <span class="dv">1</span>,</span>
<span id="cb12-17"><a href="#cb12-17"></a> <span class="st">"Your fields"</span> <span class="ot">=</span> <span class="dv">1</span></span>
<span id="cb12-18"><a href="#cb12-18"></a> )) <span class="sc">+</span></span>
<span id="cb12-19"><a href="#cb12-19"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(</span>
<span id="cb12-20"><a href="#cb12-20"></a> <span class="st">"Other fields"</span> <span class="ot">=</span> <span class="st">"#CCC29C"</span>,</span>
<span id="cb12-21"><a href="#cb12-21"></a> <span class="st">"Same crop"</span> <span class="ot">=</span> <span class="st">"#76ADBC"</span>,</span>
<span id="cb12-22"><a href="#cb12-22"></a> <span class="st">"Your fields"</span> <span class="ot">=</span> <span class="st">"#A60F2D"</span></span>
<span id="cb12-23"><a href="#cb12-23"></a> )) <span class="sc">+</span></span>
<span id="cb12-24"><a href="#cb12-24"></a> <span class="fu">scale_size_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(</span>
<span id="cb12-25"><a href="#cb12-25"></a> <span class="st">"Other fields"</span> <span class="ot">=</span> <span class="dv">2</span>,</span>
<span id="cb12-26"><a href="#cb12-26"></a> <span class="st">"Same crop"</span> <span class="ot">=</span> <span class="dv">4</span>,</span>
<span id="cb12-27"><a href="#cb12-27"></a> <span class="st">"Your fields"</span> <span class="ot">=</span> <span class="dv">4</span></span>
<span id="cb12-28"><a href="#cb12-28"></a> )) <span class="sc">+</span></span>
<span id="cb12-29"><a href="#cb12-29"></a> washi<span class="sc">::</span><span class="fu">washi_theme</span>(</span>
<span id="cb12-30"><a href="#cb12-30"></a> <span class="at">legend_position =</span> <span class="st">"bottom"</span>,</span>
<span id="cb12-31"><a href="#cb12-31"></a> <span class="at">gridline_x =</span> <span class="cn">FALSE</span>,</span>
<span id="cb12-32"><a href="#cb12-32"></a> <span class="at">gridline_y =</span> <span class="cn">FALSE</span>,</span>
<span id="cb12-33"><a href="#cb12-33"></a> <span class="at">text_scale =</span> <span class="fl">1.5</span></span>
<span id="cb12-34"><a href="#cb12-34"></a> ) <span class="sc">+</span></span>
<span id="cb12-35"><a href="#cb12-35"></a> <span class="fu">theme</span>(<span class="at">legend.title =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb12-36"><a href="#cb12-36"></a> <span class="at">axis.title.x =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb12-37"><a href="#cb12-37"></a> <span class="at">axis.title.y =</span> <span class="fu">element_blank</span>(),</span>
<span id="cb12-38"><a href="#cb12-38"></a> <span class="at">panel.border =</span> <span class="fu">element_rect</span>(<span class="at">color =</span> <span class="st">"gray"</span>, <span class="at">fill =</span> <span class="cn">NA</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<img data-src="2023_posit-parameterized-quarto_files/figure-revealjs/unnamed-chunk-13-1.png" width="960" class="r-stretch"></section>
<section id="make-your-reports-self-contained" class="slide level2">
<h2>Make your reports self-contained</h2>
<p>Provide your reader the context to understand the results.</p>
<div class="fragment">
<p><br></p>
<p>Instead of ~300 lines of markdown:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode numberSource markdown number-lines code-with-copy"><code class="sourceCode markdown"><span id="cb13-1"><a href="#cb13-1"></a><span class="fu">## What We Measured in Your Soil</span></span>
<span id="cb13-2"><a href="#cb13-2"></a></span>
<span id="cb13-3"><a href="#cb13-3"></a>{{< include soil_health_measurements.qmd >}}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p><br></p>
<p><code>Includes</code> shortcodes make it easy to reuse information across reports.</p>
</div>
</section>
<section id="make-your-html-reports-self-contained" class="slide level2">
<h2>Make your HTML reports self-contained</h2>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode numberSource yaml number-lines code-with-copy"><code class="sourceCode yaml"><span id="cb14-1"><a href="#cb14-1"></a><span class="co"># Include in YAML</span></span>
<span id="cb14-2"><a href="#cb14-2"></a><span class="pp">---</span></span>
<span id="cb14-3"><a href="#cb14-3"></a><span class="fu">format</span><span class="kw">:</span><span class="at"> </span></span>
<span id="cb14-4"><a href="#cb14-4"></a><span class="at"> </span><span class="fu">html</span><span class="kw">:</span></span>
<span id="cb14-5"><a href="#cb14-5"></a><span class="at"> </span><span class="fu">embed-resources</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span></span>