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demo.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.513">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>Demo</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
}
pre.numberSource { margin-left: 3em; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
</style>
<script src="demo_files/libs/clipboard/clipboard.min.js"></script>
<script src="demo_files/libs/quarto-html/quarto.js"></script>
<script src="demo_files/libs/quarto-html/popper.min.js"></script>
<script src="demo_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="demo_files/libs/quarto-html/anchor.min.js"></script>
<link href="demo_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="demo_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="demo_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="demo_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="demo_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
<script src="demo_files/libs/htmlwidgets-1.6.2/htmlwidgets.js"></script>
<link href="demo_files/libs/vis-9.1.0/vis-network.min.css" rel="stylesheet">
<script src="demo_files/libs/vis-9.1.0/vis-network.min.js"></script>
<script src="demo_files/libs/visNetwork-binding-2.1.2/visNetwork.js"></script>
<link href="demo_files/libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet">
<script src="demo_files/libs/datatables-binding-0.30/datatables.js"></script>
<script src="demo_files/libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<link href="demo_files/libs/dt-core-1.13.4/css/jquery.dataTables.min.css" rel="stylesheet">
<link href="demo_files/libs/dt-core-1.13.4/css/jquery.dataTables.extra.css" rel="stylesheet">
<script src="demo_files/libs/dt-core-1.13.4/js/jquery.dataTables.min.js"></script>
<link href="demo_files/libs/crosstalk-1.2.0/css/crosstalk.min.css" rel="stylesheet">
<script src="demo_files/libs/crosstalk-1.2.0/js/crosstalk.min.js"></script>
</head>
<body class="fullcontent">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Demo</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="a-modal-editor" class="level1">
<h1>A Modal Editor</h1>
<p>This is an example sentence. It lives in this example paragraph. Lorem ipsum dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia. Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est proident. Nostrud officia pariatur ut officia. Sit irure elit esse ea nulla sunt ex occaecat reprehenderit commodo officia dolor Lorem duis laboris cupidatat officia voluptate. Culpa proident adipisicing id nulla nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non excepteur duis sunt velit enim. Voluptate laboris sint cupidatat ullamco ut ea consectetur et est culpa et culpa duis.</p>
<p>Lorem ipsum dolor sit amet, officia excepteur ex fugiat reprehenderit enim labore culpa sint ad nisi Lorem pariatur mollit ex esse exercitation amet. Nisi anim cupidatat excepteur officia. Reprehenderit nostrud nostrud ipsum Lorem est aliquip amet voluptate voluptate dolor minim nulla est proident. Nostrud officia pariatur ut officia. Sit irure elit esse ea nulla sunt ex occaecat reprehenderit commodo officia dolor Lorem duis laboris cupidatat officia voluptate. Culpa proident adipisicing id nulla nisi laboris ex in Lorem sunt duis officia eiusmod. Aliqua reprehenderit commodo ex non excepteur duis sunt velit enim. Voluptate laboris sint cupidatat ullamco ut ea consectetur et est culpa et culpa duis.</p>
</section>
<section id="targets" class="level1">
<h1>Targets</h1>
<section id="setup" class="level2">
<h2 class="anchored" data-anchor-id="setup">Setup</h2>
<p>Load packages.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(targets)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Generate the <code>_targets.R</code> file.</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">tar_script</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Run the pipeline.</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="fu">tar_make</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Visualize the pipeline.</p>
<div class="cell">
<div class="sourceCode cell-code" 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><span class="fu">tar_visnetwork</span>(<span class="at">callr_arguments =</span> <span class="fu">list</span>(<span class="at">show =</span> <span class="cn">FALSE</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="visNetwork html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-86940da6d33ea422283f" style="width:100%;height:464px;"></div>
<script type="application/json" data-for="htmlwidget-86940da6d33ea422283f">{"x":{"nodes":{"name":["penguins","penguins_clean","species_colors","clean_data"],"type":["stem","stem","stem","function"],"status":["uptodate","uptodate","uptodate","uptodate"],"seconds":[0.002,0.01,0,null],"bytes":[2917,3116,123,null],"branches":[null,null,null,null],"label":["penguins","penguins_clean","species_colors","clean_data"],"color":["#354823","#354823","#354823","#354823"],"id":["penguins","penguins_clean","species_colors","clean_data"],"level":[1,2,0,1],"shape":["dot","dot","dot","triangle"]},"edges":{"from":["clean_data","penguins"],"to":["penguins_clean","penguins_clean"],"arrows":["to","to"]},"nodesToDataframe":true,"edgesToDataframe":true,"options":{"width":"100%","height":"100%","nodes":{"shape":"dot","physics":false},"manipulation":{"enabled":false},"edges":{"smooth":{"type":"cubicBezier","forceDirection":"horizontal"}},"physics":{"stabilization":false},"interaction":{"zoomSpeed":1},"layout":{"hierarchical":{"enabled":true,"direction":"LR"}}},"groups":null,"width":null,"height":null,"idselection":{"enabled":false,"style":"width: 150px; height: 26px","useLabels":true,"main":"Select by id"},"byselection":{"enabled":false,"style":"width: 150px; height: 26px","multiple":false,"hideColor":"rgba(200,200,200,0.5)","highlight":false},"main":{"text":"","style":"font-family:Georgia, Times New Roman, Times, serif;font-weight:bold;font-size:20px;text-align:center;"},"submain":null,"footer":null,"background":"rgba(0, 0, 0, 0)","highlight":{"enabled":true,"hoverNearest":false,"degree":{"from":1,"to":1},"algorithm":"hierarchical","hideColor":"rgba(200,200,200,0.5)","labelOnly":true},"collapse":{"enabled":true,"fit":false,"resetHighlight":true,"clusterOptions":null,"keepCoord":true,"labelSuffix":"(cluster)"},"legend":{"width":0.2,"useGroups":false,"position":"right","ncol":1,"stepX":100,"stepY":100,"zoom":true,"nodes":{"label":["Up to date","Stem","Function"],"color":["#354823","#899DA4","#899DA4"],"shape":["dot","dot","triangle"]},"nodesToDataframe":true},"tooltipStay":300,"tooltipStyle":"position: fixed;visibility:hidden;padding: 5px;white-space: nowrap;font-family: verdana;font-size:14px;font-color:#000000;background-color: #f5f4ed;-moz-border-radius: 3px;-webkit-border-radius: 3px;border-radius: 3px;border: 1px solid #808074;box-shadow: 3px 3px 10px rgba(0, 0, 0, 0.2);"},"evals":[],"jsHooks":[]}</script>
</div>
</div>
<p>Load the updated targets.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">tar_load</span>(penguins)</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">tar_load</span>(penguins_clean)</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar_load</span>(species_colors)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="visualize-the-dataset" class="level2">
<h2 class="anchored" data-anchor-id="visualize-the-dataset">Visualize the dataset</h2>
<p><img src="./img/lter_penguins.png" class="img-fluid"></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>DT<span class="sc">::</span><span class="fu">datatable</span>(penguins)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-e10a4026cd9265aa15be" style="width:100%;height:auto;"></div>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>species<\/th>\n <th>island<\/th>\n <th>bill_length_mm<\/th>\n <th>bill_depth_mm<\/th>\n <th>flipper_length_mm<\/th>\n <th>body_mass_g<\/th>\n <th>sex<\/th>\n <th>year<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[3,4,5,6,8]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
</div>
<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>penguins_clean <span class="sc">|></span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(bill_length_cm, bill_depth_cm)) <span class="sc">+</span></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="fu">aes</span>(<span class="at">color =</span> species, <span class="at">shape =</span> sex), <span class="at">size =</span> <span class="dv">5</span>) <span class="sc">+</span></span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> species_colors)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="demo_files/figure-html/unnamed-chunk-7-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="build-a-model" class="level2">
<h2 class="anchored" data-anchor-id="build-a-model">Build a model</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>anova_model <span class="ot"><-</span> <span class="fu">aov</span>(bill_length_cm <span class="sc">~</span> species <span class="sc">+</span> sex, penguins_clean)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(anova_model)</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> Df Sum Sq Mean Sq F value Pr(>F)
species 2 70.15 35.08 649.1 <2e-16 ***
sex 1 11.36 11.36 210.2 <2e-16 ***
Residuals 329 17.78 0.05
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11 observations deleted due to missingness</code></pre>
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<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">TukeyHSD</span>(anova_model)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<pre><code> Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = bill_length_cm ~ species + sex, data = penguins_clean)
$species
diff lwr upr p adj
Chinstrap-Adelie 1.0009851 0.9206328 1.08133739 0.0000000
Gentoo-Adelie 0.8744095 0.8068175 0.94200147 0.0000000
Gentoo-Chinstrap -0.1265756 -0.2097741 -0.04337719 0.0011404
$sex
diff lwr upr p adj
male-female 0.3693368 0.3192155 0.419458 0</code></pre>
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<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>penguins_clean <span class="sc">|></span></span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(species, bill_length_cm, <span class="at">color =</span> species, <span class="at">group =</span> species)) <span class="sc">+</span></span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a> ggbeeswarm<span class="sc">::</span><span class="fu">geom_quasirandom</span>() <span class="sc">+</span></span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">stat_summary</span>(<span class="at">color =</span> <span class="st">"black"</span>) <span class="sc">+</span></span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> species_colors) <span class="sc">+</span></span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">guides</span>(<span class="at">color =</span> <span class="cn">FALSE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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