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<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Creating data plots for effective decision-making using statistical inference with R</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Dianne Cook <br> Monash University
</div>
</div>
</div>
</section>
<section id="session-1-making-effective-plots-using-ggplot2s-grammar-of-graphics" class="slide level2 center center-align">
<h2>Session 1: Making effective plots using ggplot2’s grammar of graphics</h2>
</section>
<section id="outline" class="slide level2">
<h2>Outline</h2>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<table>
<thead>
<tr class="header">
<th style="text-align: left;">time</th>
<th style="text-align: left;">topic</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">1:40-1:55</td>
<td style="text-align: left;">Why, philosophy and benefits</td>
</tr>
<tr class="even">
<td style="text-align: left;">1:55-2:15</td>
<td style="text-align: left;">Organising data to map variables to plots</td>
</tr>
<tr class="odd">
<td style="text-align: left;">2:15-2:45</td>
<td style="text-align: left;">Making a variety of plots</td>
</tr>
<tr class="even">
<td style="text-align: left;">2:45-3:10</td>
<td style="text-align: left;">Do but don’t, and cognitive principles</td>
</tr>
<tr class="odd">
<td style="text-align: left;">3:10-3:40</td>
<td style="text-align: left;">COFFEE BREAK</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
<section id="why" class="slide level2">
<h2>Why</h2>
<div class="columns">
<div class="column" style="width:60%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/unnamed-chunk-4-1.png" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:40%;">
<p>Is there any pattern in the residuals that indicate a problem with the model fit?</p>
</div>
</div>
</section>
<section id="why-1" class="slide level2">
<h2>Why</h2>
<div class="columns">
<div class="column" style="width:60%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/unnamed-chunk-5-1.png" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:40%;">
<p><br><br> Do the teams have different shot styles?</p>
<div style="font-size: 60%;">
<p>(From the Women’s 2019 World Cup Soccer)</p>
</div>
</div>
</div>
</section>
<section id="why-2" class="slide level2">
<h2>Why</h2>
<img data-src="slides1_files/figure-revealjs/tb-trend-1.png" style="width:100.0%" class="r-stretch quarto-figure-center"><center>
<p><br> Is TB getting worse? (In Australia and Uruguay)</p>
<div style="font-size: 60%;">
<p>(From the <a href="https://www.who.int/teams/global-tuberculosis-programme/data.">World Health Organisation (WHO)</a>]</p>
</div>
</center>
</section>
<section id="why-3" class="slide level2">
<h2>Why</h2>
<center>
<p><br> Which is the best display to answer the previous question?</p>
</center>
<img data-src="slides1_files/figure-revealjs/ury-tb-trend-1.png" style="width:100.0%" class="r-stretch quarto-figure-center"></section>
<section id="whats-the-goal" class="slide level2">
<h2>What’s the goal?</h2>
<p><br></p>
<p>Reading data plots is <span style="color: #F5191C;">subjective</span>.</p>
<div class="fragment">
<p><br> Making decisions based on data visualisations is common, where <span style="color: #3B99B1;"> we need to be objective </span>.</p>
</div>
<div class="fragment" style="margin-left:230px">
<p><br><br><br> It is possible, and <span style="color: #3B99B1;"> here is how we do that …</span></p>
</div>
</section>
<section id="these-are-the-tools-you-need" class="slide level2">
<h2>These are the tools you need</h2>
<div class="{.columns]">
<div class="column" style="width:45%;">
<div class="textbox">
<p><img data-src="https://ggplot2.tidyverse.org/logo.png" width="150"></p>
<div class="cell" data-layout-align="center">
<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">install.packages</span>(<span class="st">"ggplot2"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div style="font-size: 60%;">
<p>or better yet:</p>
</div>
<div class="cell" data-layout-align="center">
<div class="sourceCode cell-code" id="cb2" data-code-line-numbers="false"><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">install.packages</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>
<div style="font-size: 60%;">
<ul>
<li>Define your plots using a grammar that maps variables in tidy data to elements of the plot.</li>
<li>Wrangle your data into tidy form for clarity of plot specification.</li>
</ul>
</div>
</div>
</div>
<div class="column" style="width:8%;">
<p><span style="color: #FFFFFF;"> space </span></p>
</div>
<div class="column" style="width:45%;">
<div class="textbox">
<p><img data-src="https://dicook.github.io/nullabor/reference/figures/nullabor_hex.png" width="170"></p>
<div class="cell" data-layout-align="center">
<div class="sourceCode cell-code" id="cb3" data-code-line-numbers="false"><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">install.packages</span>(<span class="st">"nullabor"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div style="font-size: 60%;">
<ul>
<li>Compare your data plot to plots of null data.</li>
<li>This checks whether what we see is real or spurious.</li>
<li>Also allows for measuring the effectiveness of one plot design vs another.</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="organising-your-data-to-enable-mapping-variables-to-graphical-elements" class="slide level2 center">
<h2>Organising your data to enable mapping variables to graphical elements</h2>
</section>
<section id="tidy-data" class="slide level2">
<h2>Tidy data</h2>
<p><img data-src="https://cdn.myportfolio.com/45214904-6a61-4e23-98d6-b140f8654a40/6e297111-efb7-4555-93d2-085071d1853c_rw_1920.jpg?h=f1951b118eaddaaab8a572422bc16566" class="absolute" style="top: 0px; right: 0px; width: 550px; "></p>
<p><br><br><br><br></p>
<ol type="1">
<li><strong>Each variable forms a column</strong></li>
<li><strong>Each observation forms a row</strong></li>
<li><strong>Each type of observational unit forms a table.</strong> If you have data on multiple levels (e.g. data about houses and data about the rooms within those houses), these should be in separate tables.</li>
</ol>
<div style="font-size: 40%;">
<p>Illustrations from the Openscapes blog Tidy Data for reproducibility, efficiency, and collaboration by <a href="https://allisonhorst.com/other-r-fun">Julia Lowndes and Allison Horst</a></p>
</div>
</section>
<section id="your-turn" class="slide level2 center">
<h2>YOUR TURN</h2>
<p>For each of the following data discuss whether it is in tidy form.</p>
</section>
<section id="data-1-tuberculosis-from-who" class="slide level2">
<h2>Data 1: tuberculosis from WHO</h2>
<div style="font-size: 50%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-67602451c3924e7694f1" style="width:100%;height:auto;"></div>
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</div>
</div>
</div>
</section>
<section id="data-2-graduate-programs" class="slide level2">
<h2>Data 2: Graduate programs</h2>
<div style="font-size: 40%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-46afe7d9819f694888eb" style="width:100%;height:auto;"></div>
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</div>
</div>
</div>
</section>
<section id="data-3-ghcn-weather-station-records" class="slide level2">
<h2>Data 3: GHCN weather station records</h2>
<div style="font-size: 50%;">
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-3eccf5a395ca4bc59106" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-3eccf5a395ca4bc59106">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6","7","8","9","10","11"],["UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560","UYM00086560"],[2021,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021],[6,6,7,7,8,8,9,9,10,10,11],["PRCP","TAVG","PRCP","TAVG","PRCP","TAVG","PRCP","TAVG","PRCP","TAVG","PRCP"],[0,164,0,95,0,100,0,163,272,188,0],[8,129,0,109,0,77,450,137,0,160,112],[0,143,null,112,0,117,0,146,5,136,36],[5,176,null,114,0,111,0,139,0,160,0],[610,127,0,111,null,131,5,142,0,186,8],[0,107,0,143,0,179,0,147,0,148,0],[0,113,0,160,0,199,109,147,0,125,3],[0,147,10,179,0,110,526,149,0,129,0],[0,155,0,208,531,83,211,142,0,153,0],[3,156,0,145,74,78,0,132,0,171,0],[0,111,0,111,0,103,0,159,46,163,0],[0,159,30,162,0,92,0,191,33,174,0],[0,173,0,116,0,87,0,142,0,177,0],[0,139,0,112,0,111,30,151,381,194,290],[0,96,295,111,null,91,0,144,0,149,0],[0,90,0,102,0,142,0,184,0,157,0],[0,85,5,105,0,142,0,194,0,174,0],[0,81,0,98,0,131,0,174,0,167,0],[0,93,0,84,0,131,0,169,0,166,0],[0,96,0,111,0,150,15,160,0,201,0],[0,107,0,121,0,144,0,126,0,211,0],[0,122,0,152,0,157,0,133,0,206,0],[0,144,0,181,0,123,0,153,23,181,0],[48,133,0,129,0,121,0,150,0,199,0],[3,133,249,159,0,121,0,162,0,240,0],[0,112,0,109,0,141,0,193,0,279,246],[0,71,0,85,0,118,0,159,0,283,0],[0,83,0,76,0,165,8,149,0,288,0],[0,89,null,82,0,153,3,178,0,241,632],[0,78,0,107,0,208,0,164,0,251,0],[null,null,0,107,0,244,null,null,0,185,null]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>id<\/th>\n <th>year<\/th>\n <th>month<\/th>\n <th>element<\/th>\n <th>VALUE1<\/th>\n <th>VALUE2<\/th>\n <th>VALUE3<\/th>\n <th>VALUE4<\/th>\n <th>VALUE5<\/th>\n <th>VALUE6<\/th>\n <th>VALUE7<\/th>\n <th>VALUE8<\/th>\n <th>VALUE9<\/th>\n <th>VALUE10<\/th>\n <th>VALUE11<\/th>\n <th>VALUE12<\/th>\n <th>VALUE13<\/th>\n <th>VALUE14<\/th>\n <th>VALUE15<\/th>\n <th>VALUE16<\/th>\n <th>VALUE17<\/th>\n <th>VALUE18<\/th>\n <th>VALUE19<\/th>\n <th>VALUE20<\/th>\n <th>VALUE21<\/th>\n <th>VALUE22<\/th>\n <th>VALUE23<\/th>\n <th>VALUE24<\/th>\n <th>VALUE25<\/th>\n <th>VALUE26<\/th>\n <th>VALUE27<\/th>\n <th>VALUE28<\/th>\n <th>VALUE29<\/th>\n <th>VALUE30<\/th>\n <th>VALUE31<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"t","columnDefs":[{"className":"dt-right","targets":[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
</div>
</div>
</section>
<section id="answers" class="slide level2">
<h2>Answers</h2>
<div class="columns">
<div class="column" style="width:33%;">
<div class="textbox">
<p><strong>Data 1</strong>: <br><span style="color: #F5191C;">Not in tidy form</span></p>
<ul>
<li>iso3</li>
<li>year</li>
<li>gender</li>
<li>age</li>
</ul>
</div>
</div><div class="column" style="width:33%;">
<div class="fragment fade-in">
<div class="textbox">
<p><strong>Data 2</strong>: <br><span style="color: #3B99B1;">It’s in tidy form!</span></p>
<ul>
<li>subject</li>
<li>inst</li>
<li>AvNumPubs</li>
<li>AvNumCits</li>
<li>…</li>
</ul>
</div>
</div>
</div><div class="column" style="width:33%;">
<div class="fragment fade-in">
<div class="textbox">
<p><strong>Data 3</strong>: <br><span style="color: #F5191C;">Not in tidy form</span></p>
<ul>
<li>station</li>
<li>year</li>
<li>month</li>
<li>day</li>
<li>TMAX</li>
<li>TMIN</li>
<li>PRCP</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="statistical-data" class="slide level2">
<h2>Statistical data</h2>
<p><span class="math display">\[X = \left[ \begin{array}{rrrr}
X_{~1} & X_{~2} & ... & X_{~p}
\end{array} \right] \\
= \left[ \begin{array}{rrrr}
X_{~11} & X_{~12} & ... & X_{~1p} \\
X_{~21} & X_{~22} & ... & X_{~2p} \\
\vdots & \vdots & \ddots& \vdots \\
X_{~n1} & X_{~n2} & ... & X_{~np}
\end{array} \right]\]</span></p>
<ul>
<li><span style="color: #3B99B1;">This is tidy data!</span></li>
<li>You might also make assumptions about the distribution of each variable, e.g. <span class="math inline">\(X_{~1} \sim N(0,1), ~~X_{~2} \sim \text{Exp}(1) ...\)</span></li>
</ul>
</section>
<section id="mapping" class="slide level2">
<h2>Mapping</h2>
<p>In <code>ggplot2</code>, the variables from tidy data are explicitly mapped to elements of the plot, using <code>aesthetics</code>.</p>
<div class="columns">
<div class="column" style="width:49%;">
<div style="font-size: 50%;">
<p><strong>Basic Mappings</strong></p>
<ul>
<li><code>x</code> and <code>y</code> to plot points in a two-dimensional space</li>
<li><code>color</code>, <code>fill</code> to render as a color scale</li>
<li><code>size</code> maps variable to size of object</li>
<li><code>shape</code> maps variable to different shapes</li>
</ul>
<p>Depending on the <code>geom</code> different mappings are possible, <code>xmin</code>, <code>xend</code>, <code>linetype</code>, <code>alpha</code>, <code>stroke</code>, <code>weight</code> …</p>
<p><strong>Facets</strong></p>
<p>Variables are used to subset (or condition)</p>
<p><strong>Layers</strong></p>
<p>Different data can be mapped onto the same plot, eg observations, and means</p>
</div>
</div><div class="column" style="width:49%;">
<div class="fragment">
<p><strong>Example</strong></p>
<div class="cell" data-layout-align="center">
<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">ggplot</span>(mpg, </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="at">x=</span>displ, </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="at">y=</span>hwy, </span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="at">color=</span>class)) <span class="sc">+</span> </span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div style="font-size: 60%;">
<p><code>displ</code> is mapped to <code>x</code><br> <code>hwy</code> is mapped to <code>y</code><br> <code>class</code> is mapped to <code>color</code>.</p>
</div>
</div>
</div>
</div>
</section>
<section id="common-plot-descriptions-as-scripts" class="slide level2 center">
<h2>Common plot descriptions as scripts</h2>
</section>
<section id="example-1a" class="slide level2">
<h2>Example 1A</h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>How are variables mapped to create this plot?</p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/ury-tb-1.png" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:49%;">
<p><br><br></p>
<div class="cell" data-layout-align="center">
<details>
<summary>Code for URY TB plot</summary>
<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">ggplot</span>(tb_ury, </span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">x=</span>year, </span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="at">y=</span>c_newinc)) <span class="sc">+</span> </span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_continuous</span>(<span class="st">"Year"</span>, </span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">1980</span>, <span class="dv">2020</span>, <span class="dv">10</span>), </span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"80"</span>, <span class="st">"90"</span>, <span class="st">"00"</span>, <span class="st">"10"</span>, <span class="st">"20"</span>)) <span class="sc">+</span></span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"TB incidence"</span>) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</div>
</div>
</section>
<section id="example-1b" class="slide level2">
<h2>Example 1B</h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>How are variables mapped to create this plot?</p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/ury-tb-bar-1.png" style="width:100.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:49%;">
<p><br><br></p>
<div class="cell" data-layout-align="center">
<details>
<summary>Code for URY TB plot</summary>
<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><span class="fu">ggplot</span>(tb_ury, <span class="fu">aes</span>(<span class="at">x=</span>year, <span class="at">y=</span>c_newinc)) <span class="sc">+</span> </span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_smooth</span>(<span class="at">se=</span>F, <span class="at">colour=</span><span class="st">"#F5191C"</span>) <span class="sc">+</span></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_continuous</span>(<span class="st">"Year"</span>, <span class="at">breaks =</span> <span class="fu">seq</span>(<span class="dv">1980</span>, <span class="dv">2020</span>, <span class="dv">10</span>), <span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"80"</span>, <span class="st">"90"</span>, <span class="st">"00"</span>, <span class="st">"10"</span>, <span class="st">"20"</span>)) <span class="sc">+</span></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"TB incidence"</span>) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</div>
</div>
</section>
<section id="example-2a" class="slide level2">
<h2>Example 2A</h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>How are variables mapped to create this plot?</p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/penguins1-1.png" style="width:80.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:49%;">
<p><br><br></p>
<div class="cell" data-layout-align="center">
<details>
<summary>Code for penguins plot</summary>
<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><span class="fu">ggplot</span>(penguins, </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">x=</span>flipper_length_mm, </span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> <span class="at">y=</span>bill_length_mm, </span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> <span class="at">color=</span>species)) <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="at">alpha=</span><span class="fl">0.8</span>) <span class="sc">+</span></span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_discrete_divergingx</span>(<span class="at">palette=</span><span class="st">"Zissou 1"</span>) <span class="sc">+</span></span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.title =</span> <span class="fu">element_blank</span>(), </span>
<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"bottom"</span>,</span>
<span id="cb7-9"><a href="#cb7-9" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.direction =</span> <span class="st">"horizontal"</span>,</span>
<span id="cb7-10"><a href="#cb7-10" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="st">"8"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</div>
</div>
</section>
<section id="example-2b" class="slide level2">
<h2>Example 2B</h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>How are variables mapped to create this plot?</p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/penguins2-1.png" style="width:80.0%"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:49%;">
<p><br><br></p>
<div class="cell" data-layout-align="center">
<details>
<summary>Code for penguins plot</summary>
<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><span class="fu">ggplot</span>(penguins, </span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">x=</span>flipper_length_mm, </span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a> <span class="at">y=</span>bill_length_mm, </span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a> <span class="at">color=</span>species)) <span class="sc">+</span> </span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_density2d</span>(<span class="at">alpha=</span><span class="fl">0.8</span>) <span class="sc">+</span></span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_discrete_divergingx</span>(<span class="at">palette=</span><span class="st">"Zissou 1"</span>) <span class="sc">+</span></span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.title =</span> <span class="fu">element_blank</span>(), </span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.position =</span> <span class="st">"bottom"</span>,</span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.direction =</span> <span class="st">"horizontal"</span>,</span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a> <span class="at">legend.text =</span> <span class="fu">element_text</span>(<span class="at">size=</span><span class="st">"8"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</div>
</div>
</section>
<section id="example-3-15" class="slide level2">
<h2>Example 3 <span style="font-size: 70%;"> (1/5) </span></h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>First get the data in tidy form</p>
<div class="cell" data-layout-align="center">
<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>tb_ury_sa <span class="ot"><-</span> tb_ury <span class="sc">%>%</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(year <span class="sc">></span> <span class="dv">2012</span>) <span class="sc">%>%</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(iso3, year, </span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a> newrel_f014<span class="sc">:</span>newrel_f65, </span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a> newrel_m014<span class="sc">:</span>newrel_m65) <span class="sc">%>%</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">pivot_longer</span>(<span class="at">cols=</span>newrel_f014<span class="sc">:</span>newrel_m65,</span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a> <span class="at">names_to =</span> <span class="st">"sex_age"</span>, </span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a> <span class="at">values_to =</span> <span class="st">"count"</span>) <span class="sc">%>%</span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(<span class="sc">!</span><span class="fu">is.na</span>(count)) <span class="sc">%>%</span></span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">separate</span>(sex_age, <span class="at">into=</span><span class="fu">c</span>(<span class="st">"stuff"</span>, </span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a> <span class="st">"sex_age"</span>)) <span class="sc">%>%</span></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">sex =</span> <span class="fu">str_sub</span>(sex_age, <span class="dv">1</span>, <span class="dv">1</span>),</span>
<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a> <span class="at">age =</span> <span class="fu">str_sub</span>(sex_age, <span class="dv">2</span>, </span>
<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">str_length</span>(sex_age))) <span class="sc">%>%</span></span>
<span id="cb9-15"><a href="#cb9-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">age =</span> <span class="fu">case_when</span>(</span>
<span id="cb9-16"><a href="#cb9-16" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"014"</span> <span class="sc">~</span> <span class="st">"0-14"</span>,</span>
<span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"1524"</span> <span class="sc">~</span> <span class="st">"15-24"</span>,</span>
<span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"2534"</span> <span class="sc">~</span> <span class="st">"25-34"</span>,</span>
<span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"3544"</span> <span class="sc">~</span> <span class="st">"35-44"</span>,</span>
<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"4554"</span> <span class="sc">~</span> <span class="st">"45-54"</span>,</span>
<span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"5564"</span> <span class="sc">~</span> <span class="st">"55-64"</span>,</span>
<span id="cb9-22"><a href="#cb9-22" aria-hidden="true" tabindex="-1"></a> age <span class="sc">==</span> <span class="st">"65"</span> <span class="sc">~</span> <span class="st">"65"</span>)) <span class="sc">%>%</span></span>
<span id="cb9-23"><a href="#cb9-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(iso3, year, sex, age, count)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div><div class="column" style="width:49%;">
<div class="fragment">
<div style="font-size: 50%;">
<p><br></p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-88b39e999738327054d9" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-88b39e999738327054d9">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126"],["URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY","URY"],[2013,2013,2013,2013,2013,2013,2013,2013,2013,2013,2013,2013,2013,2013,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2017,2017,2017,2017,2017,2017,2017,2017,2017,2017,2017,2017,2017,2017,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2019,2019,2019,2019,2019,2019,2019,2019,2019,2019,2019,2019,2019,2019,2020,2020,2020,2020,2020,2020,2020,2020,2020,2020,2020,2020,2020,2020,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021,2021],["f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m","f","f","f","f","f","f","f","m","m","m","m","m","m","m"],["0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65","0-14","15-24","25-34","35-44","45-54","55-64","65"],[30,35,71,44,31,40,35,22,80,142,102,100,83,66,24,60,59,34,26,23,48,33,73,138,109,97,75,63,27,50,61,57,40,32,32,26,83,135,115,86,87,69,23,46,45,58,29,38,47,28,69,135,122,98,77,64,30,52,81,62,37,30,35,21,82,127,128,104,73,71,27,53,66,62,30,35,39,20,83,155,155,119,80,78,18,46,57,56,38,27,56,24,103,157,152,124,100,99,30,56,58,42,44,35,40,31,101,137,126,103,65,100,20,55,58,49,41,32,30,14,85,153,129,100,96,89]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>iso3<\/th>\n <th>year<\/th>\n <th>sex<\/th>\n <th>age<\/th>\n <th>count<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"t","columnDefs":[{"className":"dt-right","targets":[2,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="example-3-25" class="slide level2">
<h2>Example 3 <span style="font-size: 70%;"> (2/5) </span></h2>
<div class="columns">
<div class="column" style="width:49%;">
<p>How many ways can we plot all three variables?</p>
<div style="font-size: 40%;">
<p><br></p>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-abda2b74508f87bc7ddf" style="width:100%;height:auto;"></div>
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</div>
</div>
</div>
</div><div class="column" style="width:15%;">
</div><div class="column" style="width:25%;">
<div class="fragment textbox" style="font-size: 50%;">
<p><code>geom</code>: bar + position (stack, dodge, fill)</p>
<p><code>aes</code>:</p>
<ul>
<li>Var 1 to <code>x</code></li>
<li><code>count</code> to <code>y</code></li>
<li>Var 2 to <code>color</code></li>
<li>Var 3 to <code>facet</code></li>
</ul>
</div>
<div class="fragment textbox" style="font-size: 50%;">
<p><code>geom</code>: point + smooth</p>
<p><code>aes</code>:</p>
<ul>
<li>Var 1 to <code>x</code></li>
<li><code>count</code> to <code>y</code></li>
<li>Var 2 to <code>color</code></li>
<li>Var 3 to <code>facet</code></li>
</ul>
</div>
</div>
</div>
</section>
<section id="example-3-35" class="slide level2">
<h2>Example 3 <span style="font-size: 70%;"> (3/5) </span></h2>
<img data-src="slides1_files/figure-revealjs/unnamed-chunk-28-1.png" style="width:100.0%" class="r-stretch quarto-figure-center"><div style="font-size: 60%;">
<p>How are variables mapped to create this plot?</p>
<p><code>geom</code>: bar/position=“fill”</p>
<p><code>year</code> to <code>x</code> <span class="math inline">\(~~~~\)</span> <code>count</code> to <code>y</code> <span class="math inline">\(~~~~\)</span> <code>fill</code> to <code>sex</code> <span class="math inline">\(~~~~\)</span> <code>facet</code> by <code>age</code></p>
</div>
<div class="fragment" style="font-size: 60%;">
<p><br> Observations: More incidence among males, especially with age. No clear temporal trend.</p>
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</section>
<section id="example-3-45" class="slide level2">
<h2>Example 3 <span style="font-size: 70%;"> (4/5) </span></h2>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/unnamed-chunk-29-1.png" style="width:80.0%"></p>
</figure>
</div>
</div>
</div>
<div class="columns">
<div class="column" style="width:50%;">
<div style="font-size: 60%;">
<p><code>geom</code>: bar</p>
<p><code>year</code> to <code>x</code> <span class="math inline">\(~\)</span> <code>count</code> to <code>y</code> <span class="math inline">\(~\)</span> <code>fill</code> and <code>facet</code> to <code>sex</code> <span class="math inline">\(~\)</span> <code>facet</code> by <code>age</code></p>
</div>
</div><div class="column" style="width:30%;">
<div class="fragment" style="font-size: 60%;">
<p>Incidence is higher in the middle age groups.</p>
</div>
<div class="fragment" style="font-size: 60%;">
<p>Where’s the temporal trend?</p>
</div>
</div>
</div>
<div class="fragment">
<p><img data-src="slides1_files/figure-revealjs/ury-tb-trend-1.png" class="absolute" style="top: 540px; left: 850px; width: 250px; "></p>
</div>
</section>
<section id="example-3-55" class="slide level2">
<h2>Example 3 <span style="font-size: 70%;"> (5/5) </span></h2>
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="slides1_files/figure-revealjs/unnamed-chunk-30-1.png" style="width:80.0%"></p>
</figure>
</div>
</div>
</div>
<div class="columns">
<div class="column" style="width:50%;">
<div style="font-size: 60%;">
<p><code>geom</code>: point, smooth</p>
<p><code>year</code> to <code>x</code> <span class="math inline">\(~\)</span> <code>count</code> to <code>y</code> <span class="math inline">\(~\)</span> <code>colour</code> and <code>facet</code> to <code>sex</code> <span class="math inline">\(~\)</span> <code>facet</code> by <code>age</code></p>
</div>
</div><div class="column" style="width:30%;">
<div class="fragment" style="font-size: 60%;">
<p><br> Temporal trend is mostly with males.</p>
</div>