Updates to GIS chapter and Quarto

_quarto.yml

@@ -66,7 +66,7 @@ book:
       - icon: twitter
         href: "https://twitter.com/appliedepi"
       - icon: linkedin
-        href: "https://www.linkedin.com/company/appliedepi/"
+        href: "https://www.linkedin.com/company/appliedepi"
       # - icon: github
       #   menu:
       #     - text: Source Code

html_outputs/index.html

@@ -254,7 +254,7 @@
       <a href="./">The Epidemiologist R Handbook</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://twitter.com/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
-    <a href="https://www.linkedin.com/company/appliedepi/" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
+    <a href="https://www.linkedin.com/company/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
     <a href="https://github.com/appliedepi/epihandbook_eng" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
     <div class="dropdown">
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@@ -725,7 +725,7 @@ <h1 class="title">The Epidemiologist R Handbook</h1>
     <div>
     <div class="quarto-title-meta-heading">Last updated</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">Oct 1, 2024</p>
+      <p class="date">Oct 2, 2024</p>
     </div>
   </div>
 
@@ -1463,7 +1463,7 @@ <h3 class="unnumbered anchored" data-anchor-id="contribution">Contribution</h3>
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","loop":false,"closeEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","loop":false,"descPosition":"bottom","closeEffect":"zoom"});
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html_outputs/new_pages/editorial_style.html

@@ -286,7 +286,7 @@
       <a href="../">The Epidemiologist R Handbook</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://twitter.com/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
-    <a href="https://www.linkedin.com/company/appliedepi/" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
+    <a href="https://www.linkedin.com/company/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
     <a href="https://github.com/appliedepi/epihandbook_eng" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
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html_outputs/new_pages/flexdashboard.html

@@ -317,7 +317,7 @@
       <a href="../">The Epidemiologist R Handbook</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://twitter.com/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
-    <a href="https://www.linkedin.com/company/appliedepi/" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
+    <a href="https://www.linkedin.com/company/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
     <a href="https://github.com/appliedepi/epihandbook_eng" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
     <div class="dropdown">
       <a href="" title="Share" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" role="link" aria-label="Share"><i class="bi bi-share"></i></a>
@@ -1920,7 +1920,7 @@ <h2 data-number="42.10" class="anchored" data-anchor-id="resources"><span class=
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"closeEffect":"zoom","descPosition":"bottom","openEffect":"zoom"});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {

html_outputs/new_pages/packages_suggested.html

@@ -286,7 +286,7 @@
       <a href="../">The Epidemiologist R Handbook</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://twitter.com/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
-    <a href="https://www.linkedin.com/company/appliedepi/" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
+    <a href="https://www.linkedin.com/company/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
     <a href="https://github.com/appliedepi/epihandbook_eng" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
     <div class="dropdown">
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@@ -857,34 +857,36 @@ <h2 data-number="5.1" class="anchored" data-anchor-id="packages-from-cran"><span
 <span id="cb1-91"><a href="#cb1-91" aria-hidden="true" tabindex="-1"></a>     sf,               <span class="co"># to manage spatial data using a Simple Feature format</span></span>
 <span id="cb1-92"><a href="#cb1-92" aria-hidden="true" tabindex="-1"></a>     tmap,             <span class="co"># to produce simple maps, works for both interactive and static maps</span></span>
 <span id="cb1-93"><a href="#cb1-93" aria-hidden="true" tabindex="-1"></a>     OpenStreetMap,    <span class="co"># to add OSM basemap in ggplot map</span></span>
-<span id="cb1-94"><a href="#cb1-94" aria-hidden="true" tabindex="-1"></a>     spdep,            <span class="co"># spatial statistics </span></span>
-<span id="cb1-95"><a href="#cb1-95" aria-hidden="true" tabindex="-1"></a>     </span>
-<span id="cb1-96"><a href="#cb1-96" aria-hidden="true" tabindex="-1"></a>     <span class="co"># routine reports</span></span>
-<span id="cb1-97"><a href="#cb1-97" aria-hidden="true" tabindex="-1"></a>     <span class="do">#################</span></span>
-<span id="cb1-98"><a href="#cb1-98" aria-hidden="true" tabindex="-1"></a>     rmarkdown,        <span class="co"># produce PDFs, Word Documents, Powerpoints, and HTML files</span></span>
-<span id="cb1-99"><a href="#cb1-99" aria-hidden="true" tabindex="-1"></a>     reportfactory,    <span class="co"># auto-organization of R Markdown outputs</span></span>
-<span id="cb1-100"><a href="#cb1-100" aria-hidden="true" tabindex="-1"></a>     officer,          <span class="co"># powerpoints</span></span>
-<span id="cb1-101"><a href="#cb1-101" aria-hidden="true" tabindex="-1"></a>     </span>
-<span id="cb1-102"><a href="#cb1-102" aria-hidden="true" tabindex="-1"></a>     <span class="co"># dashboards</span></span>
-<span id="cb1-103"><a href="#cb1-103" aria-hidden="true" tabindex="-1"></a>     <span class="do">############</span></span>
-<span id="cb1-104"><a href="#cb1-104" aria-hidden="true" tabindex="-1"></a>     flexdashboard,    <span class="co"># convert an R Markdown script into a dashboard</span></span>
-<span id="cb1-105"><a href="#cb1-105" aria-hidden="true" tabindex="-1"></a>     shiny,            <span class="co"># interactive web apps</span></span>
-<span id="cb1-106"><a href="#cb1-106" aria-hidden="true" tabindex="-1"></a>     </span>
-<span id="cb1-107"><a href="#cb1-107" aria-hidden="true" tabindex="-1"></a>     <span class="co"># tables for presentation</span></span>
-<span id="cb1-108"><a href="#cb1-108" aria-hidden="true" tabindex="-1"></a>     <span class="do">#########################</span></span>
-<span id="cb1-109"><a href="#cb1-109" aria-hidden="true" tabindex="-1"></a>     knitr,            <span class="co"># R Markdown report generation and html tables</span></span>
-<span id="cb1-110"><a href="#cb1-110" aria-hidden="true" tabindex="-1"></a>     flextable,        <span class="co"># HTML tables</span></span>
-<span id="cb1-111"><a href="#cb1-111" aria-hidden="true" tabindex="-1"></a>     <span class="co">#DT,              # HTML tables (alternative)</span></span>
-<span id="cb1-112"><a href="#cb1-112" aria-hidden="true" tabindex="-1"></a>     <span class="co">#gt,              # HTML tables (alternative)</span></span>
-<span id="cb1-113"><a href="#cb1-113" aria-hidden="true" tabindex="-1"></a>     <span class="co">#huxtable,        # HTML tables (alternative) </span></span>
-<span id="cb1-114"><a href="#cb1-114" aria-hidden="true" tabindex="-1"></a>     </span>
-<span id="cb1-115"><a href="#cb1-115" aria-hidden="true" tabindex="-1"></a>     <span class="co"># phylogenetics</span></span>
-<span id="cb1-116"><a href="#cb1-116" aria-hidden="true" tabindex="-1"></a>     <span class="do">###############</span></span>
-<span id="cb1-117"><a href="#cb1-117" aria-hidden="true" tabindex="-1"></a>     ggtree,           <span class="co"># visualization and annotation of trees</span></span>
-<span id="cb1-118"><a href="#cb1-118" aria-hidden="true" tabindex="-1"></a>     ape,              <span class="co"># analysis of phylogenetics and evolution</span></span>
-<span id="cb1-119"><a href="#cb1-119" aria-hidden="true" tabindex="-1"></a>     treeio            <span class="co"># to visualize phylogenetic files</span></span>
-<span id="cb1-120"><a href="#cb1-120" aria-hidden="true" tabindex="-1"></a> </span>
-<span id="cb1-121"><a href="#cb1-121" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb1-94"><a href="#cb1-94" aria-hidden="true" tabindex="-1"></a>     tidyterra,        <span class="co"># to plot basemaps</span></span>
+<span id="cb1-95"><a href="#cb1-95" aria-hidden="true" tabindex="-1"></a>     maptiles,         <span class="co"># for creating basemaps</span></span>
+<span id="cb1-96"><a href="#cb1-96" aria-hidden="true" tabindex="-1"></a>     spdep,            <span class="co"># spatial statistics </span></span>
+<span id="cb1-97"><a href="#cb1-97" aria-hidden="true" tabindex="-1"></a>     </span>
+<span id="cb1-98"><a href="#cb1-98" aria-hidden="true" tabindex="-1"></a>     <span class="co"># routine reports</span></span>
+<span id="cb1-99"><a href="#cb1-99" aria-hidden="true" tabindex="-1"></a>     <span class="do">#################</span></span>
+<span id="cb1-100"><a href="#cb1-100" aria-hidden="true" tabindex="-1"></a>     rmarkdown,        <span class="co"># produce PDFs, Word Documents, Powerpoints, and HTML files</span></span>
+<span id="cb1-101"><a href="#cb1-101" aria-hidden="true" tabindex="-1"></a>     reportfactory,    <span class="co"># auto-organization of R Markdown outputs</span></span>
+<span id="cb1-102"><a href="#cb1-102" aria-hidden="true" tabindex="-1"></a>     officer,          <span class="co"># powerpoints</span></span>
+<span id="cb1-103"><a href="#cb1-103" aria-hidden="true" tabindex="-1"></a>     </span>
+<span id="cb1-104"><a href="#cb1-104" aria-hidden="true" tabindex="-1"></a>     <span class="co"># dashboards</span></span>
+<span id="cb1-105"><a href="#cb1-105" aria-hidden="true" tabindex="-1"></a>     <span class="do">############</span></span>
+<span id="cb1-106"><a href="#cb1-106" aria-hidden="true" tabindex="-1"></a>     flexdashboard,    <span class="co"># convert an R Markdown script into a dashboard</span></span>
+<span id="cb1-107"><a href="#cb1-107" aria-hidden="true" tabindex="-1"></a>     shiny,            <span class="co"># interactive web apps</span></span>
+<span id="cb1-108"><a href="#cb1-108" aria-hidden="true" tabindex="-1"></a>     </span>
+<span id="cb1-109"><a href="#cb1-109" aria-hidden="true" tabindex="-1"></a>     <span class="co"># tables for presentation</span></span>
+<span id="cb1-110"><a href="#cb1-110" aria-hidden="true" tabindex="-1"></a>     <span class="do">#########################</span></span>
+<span id="cb1-111"><a href="#cb1-111" aria-hidden="true" tabindex="-1"></a>     knitr,            <span class="co"># R Markdown report generation and html tables</span></span>
+<span id="cb1-112"><a href="#cb1-112" aria-hidden="true" tabindex="-1"></a>     flextable,        <span class="co"># HTML tables</span></span>
+<span id="cb1-113"><a href="#cb1-113" aria-hidden="true" tabindex="-1"></a>     <span class="co">#DT,              # HTML tables (alternative)</span></span>
+<span id="cb1-114"><a href="#cb1-114" aria-hidden="true" tabindex="-1"></a>     <span class="co">#gt,              # HTML tables (alternative)</span></span>
+<span id="cb1-115"><a href="#cb1-115" aria-hidden="true" tabindex="-1"></a>     <span class="co">#huxtable,        # HTML tables (alternative) </span></span>
+<span id="cb1-116"><a href="#cb1-116" aria-hidden="true" tabindex="-1"></a>     </span>
+<span id="cb1-117"><a href="#cb1-117" aria-hidden="true" tabindex="-1"></a>     <span class="co"># phylogenetics</span></span>
+<span id="cb1-118"><a href="#cb1-118" aria-hidden="true" tabindex="-1"></a>     <span class="do">###############</span></span>
+<span id="cb1-119"><a href="#cb1-119" aria-hidden="true" tabindex="-1"></a>     ggtree,           <span class="co"># visualization and annotation of trees</span></span>
+<span id="cb1-120"><a href="#cb1-120" aria-hidden="true" tabindex="-1"></a>     ape,              <span class="co"># analysis of phylogenetics and evolution</span></span>
+<span id="cb1-121"><a href="#cb1-121" aria-hidden="true" tabindex="-1"></a>     treeio            <span class="co"># to visualize phylogenetic files</span></span>
+<span id="cb1-122"><a href="#cb1-122" aria-hidden="true" tabindex="-1"></a> </span>
+<span id="cb1-123"><a href="#cb1-123" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section>
 <section id="packages-from-github" class="level2" data-number="5.2">

html_outputs/new_pages/quarto.html

@@ -255,7 +255,7 @@
       <a href="../">The Epidemiologist R Handbook</a> 
         <div class="sidebar-tools-main tools-wide">
     <a href="https://twitter.com/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-twitter"></i></a>
-    <a href="https://www.linkedin.com/company/appliedepi/" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
+    <a href="https://www.linkedin.com/company/appliedepi" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-linkedin"></i></a>
     <a href="https://github.com/appliedepi/epihandbook_eng" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
     <div class="dropdown">
       <a href="" title="Share" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" role="link" aria-label="Share"><i class="bi bi-share"></i></a>
@@ -690,7 +690,10 @@
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#why-quarto-over-r-markdown" id="toc-why-quarto-over-r-markdown" class="nav-link active" data-scroll-target="#why-quarto-over-r-markdown"><span class="header-section-number">44.1</span> Why Quarto over R Markdown?</a></li>
+  <li><a href="#why-quarto-over-r-markdown" id="toc-why-quarto-over-r-markdown" class="nav-link active" data-scroll-target="#why-quarto-over-r-markdown"><span class="header-section-number">44.1</span> Why Quarto over R Markdown?</a>
+  <ul class="collapse">
+  <li><a href="#limitations-of-quarto" id="toc-limitations-of-quarto" class="nav-link" data-scroll-target="#limitations-of-quarto">Limitations of Quarto</a></li>
+  </ul></li>
   <li><a href="#getting-started" id="toc-getting-started" class="nav-link" data-scroll-target="#getting-started"><span class="header-section-number">44.2</span> Getting started</a></li>
   <li><a href="#moving-beyond-simple-reports" id="toc-moving-beyond-simple-reports" class="nav-link" data-scroll-target="#moving-beyond-simple-reports"><span class="header-section-number">44.3</span> Moving beyond simple reports</a></li>
   <li><a href="#resources" id="toc-resources" class="nav-link" data-scroll-target="#resources"><span class="header-section-number">44.4</span> Resources</a></li>
@@ -752,6 +755,22 @@ <h2 data-number="44.1" class="anchored" data-anchor-id="why-quarto-over-r-markdo
 </div>
 </div>
 <p><a href="https://quarto.org/docs/faq/rmarkdown.html">Source</a></p>
+<section id="limitations-of-quarto" class="level3 unnumbered">
+<h3 class="unnumbered anchored" data-anchor-id="limitations-of-quarto">Limitations of Quarto</h3>
+<p>There is one substantial limitation of Quarto, compared to R Markdown, when it is used to generate multiple different reports using the same dataset.</p>
+<p>In R Markdown, you can load in a dataset, run your analyses, and then generate multiple different reports from this dataset in your R environment. This means that you <em>do not need to individually import the dataset for each report</em>.</p>
+<p>However, because of the way that Quarto works, every single report needs to be self contained. That is to say that you would need to import the dataset <em>every time you want a new report</em>.</p>
+<p>This is not a problem if you are only running a single report, or a handful. But if you have a large dataset, and need to make a large number of reports, this can quickly become a real problem.</p>
+<p>Imagine a scenario where you are conducting a national outbreak response. You have a dataset which takes 5 minutes to import, and then you need to generate a report for each of the 50 provinces in the country.</p>
+<ul>
+<li><p>For R Markdown, you would only need to read in the data once, and then run your reports. This would take a minimum of 5 minutes (5 minutes to read in the data + time to run the script for the reports).</p></li>
+<li><p>For Quarto, you would need to read in the dataset each time. This would mean you would need at least 250 minutes (5 minutes for each of the 50 provinces).</p></li>
+</ul>
+<p>This quickly increasing time burden means that if you are generating multiple reports based on a large dataset, you may want to use R Markdown over Quarto!</p>
+<p>For further explanation, please see these forum posts:</p>
+<p><a href="https://forum.posit.co/t/quarto-cant-find-r-objects/156848">Quarto can’t find R-objects</a></p>
+<p><a href="https://github.com/quarto-dev/quarto-cli/discussions/1773">How to quarto_render into console environment</a></p>
+</section>
 </section>
 <section id="getting-started" class="level2" data-number="44.2">
 <h2 data-number="44.2" class="anchored" data-anchor-id="getting-started"><span class="header-section-number">44.2</span> Getting started</h2>
@@ -1417,7 +1436,7 @@ <h2 data-number="44.4" class="anchored" data-anchor-id="resources"><span class="
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","loop":false,"openEffect":"zoom","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","openEffect":"zoom","descPosition":"bottom","selector":".lightbox","loop":false});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {