From ca573fc09255023153efafd971cb341364f275e4 Mon Sep 17 00:00:00 2001
From: arranhamlet <arran.hamlet14@imperial.ac.uk>
Date: Mon, 23 Sep 2024 19:14:33 -0700
Subject: [PATCH] Flexdashboard chapter finished

---
 html_outputs/new_pages/flexdashboard.html | 194 +++++++++++++++++-----
 html_outputs/search.json                  |   2 +-
 new_pages/flexdashboard.qmd               |  58 ++++---
 3 files changed, 178 insertions(+), 76 deletions(-)
diff --git a/html_outputs/new_pages/flexdashboard.html b/html_outputs/new_pages/flexdashboard.html
index 29bb0b18..af1e63fd 100644
--- a/html_outputs/new_pages/flexdashboard.html
+++ b/html_outputs/new_pages/flexdashboard.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.550">
+<meta name="generator" content="quarto-1.4.555">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -137,78 +137,150 @@
 </script> 
   
 <script async="" src="https://www.googletagmanager.com/gtag/js?id=G-QXDW878QLX"></script>
+
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 </head><body class="nav-sidebar floating"><div class="alert alert-info alert-dismissible">
+
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+
   <strong>Need help learning R?</strong> Enroll in Applied Epi's <a href="https://www.appliedepi.org/live/"
+
     class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/tutorial/"
+
     class="alert-link">free R tutorials</a>, post in our <a href="https://community.appliedepi.org/"
+
     class="alert-link">Community Q&A forum</a>, or ask about our <a href="mailto:contact@appliedepi.org"
+
     class="alert-link">R Help Desk service</a>. -->
+
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+
+
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+
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+
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+
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+
     en: '<strong>Need help learning R?</strong> Enroll in Applied Epi\'s <a href="https://www.appliedepi.org/live/" class="alert-link">intro R course</a>, try our <a href="https://www.appliedepi.org/tutorial/" class="alert-link">free R tutorials</a>, post in our <a href="https://community.appliedepi.org/" class="alert-link">Community Q&A forum</a>, or ask about our <a href="mailto:contact@appliedepi.org" class="alert-link">R Help Desk service</a>.',
+
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+
     es: '<strong>¿Necesitas ayuda para aprender R?</strong> Inscríbete en el <a href="https://www.appliedepi.org/live/" class="alert-link">Curso de introducción a R</a> de Applied Epi, prueba nuestros <a href="https://www.appliedepi.org/tutorial/" class="alert-link">Tutoriales gratuitos de R</a>, escribe en nuestro <a href="https://community.appliedepi.org/" class="alert-link">Foro de preguntas y respuestas,</a> o pregunta por nuestra <a href="mailto:contact@appliedepi.org" class="alert-link">Asistencia técnica para R</a>.',
+
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+
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+
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+
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+
     ru: '<strong>Нужна помощь в изучении R?</strong> Запишитесь на <a href="https://www.appliedepi.org/live/" class="alert-link">вводный курс по R</a> от Applied Epi, попробуйте наши <a href="https://www.appliedepi.org/tutorial/" class="alert-link">бесплатные учебные материалы по R</a>, задайте вопрос в нашем <a href="https://community.appliedepi.org/" class="alert-link">форуме вопросов и ответов сообщества</a>, или спросите о нашей услуге <a href="mailto:contact@appliedepi.org" class="alert-link">Службы поддержки по R</a>.'
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@@ -216,6 +288,7 @@
 
 
 
+
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
   <nav class="quarto-secondary-nav">
@@ -744,20 +817,20 @@ <h1 class="title"><span class="chapter-number">42</span>&nbsp; <span class="chap
 </div>
 </div>
 </div>
-<p>This page will cover the basic use of the <strong>flexdashboard</strong> package. This package allows you to easily format R Markdown output as a dashboard with panels and pages. The dashboard content can be text, static figures/tables or interactive graphics.</p>
+<p>This page will cover the basic use of the <a href="https://pkgs.rstudio.com/flexdashboard/"><strong>flexdashboard</strong> package</a>. This package allows you to easily format R Markdown output as a dashboard with panels and pages. The dashboard content can be text, static figures/tables or interactive graphics.</p>
 <p>Advantages of <strong>flexdashboard</strong>:</p>
 <ul>
-<li>It requires minimal non-standard R coding - with very little practice you can quickly create a dashboard<br>
+<li>It requires minimal non-standard R coding - with very little practice you can quickly create a dashboard.<br>
 </li>
-<li>The dashboard can usually be emailed to colleagues as a self-contained HTML file - no server required<br>
+<li>The dashboard can usually be emailed to colleagues as a self-contained HTML file - no server required.<br>
 </li>
-<li>You can combine <strong>flexdashboard</strong> with <strong>shiny</strong>, <strong>ggplotly</strong>, and other <em>“html widgets”</em> to add interactivity</li>
+<li>You can combine <strong>flexdashboard</strong> with <a href="../new_pages/shiny_basics.html"><strong>shiny</strong></a>, <a href="../new_pages/interactive_plots.html"><strong>ggplotly</strong></a>, and other <em>“html widgets”</em> to add interactivity.</li>
 </ul>
 <p>Disadvantages of <strong>flexdashboard</strong>:</p>
 <ul>
-<li>Less customization as compared to using <strong>shiny</strong> alone to create a dashboard</li>
+<li>Less customization as compared to using <strong>shiny</strong> alone to create a dashboard.</li>
 </ul>
-<p>Very comprehensive tutorials on using <strong>flexdashboard</strong> that informed this page can be found in the Resources section. Below we describe the core features and give an example of building a dashboard to explore an outbreak, using the case <code>linelist</code> data.</p>
+<p>Very comprehensive tutorials on using <strong>flexdashboard</strong> that informed this page can be found in the <a href="../new_pages/flexdashboard.html#resources">Resources</a> section. Below we describe the core features and give an example of building a dashboard to explore an outbreak, using the case <code>linelist</code> data.</p>
 <section id="preparation" class="level2" data-number="42.1">
 <h2 data-number="42.1" class="anchored" data-anchor-id="preparation"><span class="header-section-number">42.1</span> Preparation</h2>
 <section id="load-packages" class="level3 unnumbered">
@@ -778,14 +851,23 @@ <h3 class="unnumbered anchored" data-anchor-id="load-packages">Load packages</h3
 <h3 class="unnumbered anchored" data-anchor-id="import-data">Import data</h3>
 <p>We import the dataset of cases from a simulated Ebola epidemic. If you want to follow along, <a href="https://github.com/appliedepi/epirhandbook_eng/raw/master/data/case_linelists/linelist_cleaned.rds" class="download-button">click to download the “clean” linelist</a> (as .rds file). Import data with the <code>import()</code> function from the <strong>rio</strong> package (it handles many file types like .xlsx, .csv, .rds - see the <a href="../new_pages/importing.html">Import and export</a> page for details).</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="co"># import the linelist</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>linelist <span class="ot">&lt;-</span> <span class="fu">import</span>(<span class="st">"linelist_cleaned.rds"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Warning: The `trust` argument of `import()` should be explicit for serialization formats
+as of rio 1.0.3.
+ℹ Missing `trust` will be set to FALSE by default for RDS in 2.0.0.
+ℹ The deprecated feature was likely used in the rio package.
+  Please report the issue at &lt;https://github.com/gesistsa/rio/issues&gt;.</code></pre>
+</div>
+</div>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co"># import the linelist</span></span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>linelist <span class="ot">&lt;-</span> <span class="fu">import</span>(<span class="st">"linelist_cleaned.rds"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>The first 50 rows of the linelist are displayed below.</p>
 <div class="cell">
 <div class="cell-output-display">
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 </section>
@@ -821,20 +903,20 @@ <h3 class="unnumbered anchored" data-anchor-id="yaml">YAML</h3>
 <p>At the top of the script is the “YAML” header. This must begin with three dashes <code>---</code> and must close with three dashes <code>---</code>. YAML parameters comes in <code>key:value</code> pairs. <strong>The indentation and placement of colons in YAML is important</strong> - the <code>key:value</code> pairs are separated by colons (not equals signs!).</p>
 <p>The YAML should begin with metadata for the document. The order of these primary YAML parameters (not indented) does not matter. For example:</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>title<span class="sc">:</span> <span class="st">"My document"</span></span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>author<span class="sc">:</span> <span class="st">"Me"</span></span>
-<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>date<span class="sc">:</span> <span class="st">"`r Sys.Date()`"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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>title<span class="sc">:</span> <span class="st">"My document"</span></span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>author<span class="sc">:</span> <span class="st">"Me"</span></span>
+<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>date<span class="sc">:</span> <span class="st">"`r Sys.Date()`"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>You can use R code in YAML values by putting it like in-line code (preceeded by <code>r</code> within backticks) but also within quotes (see above for Date).</p>
 <p>A required YAML parameter is <code>output:</code>, which specifies the type of file to be produced (e.g.&nbsp;<code>html_document</code>, <code>pdf_document</code>, <code>word_document</code>, or <code>powerpoint_presentation</code>). For <strong>flexdashboard</strong> this parameter value is a bit confusing - it must be set as <code>output:flexdashboard::flex_dashboard</code>. Note the single and double colons, and the underscore. This YAML output parameter is often followed by <em>an additional colon</em> and indented sub-parameters (see <code>orientation:</code> and <code>vertical_layout:</code> parameters below).</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>title<span class="sc">:</span> <span class="st">"My dashboard"</span></span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>author<span class="sc">:</span> <span class="st">"Me"</span></span>
-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>date<span class="sc">:</span> <span class="st">"`r Sys.Date()`"</span></span>
-<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>output<span class="sc">:</span></span>
-<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>  flexdashboard<span class="sc">::</span>flex_dashboard<span class="sc">:</span></span>
-<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>    orientation<span class="sc">:</span> rows</span>
-<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>    vertical_layout<span class="sc">:</span> scroll</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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>title<span class="sc">:</span> <span class="st">"My dashboard"</span></span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>author<span class="sc">:</span> <span class="st">"Me"</span></span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>date<span class="sc">:</span> <span class="st">"`r Sys.Date()`"</span></span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>output<span class="sc">:</span></span>
+<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>  flexdashboard<span class="sc">::</span>flex_dashboard<span class="sc">:</span></span>
+<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>    orientation<span class="sc">:</span> rows</span>
+<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>    vertical_layout<span class="sc">:</span> scroll</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>As shown above, indentations (2 spaces) are used for sub-parameters. In this case, do not forget to put an additional colon after the primary, like <code>key:value:</code>.</p>
 <p>If appropriate, logical values should be given in YAML in lowercase (<code>true</code>, <code>false</code>, <code>null</code>). If a colon is part of your value (e.g.&nbsp;in the title) put the value in quotes. See the examples in sections below.</p>
@@ -853,11 +935,11 @@ <h3 class="unnumbered anchored" data-anchor-id="narrative-text">Narrative text</
 <h3 class="unnumbered anchored" data-anchor-id="headings">Headings</h3>
 <p>Different heading levels are established with different numbers of hash symbols, as described in the <a href="../new_pages/rmarkdown.html">Reports with R Markdown</a> page.</p>
 <p>In <strong>flexdashboard</strong>, a primary heading (#) creates a “page” of the dashboard. Second-level headings (##) create a column or a row depending on your <code>orientation:</code> parameter (see details below). Third-level headings (###) create panels for plots, charts, tables, text, etc.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode md code-with-copy"><code class="sourceCode markdown"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu"># First-level heading (page)</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="fu">## Second level heading (row or column)  </span></span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a><span class="fu">### Third-level heading (pane for plot, chart, etc.)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode md code-with-copy"><code class="sourceCode markdown"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu"># First-level heading (page)</span></span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="fu">## Second level heading (row or column)  </span></span>
+<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="fu">### Third-level heading (pane for plot, chart, etc.)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </section>
 </section>
 <section id="section-attributes" class="level2" data-number="42.4">
@@ -1062,10 +1144,10 @@ <h3 class="unnumbered anchored" data-anchor-id="tables">Tables</h3>
 <p>If you want to show a dynamic table that allows the user to filter, sort, and/or click through “pages” of the data frame, use the package <strong>DT</strong> and it’s function <code>datatable()</code>, as in the code below.</p>
 <p>The example code below, the data frame <code>linelist</code> is printed. You can set <code>rownames = FALSE</code> to conserve horizontal space, and <code>filter = "top"</code> to have filters on top of every column. A list of other specifications can be provided to <code>options =</code>. Below, we set <code>pageLength =</code> so that 5 rows appear and <code>scrollX =</code> so the user can use a scroll bar on the bottom to scroll horizontally. The argument <code>class = 'white-space: nowrap'</code> ensures that each row is only one line (not multiple lines). You can read about other possible arguments and values <a href="https://rstudio.github.io/DT/?_ga=2.2810736.1321860763.1619286819-369061888.1601594705">here</a> or by entering <code>?datatable</code></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>(linelist, </span>
-<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>              <span class="at">rownames =</span> <span class="cn">FALSE</span>, </span>
-<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>              <span class="at">options =</span> <span class="fu">list</span>(<span class="at">pageLength =</span> <span class="dv">5</span>, <span class="at">scrollX =</span> <span class="cn">TRUE</span>), </span>
-<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>              <span class="at">class =</span> <span class="st">'white-space: nowrap'</span> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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>DT<span class="sc">::</span><span class="fu">datatable</span>(linelist, </span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>              <span class="at">rownames =</span> <span class="cn">FALSE</span>, </span>
+<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>              <span class="at">options =</span> <span class="fu">list</span>(<span class="at">pageLength =</span> <span class="dv">5</span>, <span class="at">scrollX =</span> <span class="cn">TRUE</span>), </span>
+<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>              <span class="at">class =</span> <span class="st">'white-space: nowrap'</span> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section>
 <section id="plots" class="level3 unnumbered">
@@ -1095,9 +1177,9 @@ <h3 class="unnumbered anchored" data-anchor-id="plots">Plots</h3>
 <h3 class="unnumbered anchored" data-anchor-id="interactive-plots">Interactive plots</h3>
 <p>You can also pass a standard ggplot or other plot object to <code>ggplotly()</code> from the <strong>plotly</strong> package (see the <a href="../new_pages/interactive_plots.html">Interactive plots</a> page). This will make your plot interactive, allow the reader to “zoom in”, and show-on-hover the value of every data point (in this scenario the number of cases per week and age group in the curve).</p>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>age_outbreak <span class="ot">&lt;-</span> <span class="fu">incidence</span>(linelist, date_onset, <span class="st">"week"</span>, <span class="at">groups =</span> age_cat)</span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(age_outbreak, <span class="at">fill =</span> age_cat, <span class="at">col_pal =</span> muted, <span class="at">title =</span> <span class="st">""</span>) <span class="sc">%&gt;%</span> </span>
-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>  plotly<span class="sc">::</span><span class="fu">ggplotly</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<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>age_outbreak <span class="ot">&lt;-</span> <span class="fu">incidence</span>(linelist, date_onset, <span class="st">"week"</span>, <span class="at">groups =</span> age_cat)</span>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(age_outbreak, <span class="at">fill =</span> age_cat, <span class="at">col_pal =</span> muted, <span class="at">title =</span> <span class="st">""</span>) <span class="sc">%&gt;%</span> </span>
+<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>  plotly<span class="sc">::</span><span class="fu">ggplotly</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>Here is what this looks like in the dashboard (gif). This interactive functionality will still work even if you email the dashboard as a static file (not online on a server).</p>
 <div class="cell">
@@ -1166,14 +1248,14 @@ <h2 data-number="42.8" class="anchored" data-anchor-id="shiny"><span class="head
 <section id="settings" class="level3 unnumbered">
 <h3 class="unnumbered anchored" data-anchor-id="settings">Settings</h3>
 <p>Enable <strong>shiny</strong> in a <strong>flexdashboard</strong> by adding the YAML parameter <code>runtime: shiny</code> at the same indentation level as <code>output:</code>, as below:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode md code-with-copy"><code class="sourceCode markdown"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Outbreak dashboard (Shiny demo)"</span></span>
-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="an">output:</span><span class="co"> </span></span>
-<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a><span class="co">  flexdashboard::flex_dashboard:</span></span>
-<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a><span class="co">    orientation: columns</span></span>
-<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a><span class="co">    vertical_layout: fill</span></span>
-<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a><span class="an">runtime:</span><span class="co"> shiny</span></span>
-<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb9"><pre class="sourceCode md code-with-copy"><code class="sourceCode markdown"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Outbreak dashboard (Shiny demo)"</span></span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="an">output:</span><span class="co"> </span></span>
+<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="co">  flexdashboard::flex_dashboard:</span></span>
+<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="co">    orientation: columns</span></span>
+<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="co">    vertical_layout: fill</span></span>
+<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="an">runtime:</span><span class="co"> shiny</span></span>
+<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>It is also convenient to enable a “side bar” to hold the shiny input widgets that will collect information from the user. As explained above, create a column and indicate the <code>{.sidebar}</code> option to create a side bar on the left side. You can add text and R chunks containing the <strong>shiny</strong> <code>input</code> commands within this column.</p>
 <p>If your app/dashboard is hosted on a server and may have multiple simultaneous users, name the first R code chunk as <code>global</code>. Include the commands to import/load your data in this chunk. This special named chunk is treated differently, and the data imported within it are only imported once (not continuously) and are available for all users. This improves the start-up speed of the app.</p>
 </section>
@@ -1476,6 +1558,24 @@ <h2 data-number="42.10" class="anchored" data-anchor-id="resources"><span class=
     // clear code selection
     e.clearSelection();
   });
+    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+    var mailtoRegex = new RegExp(/^mailto:/);
+      var filterRegex = new RegExp('/' + window.location.host + '/');
+    var isInternal = (href) => {
+        return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+    }
+    // Inspect non-navigation links and adorn them if external
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+    for (var i=0; i<links.length; i++) {
+      const link = links[i];
+      if (!isInternal(link.href)) {
+        // undo the damage that might have been done by quarto-nav.js in the case of
+        // links that we want to consider external
+        if (link.dataset.originalHref !== undefined) {
+          link.href = link.dataset.originalHref;
+        }
+      }
+    }
   function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
@@ -1510,7 +1610,11 @@ <h2 data-number="42.10" class="anchored" data-anchor-id="resources"><span class=
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
+      if (note) {
+        return note.innerHTML;
+      } else {
+        return "";
+      }
     });
   }
   const xrefs = window.document.querySelectorAll('a.quarto-xref');
@@ -1810,7 +1914,7 @@ <h2 data-number="42.10" class="anchored" data-anchor-id="resources"><span class=
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","openEffect":"zoom","loop":false,"descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"loop":false,"openEffect":"zoom","closeEffect":"zoom","selector":".lightbox","descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;
diff --git a/html_outputs/search.json b/html_outputs/search.json
index 8cbea6d3..db37f13f 100644
--- a/html_outputs/search.json
+++ b/html_outputs/search.json
@@ -3728,7 +3728,7 @@
     "href": "new_pages/flexdashboard.html#preparation",
     "title": "42  Dashboards with R Markdown",
     "section": "",
-    "text": "Load packages\nIn this handbook we emphasize p_load() from pacman, which installs the package if necessary and loads it for use. You can also load installed packages with library() from base R. See the page on R basics for more information on R packages.\n\npacman::p_load(\n  rio,             # data import/export     \n  here,            # locate files\n  tidyverse,       # data management and visualization\n  flexdashboard,   # dashboard versions of R Markdown reports\n  shiny,           # interactive figures\n  plotly           # interactive figures\n)\n\n\n\nImport data\nWe import the dataset of cases from a simulated Ebola epidemic. If you want to follow along, click to download the “clean” linelist (as .rds file). Import data with the import() function from the rio package (it handles many file types like .xlsx, .csv, .rds - see the Import and export page for details).\n\n# import the linelist\nlinelist &lt;- import(\"linelist_cleaned.rds\")\n\nThe first 50 rows of the linelist are displayed below.",
+    "text": "Load packages\nIn this handbook we emphasize p_load() from pacman, which installs the package if necessary and loads it for use. You can also load installed packages with library() from base R. See the page on R basics for more information on R packages.\n\npacman::p_load(\n  rio,             # data import/export     \n  here,            # locate files\n  tidyverse,       # data management and visualization\n  flexdashboard,   # dashboard versions of R Markdown reports\n  shiny,           # interactive figures\n  plotly           # interactive figures\n)\n\n\n\nImport data\nWe import the dataset of cases from a simulated Ebola epidemic. If you want to follow along, click to download the “clean” linelist (as .rds file). Import data with the import() function from the rio package (it handles many file types like .xlsx, .csv, .rds - see the Import and export page for details).\n\n\nWarning: The `trust` argument of `import()` should be explicit for serialization formats\nas of rio 1.0.3.\nℹ Missing `trust` will be set to FALSE by default for RDS in 2.0.0.\nℹ The deprecated feature was likely used in the rio package.\n  Please report the issue at &lt;https://github.com/gesistsa/rio/issues&gt;.\n\n\n\n# import the linelist\nlinelist &lt;- import(\"linelist_cleaned.rds\")\n\nThe first 50 rows of the linelist are displayed below.",
     "crumbs": [
       "Reports and dashboards",
       "<span class='chapter-number'>42</span>  <span class='chapter-title'>Dashboards with R Markdown</span>"
diff --git a/new_pages/flexdashboard.qmd b/new_pages/flexdashboard.qmd
index baf4fd57..9e7ca2d2 100644
--- a/new_pages/flexdashboard.qmd
+++ b/new_pages/flexdashboard.qmd
@@ -5,20 +5,20 @@
 knitr::include_graphics(here::here("images", "flexdashboard_output.png"))
 ```
 
-This page will cover the basic use of the **flexdashboard** package. This package allows you to easily format R Markdown output as a dashboard with panels and pages. The dashboard content can be text, static figures/tables or interactive graphics.  
+This page will cover the basic use of the [**flexdashboard** package](https://pkgs.rstudio.com/flexdashboard/). This package allows you to easily format R Markdown output as a dashboard with panels and pages. The dashboard content can be text, static figures/tables or interactive graphics.  
 
 Advantages of **flexdashboard**:  
 
-* It requires minimal non-standard R coding - with very little practice you can quickly create a dashboard  
-* The dashboard can usually be emailed to colleagues as a self-contained HTML file - no server required  
-* You can combine **flexdashboard** with **shiny**, **ggplotly**, and other *"html widgets"* to add interactivity  
+* It requires minimal non-standard R coding - with very little practice you can quickly create a dashboard.  
+* The dashboard can usually be emailed to colleagues as a self-contained HTML file - no server required.  
+* You can combine **flexdashboard** with [**shiny**](shiny_basics.qmd), [**ggplotly**](interactive_plots.qmd), and other *"html widgets"* to add interactivity.  
 
 Disadvantages of **flexdashboard**:  
 
-* Less customization as compared to using **shiny** alone to create a dashboard  
+* Less customization as compared to using **shiny** alone to create a dashboard.  
 
 
-Very comprehensive tutorials on using **flexdashboard** that informed this page can be found in the Resources section. Below we describe the core features and give an example of building a dashboard to explore an outbreak, using the case `linelist` data.  
+Very comprehensive tutorials on using **flexdashboard** that informed this page can be found in the [Resources](flexdashboard.qmd#resources) section. Below we describe the core features and give an example of building a dashboard to explore an outbreak, using the case `linelist` data.  
 
 
 ## Preparation
@@ -159,8 +159,8 @@ Section attributes specific to **flexdashboard** include:
 * `{data-orientation=}` Set to either `rows` or `columns`. If your dashboard has multiple pages, add this attribute to each page to indicate orientation (further explained in [layout section](#layout)).  
 * `{data-width=}` and `{data-height=}` set relative size of charts, columns, rows laid out in the same dimension (horizontal or vertical). Absolute sizes are adjusted to best fill the space on any display device thanks to the [flexbox](https://developer.mozilla.org/en-US/docs/Web/CSS/CSS_Flexible_Box_Layout/Using_CSS_flexible_boxes) engine.  
      * Height of charts also depends on whether you set the YAML parameter `vertical_layout: fill` or `vertical_layout: scroll`. If set to scroll, figure height will reflect the traditional `fig.height = ` option in the R code chunk.  
-     * See complete size documentation at the [flexdashboard website](https://rmarkdown.rstudio.com/flexdashboard/using.html#sizing)  
-* `{.hidden}` Use this to exclude a specific page from the navigation bar  
+     * See complete size documentation at the [flexdashboard website](https://pkgs.rstudio.com/flexdashboard/articles/using.html#sizing)  
+* `{.hidden}` Use this to exclude a specific page from the navigation bar.  
 * `{data-navbar=}` Use this in a page-level heading to nest it within a navigation bar drop-down menu. Provide the name (in quotes) of the drop-down menu. See example below.  
 
 
@@ -168,10 +168,10 @@ Section attributes specific to **flexdashboard** include:
 
 Adjust the layout of your dashboard in the following ways:  
 
-* Add pages, columns/rows, and charts with R Markdown headings (e.g. #, ##, or ###)  
-* Adjust the YAML parameter `orientation:` to either `rows` or `columns`  
-* Specify whether the layout fills the browser or allows scrolling  
-* Add tabs to a particular section heading  
+* Add pages, columns/rows, and charts with R Markdown headings (e.g. #, ##, or ###).  
+* Adjust the YAML parameter `orientation:` to either `rows` or `columns`.  
+* Specify whether the layout fills the browser or allows scrolling.  
+* Add tabs to a particular section heading.  
 
 
 ### Pages {.unnumbered}  
@@ -314,7 +314,7 @@ DT::datatable(linelist,
 
 ### Plots {.unnumbered}  
 
-You can print plots to a dashboard pane as you would in an R script. In our example, we use the **incidence2** package to create an "epicurve" by age group with two simple commands (see [Epidemic curves](epicurves.qmd) page). However, you could use `ggplot()` and print a plot in the same manner.  
+You can print plots to a dashboard pane as you would in an R script. In our example, we use the **incidence2** package to create an "epicurve" by age group with two simple commands (see [An Introduction to incidence2](https://www.reconverse.org/incidence2/articles/incidence2.html) page). However, you could use `ggplot()` and print a plot in the same manner.  
 
 ```{r, out.width = c('100%'), out.height = c('100%'), echo=F}
 knitr::include_graphics(here::here("images", "flexdashboard_plots_script.png"))
@@ -349,11 +349,11 @@ knitr::include_graphics(here::here("images", "flexdashboard_ggplotly.gif"))
 
 Some common examples of these widgets include:  
 
-* Plotly (used in this handbook page and in the [Interative plots](interactive_plots.qmd) page)
-* visNetwork (used in the [Transmission Chains](transmission_chains.qmd) page of this handbook)  
-* Leaflet (used in the [GIS Basics](gis.qmd) page of this handbook)  
-* dygraphs (useful for interactively showing time series data)  
-* DT (`datatable()`) (used to show dynamic tables with filter, sort, etc.)  
+* Plotly (used in this handbook page and in the [Interative plots](interactive_plots.qmd) page).
+* visNetwork (used in the [Transmission Chains](transmission_chains.qmd) page of this handbook). 
+* Leaflet (used in the [GIS Basics](gis.qmd) page of this handbook).  
+* dygraphs (useful for interactively showing time series data).  
+* DT (`datatable()`) (used to show dynamic tables with filter, sort, etc.).  
 
 Below we demonstrate adding an epidemic transmission chain which uses visNetwork to the dashboard. The script shows only the new code added to the "Column 2" section of the R Markdown script. You can find the code in the [Transmission chains](transmission_chains.qmd)  page of this handbook.  
 
@@ -385,7 +385,7 @@ Embedding **shiny** in **flexdashboard** is however, a fundamental change to you
 Sharing your dashboard will now require that you either:  
 
 * Send the Rmd script to the viewer, they open it in R on their computer, and run the app, or  
-* The app/dashboard is hosted on a server accessible to the viewer  
+* the app/dashboard is hosted on a server accessible to the viewer.  
 
 Thus, there are benefits to integrating **shiny**, but also complications. If easy sharing by email is a priority and you don't need **shiny** reactive capabilities, consider the reduced interactivity offered by `ggplotly()` as demonstrated above.    
 
@@ -417,14 +417,14 @@ If your app/dashboard is hosted on a server and may have multiple simultaneous u
 
 Here we adapt the flexdashboard script "outbreak_dashboard.Rmd" to include **shiny**. We will add the capability for the user to select a hospital from a drop-down menu, and have the epidemic curve reflect only cases from that hospital, with a dynamic plot title. We do the following:  
 
-* Add `runtime: shiny` to the YAML  
-* Re-name the setup chunk as `global`  
+* Add `runtime: shiny` to the YAML.  
+* Re-name the setup chunk as `global`.  
 * Create a sidebar containing:  
-  * Code to create a vector of unique hospital names  
-  * A `selectInput()` command (**shiny** drop-down menu) with the choice of hospital names. The selection is saved as `hospital_choice`, which can be referenced in later code as `input$hospital_choice`  
+  * Code to create a vector of unique hospital names.  
+  * A `selectInput()` command (**shiny** drop-down menu) with the choice of hospital names. The selection is saved as `hospital_choice`, which can be referenced in later code as `input$hospital_choice`.  
 * The epidemic curve code (column 2) is wrapped within `renderPlot({ })`, including:  
-  * A filter on the dataset restricting the column `hospital` to the current value of `input$hospital_choice`  
-  * A dynamic plot title that incorporates `input$hospital_choice`  
+  * A filter on the dataset restricting the column `hospital` to the current value of `input$hospital_choice`.  
+  * A dynamic plot title that incorporates `input$hospital_choice`.  
   
 Note that any code referencing an `input$` value must be within a `render({})` function (to be reactive).  
 
@@ -467,10 +467,8 @@ If you have embedded **shiny**, you will not be able to send an output by email,
 
 Excellent tutorials that informed this page can be found below. If you review these, most likely within an hour you can have your own dashboard.  
 
-https://bookdown.org/yihui/rmarkdown/dashboards.html
+[Rmarkdown and Dashboards](https://bookdown.org/yihui/rmarkdown/dashboards.html)
 
-https://rmarkdown.rstudio.com/flexdashboard/
+[Flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/)
 
-https://rmarkdown.rstudio.com/flexdashboard/using.html
-
-https://rmarkdown.rstudio.com/flexdashboard/examples.html
+[Flexdashboard gallery](https://rmarkdown.rstudio.com/flexdashboard/examples.html)
