From f5f1923383085845677d7f8699ecccdcb37ed00e Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 3 Sep 2024 00:41:06 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 73c5714f8a11a1e1192f1e0bbdd9616e9112a717
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-09 00:38:49 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 4b92374e2e8ab99d4719e9c5cd1a5479bb846f4f
Branch  : main
Author  : Bisaloo <Bisaloo@users.noreply.github.com>
Time    : 2024-02-06 21:00:56 +0000
Message : [actions] update 23 packages
---
 404.html                                  |   9 +-
 CODE_OF_CONDUCT.html                      |   4 +-
 LICENSE.html                              |  10 +-
 aio.html                                  | 243 +++++++--------------
 compare-interventions.html                |  31 ++-
 create-forecast.html                      |  37 ++--
 images.html                               |   6 +-
 index.html                                |  24 +--
 instructor-notes.html                     |   6 +-
 instructor/404.html                       |   9 +-
 instructor/CODE_OF_CONDUCT.html           |   4 +-
 instructor/LICENSE.html                   |  10 +-
 instructor/aio.html                       | 247 +++++++---------------
 instructor/compare-interventions.html     |  33 ++-
 instructor/create-forecast.html           |  37 ++--
 instructor/images.html                    |   6 +-
 instructor/index.html                     |  26 +--
 instructor/instructor-notes.html          |   6 +-
 instructor/introduction.html              |  31 +--
 instructor/key-points.html                |   6 +-
 instructor/model-choices.html             |  30 +--
 instructor/modelling-interventions.html   |  35 ++-
 instructor/profiles.html                  |   9 +-
 instructor/quantify-transmissibility.html |  43 ++--
 instructor/read-delays.html               |  99 +++------
 instructor/reference.html                 |  55 ++---
 instructor/simulating-transmission.html   |  45 ++--
 introduction.html                         |  31 +--
 key-points.html                           |   6 +-
 model-choices.html                        |  30 +--
 modelling-interventions.html              |  33 ++-
 pkgdown.yml                               |   2 +-
 profiles.html                             |   9 +-
 quantify-transmissibility.html            |  43 ++--
 read-delays.html                          |  99 +++------
 reference.html                            |  55 ++---
 simulating-transmission.html              |  45 ++--
 37 files changed, 502 insertions(+), 952 deletions(-)

diff --git a/404.html b/404.html
index 070f0f5e..679172ea 100644
--- a/404.html
+++ b/404.html
@@ -343,8 +343,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Page not found</h1>
         
-<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
 <hr class="half-width"><p>We cannot seem to find the page you are looking for. Here are some
 tips that may help:</p>
 <ol style="list-style-type: decimal"><li>try going back to the <a href="javascript:history.back()">previous
@@ -383,7 +382,7 @@ <h1>Page not found</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -405,8 +404,8 @@ <h1>Page not found</h1>
   "url": "https://epiverse-trace.github.io/tutorials/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/404.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index e35532be..f8c1b802 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -401,7 +401,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -424,7 +424,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index b2e87cce..f50e3d98 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -351,8 +351,7 @@ <h1>Licenses</h1>
 
         
 
-<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>The tutorials in this repository are developed by Epiverse-TRACE,
 based on the <a href="https://github.com/carpentries/workbench-template-rmd" class="external-link">lesson
 template from the Carpentries</a> (template under CC BY license).</p>
@@ -388,8 +387,7 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-<a class="anchor" aria-label="anchor" href="#software"></a></h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by Epiverse-TRACE are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -449,7 +447,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -472,7 +470,7 @@ <h1>Licenses</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/LICENSE.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index c28dde6c..0841c3db 100644
--- a/aio.html
+++ b/aio.html
@@ -441,8 +441,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -451,7 +450,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
-<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
 </h2>
 <hr class="half-width">
 <p>Outbreaks appear with different diseases and in different contexts,
@@ -490,8 +488,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="questions-to-think-about" class="callout-inner">
-<h3 class="callout-title">Questions to think about<a class="anchor" aria-label="anchor" href="#questions-to-think-about"></a>
-</h3>
+<h3 class="callout-title">Questions to think about</h3>
 <div class="callout-content">
 <p>Remember your last experience with outbreak data and reflect on these
 questions:</p>
@@ -506,7 +503,6 @@ <h3 class="callout-title">Questions to think about<a class="anchor" aria-label="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
-<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="https://epiforecasts.io/EpiNow2/" class="external-link">EpiNow2</a> package provides a three-step solution to
@@ -616,8 +612,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="is-this-rt-estimation-biased" class="callout-inner">
-<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?<a class="anchor" aria-label="anchor" href="#is-this-rt-estimation-biased"></a>
-</h3>
+<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?</h3>
 <div class="callout-content">
 <p>Review <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008409" class="external-link">Gostic
 et al., 2020</a> about what additional adjustments this estimation
@@ -627,7 +622,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 </div>
 </div>
 </section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a>
-<a class="anchor" aria-label="anchor" href="#the-problem"></a>
 </h2>
 <hr class="half-width">
 <p>However, <em>quantifying the transmissibility</em> during a real-life
@@ -655,7 +649,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <p>So, all these tasks can be interconnected in a pipeline:</p>
 <figure><img src="https://epiverse-trace.github.io/task_pipeline-minimal.svg" alt="The outbreak analytics pipeline." class="figure mx-auto d-block"><div class="figcaption">The outbreak analytics pipeline.</div>
 </figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
-<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
 </h2>
 <hr class="half-width">
 <p>Our strategy is gradually incorporating specialised R packages into
@@ -666,7 +659,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 existing ones interoperable for the user experience, and stimulate a
 community of practice.</p>
 <figure><img src="fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
-<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
 </h2>
 <hr class="half-width">
 <p>Our plan for these tutorials is to introduce key solutions from
@@ -697,8 +689,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Our vision is to have pipelines of R packages for outbreak
@@ -761,8 +752,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -772,7 +762,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="reference.html#naturalhistory">natural history</a> of an
@@ -787,8 +776,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="definitions" class="callout-inner">
-<h3 class="callout-title">Definitions<a class="anchor" aria-label="anchor" href="#definitions"></a>
-</h3>
+<h3 class="callout-title">Definitions</h3>
 <div class="callout-content">
 <p>Look at the <a href="reference.html">glossary</a> for the definitions
 of all the time periods of the figure above!</p>
@@ -853,7 +841,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="kw">library</span><span class="op">(</span><span class="va">tidyverse</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
-<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
 </h2>
 <hr class="half-width">
 <p>The generation time, jointly with the <span class="math inline">\(R\)</span>, can inform about the speed of spread
@@ -892,8 +879,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="from-time-periods-to-probability-distributions." class="callout-inner">
-<h3 class="callout-title">From time periods to probability distributions.<a class="anchor" aria-label="anchor" href="#from-time-periods-to-probability-distributions."></a>
-</h3>
+<h3 class="callout-title">From time periods to probability distributions.</h3>
 <div class="callout-content">
 <p>When we calculate the <em>serial interval</em>, we see that not all
 case pairs have the same time length. We will observe this variability
@@ -997,8 +983,7 @@ <h3 class="callout-title">From time periods to probability distributions.<a clas
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="serial-interval" class="callout-inner">
-<h3 class="callout-title">Serial interval<a class="anchor" aria-label="anchor" href="#serial-interval"></a>
-</h3>
+<h3 class="callout-title">Serial interval</h3>
 <div class="callout-content">
 <p>Assume that COVID-19 and SARS have similar reproduction number values
 and that the serial interval approximates the generation time.</p>
@@ -1052,7 +1037,6 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 
 </section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
-<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
 </h2>
 <hr class="half-width">
 <p>First, let’s assume that the data set <code>example_confirmed</code>
@@ -1206,8 +1190,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="case-insensitive" class="callout-inner">
-<h3 class="callout-title">CASE-INSENSITIVE<a class="anchor" aria-label="anchor" href="#case-insensitive"></a>
-</h3>
+<h3 class="callout-title">CASE-INSENSITIVE</h3>
 <div class="callout-content">
 <p><code>epidist_db</code> is <a href="https://dillionmegida.com/p/case-sensitivity-vs-case-insensitivity/#case-insensitivity" class="external-link">case-insensitive</a>.
 This means that you can use strings with letters in upper or lower case
@@ -1250,8 +1233,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-periods" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation periods<a class="anchor" aria-label="anchor" href="#ebolas-incubation-periods"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation periods</h3>
 <div class="callout-content">
 <p>Take 5 minutes:</p>
 <ul>
@@ -1314,7 +1296,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
 </h2>
 <hr class="half-width">
 <p>The <code>epiparameter::epidist_db()</code> function works as a
@@ -1389,8 +1370,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-does-single_epidist-works" class="callout-inner">
 <h3 class="callout-title">How does <code>single_epidist</code>
-works?<a class="anchor" aria-label="anchor" href="#how-does-single_epidist-works"></a>
-</h3>
+works?</h3>
 <div class="callout-content">
 <p>Looking at the help documentation for
 <code>?epiparameter::epidist_db()</code>:</p>
@@ -1458,8 +1438,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-period" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation period<a class="anchor" aria-label="anchor" href="#ebolas-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation period</h3>
 <div class="callout-content">
 <p>Take 2 minutes:</p>
 <ul>
@@ -1527,7 +1506,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
-<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
 </h2>
 <hr class="half-width">
 <p>We can get the <code>mean</code> and standard deviation
@@ -1551,8 +1529,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-to-get-the-sd-and-other-nested-elements" class="callout-inner">
 <h3 class="callout-title">How to get the <code>sd</code> and other
-nested elements?<a class="anchor" aria-label="anchor" href="#how-to-get-the-sd-and-other-nested-elements"></a>
-</h3>
+nested elements?</h3>
 <div class="callout-content">
 <p>Take 1 minute to:</p>
 <ol style="list-style-type: decimal">
@@ -1640,8 +1617,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-severity-parameter" class="callout-inner">
-<h3 class="callout-title">Ebola’s severity parameter<a class="anchor" aria-label="anchor" href="#ebolas-severity-parameter"></a>
-</h3>
+<h3 class="callout-title">Ebola’s severity parameter</h3>
 <div class="callout-content">
 <p>A severity parameter like the duration of hospitalization could add
 to the information needed about the bed capacity in response to an
@@ -1702,7 +1678,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
-<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
 </h2>
 <hr class="half-width">
 <p>The following output has four entries with different content in the
@@ -1821,8 +1796,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="the-distribution-zoo" class="callout-inner">
-<h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anchor" href="#the-distribution-zoo"></a>
-</h3>
+<h3 class="callout-title">The distribution Zoo</h3>
 <div class="callout-content">
 <p>Explore this shinyapp called <strong>The Distribution
 Zoo</strong>!</p>
@@ -1854,7 +1828,6 @@ <h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anch
 </div>
 <!-- A slider, in the context of user interfaces and graphical user interfaces (GUIs), is a graphical control element that allows users to adjust a value by moving a handle along a track or bar. Conceptually, it provides a way to select a numeric value within a specified range by visually sliding or dragging a pointer (the handle) along a continuous axis. -->
 </section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
-<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
 </h2>
 <hr class="half-width">
 <p>In R, all the statistical distributions have functions to access
@@ -1954,8 +1927,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="window-for-contact-tracing-and-the-serial-interval" class="callout-inner">
-<h3 class="callout-title">Window for contact tracing and the Serial interval<a class="anchor" aria-label="anchor" href="#window-for-contact-tracing-and-the-serial-interval"></a>
-</h3>
+<h3 class="callout-title">Window for contact tracing and the Serial interval</h3>
 <div class="callout-content">
 <p>The <strong>serial interval</strong> is important in the optimization
 of contact tracing since it provides a time window for the containment
@@ -2050,7 +2022,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
 </h2>
 <hr class="half-width">
 <p>We are getting closer to the end! <code>EpiNow2::dist_spec()</code>
@@ -2124,8 +2095,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="lenght-of-quarantine-and-incubation-period" class="callout-inner">
-<h3 class="callout-title">Lenght of quarantine and Incubation period<a class="anchor" aria-label="anchor" href="#lenght-of-quarantine-and-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Lenght of quarantine and Incubation period</h3>
 <div class="callout-content">
 <p>The <strong>incubation period</strong> distribution is a useful delay
 to assess the length of active monitoring or quarantine (<a href="https://www.acpjournals.org/doi/10.7326/M20-0504" class="external-link">Lauer et al.,
@@ -2246,7 +2216,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code><a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
+</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code>
 <a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
 </h2>
 <hr class="half-width">
@@ -2277,8 +2247,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="warning" class="callout-inner">
-<h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#warning"></a>
-</h3>
+<h3 class="callout-title">Warning</h3>
 <div class="callout-content">
 <p>Using the serial interval instead of the generation time is an
 alternative that can propagate bias in your estimates, even more so in
@@ -2311,8 +2280,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number</h3>
 <div class="callout-content">
 <p>Download and read the <a href="data/ebola_cases.csv">Ebola
 dataset</a>:</p>
@@ -2408,7 +2376,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
-<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
 </h2>
 <hr class="half-width">
 <p>Estimating <span class="math inline">\(R_t\)</span> requires data on
@@ -2439,8 +2406,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="reuse-an-incubation-period-for-covid-19" class="callout-inner">
-<h3 class="callout-title">Reuse an Incubation period for COVID-19<a class="anchor" aria-label="anchor" href="#reuse-an-incubation-period-for-covid-19"></a>
-</h3>
+<h3 class="callout-title">Reuse an Incubation period for COVID-19</h3>
 <div class="callout-content">
 <p>Use <code>{epiparameter}</code> to:</p>
 <ul>
@@ -2554,8 +2520,7 @@ <h4 class="accordion-header" id="headingSolution12"> How much has it changed? </
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays</h3>
 <div class="callout-content">
 <p>Using the same <a href="data/ebola_cases.csv">Ebola dataset</a>:</p>
 <ul>
@@ -2659,8 +2624,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="extract-parameters" class="callout-inner">
-<h3 class="callout-title">Extract parameters<a class="anchor" aria-label="anchor" href="#extract-parameters"></a>
-</h3>
+<h3 class="callout-title">Extract parameters</h3>
 <div class="callout-content">
 <p>Use the <code>influenza_england_1978_school</code> from the
 <a href="https://github.com/reconhub/outbreaks" class="external-link">outbreaks</a> package to calculate the effective reproduction
@@ -2763,7 +2727,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
-<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
 </h2>
 <hr class="half-width">
 <p>In the early stage of an outbreak, we can rely on reusing parameters
@@ -2812,8 +2775,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="heart"></i>
 </div>
 <div id="how-to-estimate-delay-distributions-for-disease-x" class="callout-inner">
-<h3 class="callout-title">How to estimate delay distributions for Disease X?<a class="anchor" aria-label="anchor" href="#how-to-estimate-delay-distributions-for-disease-x"></a>
-</h3>
+<h3 class="callout-title">How to estimate delay distributions for Disease X?</h3>
 <div class="callout-content">
 <p>Refer to this excellent tutorial on estimating the serial interval
 and incubation period of Disease X accounting for <em>censoring</em>
@@ -2872,8 +2834,7 @@ <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-type-of-transmission" class="callout-inner">
-<h3 class="callout-title">What type of transmission?<a class="anchor" aria-label="anchor" href="#what-type-of-transmission"></a>
-</h3>
+<h3 class="callout-title">What type of transmission?</h3>
 <div class="callout-content">
 <p>Compare the serial interval and incubation period of Influenza and
 MERS:</p>
@@ -3005,8 +2966,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Use <code>{epiparameter}</code> to access the systematic review
@@ -3069,8 +3029,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -3086,7 +3045,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 <div id="reminder-the-effective-reproduction-number-r_t" class="callout-inner">
 <h3 class="callout-title">Reminder: the Effective Reproduction Number,
-<span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#reminder-the-effective-reproduction-number-r_t"></a>
+<span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>The <a href="reference.html#basic">basic reproduction number</a>,
@@ -3104,7 +3063,6 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Quantifying transmission metrics at the start of an outbreak can give
@@ -3127,8 +3085,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference" class="callout-inner">
-<h3 class="callout-title">Bayesian inference<a class="anchor" aria-label="anchor" href="#bayesian-inference"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference</h3>
 <div class="callout-content">
 <p>The R package <code>EpiNow2</code> uses a <a href="reference.html#bayesian">Bayesian inference</a> framework to
 estimate reproduction numbers and infection times based on reporting
@@ -3152,7 +3109,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 
 </section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
-<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -3243,8 +3199,7 @@ <h3 id="delay-distributions">Delay distributions<a class="anchor" aria-label="an
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="delays-and-data" class="callout-inner">
-<h3 class="callout-title">Delays and data<a class="anchor" aria-label="anchor" href="#delays-and-data"></a>
-</h3>
+<h3 class="callout-title">Delays and data</h3>
 <div class="callout-content">
 <p>The number of delays and type of delay is a flexible input that
 depends on the data. The examples below highlight how the delays can be
@@ -3311,8 +3266,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-a-gamma-distrubution" class="callout-inner">
-<h3 class="callout-title">Why a gamma distrubution?<a class="anchor" aria-label="anchor" href="#why-a-gamma-distrubution"></a>
-</h3>
+<h3 class="callout-title">Why a gamma distrubution?</h3>
 <div class="callout-content">
 <p>The incubation period has to be positive in value. Therefore we must
 specific a distribution in <code>dist_spec</code> which is for positive
@@ -3442,7 +3396,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
-<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
 </h2>
 <hr class="half-width">
 <p>The function <code>epinow()</code> is a wrapper for the function
@@ -3469,8 +3422,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference-using-stan" class="callout-inner">
-<h3 class="callout-title">Bayesian inference using Stan<a class="anchor" aria-label="anchor" href="#bayesian-inference-using-stan"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference using Stan</h3>
 <div class="callout-content">
 <p>The Bayesian inference is performed using MCMC methods with the
 program <a href="https://mc-stan.org/" class="external-link">Stan</a>. There are a number of
@@ -3581,9 +3533,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="expected-change-in-daily-cases" class="callout-inner">
-<h3 class="callout-title">
-<code>Expected change in daily cases</code><a class="anchor" aria-label="anchor" href="#expected-change-in-daily-cases"></a>
-</h3>
+<h3 class="callout-title"><code>Expected change in daily cases</code></h3>
 <div class="callout-content">
 <p>A factor describing expected change in daily cases based on the
 posterior probability that <span class="math inline">\(R_t &lt;
@@ -3623,7 +3573,6 @@ <h3 class="callout-title">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
-<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
 </h2>
 <hr class="half-width">
 <p>The outbreak data of the start of the COVID-19 pandemic from the
@@ -3756,7 +3705,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">estimates_regional</span><span class="op">$</span><span class="va">summary</span><span class="op">$</span><span class="va">plots</span><span class="op">$</span><span class="va">R</span></span></code></pre>
 </div>
 <figure><img src="fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> can be used to estimate transmission metrics
@@ -3770,8 +3718,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Transmission metrics can be estimated from case data after
@@ -3827,8 +3774,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="quantify-transmissibility.html">Quantifying transmission</a>
@@ -3843,7 +3789,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Given case data, we can create estimates of the current and future
@@ -3856,7 +3801,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 assuming the reproduction number will remain the same as it was
 estimated to be on the final date for which data was available.</p>
 </section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
-<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
 </h2>
 <hr class="half-width">
 <p>The function <code>epinow()</code> described in the previous tutorial
@@ -3906,7 +3850,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="forecasting-with-estimates-of-r_t" class="callout-inner">
-<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#forecasting-with-estimates-of-r_t"></a>
+<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>By default, the short-term forecasts are created using the latest
@@ -4012,7 +3956,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <code>?EpiNow2::obs_opts</code> for more detail.</p>
 </div>
 </section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
-<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> also has the ability to estimate and forecast
@@ -4090,8 +4033,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="be-cautious-of-timescale" class="callout-inner">
-<h3 class="callout-title">Be cautious of timescale<a class="anchor" aria-label="anchor" href="#be-cautious-of-timescale"></a>
-</h3>
+<h3 class="callout-title">Be cautious of timescale</h3>
 <div class="callout-content">
 <p>In the early stages of an outbreak there can be substantial changes
 in testing and reporting. If there are testing changes from one month to
@@ -4147,7 +4089,6 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 as the <code>estimates</code> output from
 <code>estimate_infections()</code>.</p>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <div id="challenge1" class="callout challenge">
@@ -4155,8 +4096,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Download the file <a href="data/ebola_cases.csv">ebola_cases.csv</a>
 and read it into R. The simulated data consists of the date of symptom
@@ -4190,7 +4130,7 @@ <h4 class="accordion-header" id="headingHint1">
   HINT : data format
   </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Ensure the data is in the correct format :</p>
 <ul>
@@ -4211,7 +4151,7 @@ <h4 class="accordion-header" id="headingSolution1">
   SOLUTION
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To estimate the effective reproduction number and growth rate, we
 will use the function <code>epinow()</code>.</p>
@@ -4305,7 +4245,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> can be used to create short term forecasts and
@@ -4320,8 +4259,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>We can create short-term forecasts by making assumptions about the
@@ -4383,8 +4321,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -4397,7 +4334,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Mathematical models are useful tools for generating future
@@ -4407,7 +4343,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 you will be able to generate the trajectory below showing the number of
 infectious individuals in different age categories over time.</p>
 <figure><img src="fig/simulating-transmission-rendered-traj-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
-<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
 </h2>
 <hr class="half-width">
 <p>To generate predictions of infectious disease trajectories, we must
@@ -4432,8 +4367,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="model-parameters-rates" class="callout-inner">
-<h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="anchor" href="#model-parameters-rates"></a>
-</h3>
+<h3 class="callout-title">Model parameters : rates</h3>
 <div class="callout-content">
 <p>In ODE models, model parameters are often (but not always) specified
 as rates. The rate at which an event occurs is the inverse of the
@@ -4481,8 +4415,7 @@ <h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="exposed-infected-infectious" class="callout-inner">
-<h3 class="callout-title">Exposed, infected, infectious<a class="anchor" aria-label="anchor" href="#exposed-infected-infectious"></a>
-</h3>
+<h3 class="callout-title">Exposed, infected, infectious</h3>
 <div class="callout-content">
 <p>Confusion sometimes arises when referring to the terms ‘exposed’,
 ‘infected’ and ‘infectious’ in mathematical modelling. Infection occurs
@@ -4521,8 +4454,7 @@ <h3 id="contact-matrix">1. Contact matrix<a class="anchor" aria-label="anchor" h
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="load-contact-and-population-data" class="callout-inner">
-<h3 class="callout-title">Load contact and population data<a class="anchor" aria-label="anchor" href="#load-contact-and-population-data"></a>
-</h3>
+<h3 class="callout-title">Load contact and population data</h3>
 <div class="callout-content">
 <p>Using the R package <code>socialmixr</code>, run the following lines
 of R code to obtain the contact matrix for the United Kingdom for the
@@ -4578,8 +4510,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-would-a-contact-matrix-be-non-symmetric" class="callout-inner">
-<h3 class="callout-title">Why would a contact matrix be non-symmetric?<a class="anchor" aria-label="anchor" href="#why-would-a-contact-matrix-be-non-symmetric"></a>
-</h3>
+<h3 class="callout-title">Why would a contact matrix be non-symmetric?</h3>
 <div class="callout-content">
 <p>One of the arguments of the function <code>contact_matrix()</code> is
 <code>symmetric=TRUE</code>. This means that the total number of
@@ -4726,7 +4657,7 @@ <h3 id="model-parameters">4. Model parameters<a class="anchor" aria-label="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-basic-reproduction-number-r_0" class="callout-inner">
-<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span><a class="anchor" aria-label="anchor" href="#the-basic-reproduction-number-r_0"></a>
+<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span>
 </h3>
 <div class="callout-content">
 <p>The basic reproduction number, <span class="math inline">\(R_0\)</span>, for the SEIR model is:</p>
@@ -4739,7 +4670,6 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 </div>
 </div>
 </section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
 </h2>
 <hr class="half-width">
 <div id="running-solving-the-model" class="callout">
@@ -4747,8 +4677,7 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="running-solving-the-model" class="callout-inner">
-<h3 class="callout-title">Running (solving) the model<a class="anchor" aria-label="anchor" href="#running-solving-the-model"></a>
-</h3>
+<h3 class="callout-title">Running (solving) the model</h3>
 <div class="callout-content">
 <p>For models that are described by ODEs, running the model actually
 means to solve the system of ODEs. ODEs describe the rate of change in
@@ -4849,8 +4778,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="time-increments" class="callout-inner">
-<h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" href="#time-increments"></a>
-</h3>
+<h3 class="callout-title">Time increments</h3>
 <div class="callout-content">
 <p>Note that there is a default argument of <code>increment = 1</code>.
 This relates to the time step of the ODE solver. When the parameters are
@@ -4866,7 +4794,6 @@ <h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
-<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
 </h2>
 <hr class="half-width">
 <p>As the epidemic model is <a href="reference.html#deterministic">deterministic</a>, we have one
@@ -4959,7 +4886,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 al. 2021</a> to learn about different types of uncertainty in infectious
 disease modelling.</p>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>In this tutorial, we have learnt how to simulate disease spread using
@@ -4972,8 +4898,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Disease trajectories can be generated using the R package
@@ -5029,8 +4954,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="simulating-transmission.html">Simulating
@@ -5041,7 +4965,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>There are existing mathematical models for different infections,
@@ -5054,8 +4977,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="choosing-a-model" class="callout-inner">
-<h3 class="callout-title">Choosing a model<a class="anchor" aria-label="anchor" href="#choosing-a-model"></a>
-</h3>
+<h3 class="callout-title">Choosing a model</h3>
 <div class="callout-content">
 <p>When deciding which mathematical model to use, there are a number of
 questions we must consider :</p>
@@ -5157,7 +5079,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code><a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
+</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code>
 <a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
 </h2>
 <hr class="half-width">
@@ -5171,8 +5093,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-model" class="callout-inner">
-<h3 class="callout-title">What model?<a class="anchor" aria-label="anchor" href="#what-model"></a>
-</h3>
+<h3 class="callout-title">What model?</h3>
 <div class="callout-content">
 <p>You have been asked to explore the variation in numbers of infectious
 individuals in the early stages of an Ebola outbreak.</p>
@@ -5198,8 +5119,7 @@ <h4 class="accordion-header" id="headingHint1"> HINT </h4>
 <i class="callout-icon" data-feather="check-square"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#checklist1"></a>
-</h3>
+<h3 class="callout-title">Checklist</h3>
 <div class="callout-content">
 <ul>
 <li>What is the infection/disease of interest?</li>
@@ -5293,7 +5213,6 @@ <h4 id="model_ebola_r">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <div id="running-the-model" class="callout challenge">
@@ -5301,8 +5220,7 @@ <h4 id="model_ebola_r">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-the-model" class="callout-inner">
-<h3 class="callout-title">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-</h3>
+<h3 class="callout-title">Running the model</h3>
 <div class="callout-content">
 <p>You have been tasked to generate initial trajectories of an Ebola
 outbreak in Guinea. Using <code>model_ebola_r()</code> and the the
@@ -5500,8 +5418,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Existing mathematical models should be selected according to the
@@ -5556,8 +5473,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="simulating-transmission.html">Simulating
@@ -5572,7 +5488,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Mathematical models can be used to generate trajectories of disease
@@ -5589,7 +5504,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 interventions in model of COVID-19 transmission.</p>
 
 </section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
 </h2>
 <hr class="half-width">
 <p><a href="reference.html#NPIs">Non-pharmaceutical interventions</a>
@@ -5697,8 +5611,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="effect-of-interventions-on-contacts" class="callout-inner">
-<h3 class="callout-title">Effect of interventions on contacts<a class="anchor" aria-label="anchor" href="#effect-of-interventions-on-contacts"></a>
-</h3>
+<h3 class="callout-title">Effect of interventions on contacts</h3>
 <div class="callout-content">
 <p>In <code>epidemics</code>, the contact matrix is scaled down by
 proportions for the period in which the intervention is in place. To
@@ -5919,8 +5832,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="intervention-types" class="callout-inner">
-<h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor" href="#intervention-types"></a>
-</h3>
+<h3 class="callout-title">Intervention types</h3>
 <div class="callout-content">
 <p>There are two intervention types for
 <code>model_default_cpp()</code>. Rate interventions on model parameters
@@ -5939,7 +5851,6 @@ <h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor
 </div>
 </div>
 </section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
 </h2>
 <hr class="half-width">
 <p>Pharmaceutical interventions (PIs) are measures such as vaccination
@@ -6006,8 +5917,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="compare-interventions" class="callout-inner">
-<h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anchor" href="#compare-interventions"></a>
-</h3>
+<h3 class="callout-title">Compare interventions</h3>
 <div class="callout-content">
 <p>Plot the three interventions vaccination, school closure and mask
 mandate and the baseline simulation on one plot. Which intervention
@@ -6020,7 +5930,7 @@ <h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anc
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Output </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6061,7 +5971,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Different types of intervention can be implemented using mathematical
@@ -6077,8 +5986,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The effect of NPIs can be modelled as reducing contact rates between
@@ -6132,8 +6040,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorials <a href="simulating-transmission.html">Simulating
@@ -6149,7 +6056,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>In this tutorial we will compare intervention scenarios against each
@@ -6168,7 +6074,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <li>a metric such as the epidemic peak time or size,</li>
 <li>a measure that uses the model outcomes such as QALY/DALYs.</li>
 </ul></section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
-<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
 </h2>
 <hr class="half-width">
 <p>The Vacamole model is a deterministic model based on a system of ODEs
@@ -6196,8 +6101,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-a-counterfactual-scenario-using-the-vacamole-model" class="callout-inner">
-<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model<a class="anchor" aria-label="anchor" href="#running-a-counterfactual-scenario-using-the-vacamole-model"></a>
-</h3>
+<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model</h3>
 <div class="callout-content">
 <ol style="list-style-type: decimal">
 <li>Run the model with the default parameter values for the UK
@@ -6226,7 +6130,7 @@ <h3 class="callout-title">Running a counterfactual scenario using the Vacamole m
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Vaccination code </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>To run the model with no vaccination in place we can <em>either</em>
 create two vaccination objects (one for each dose) using
@@ -6249,7 +6153,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> HINT : Running the model with default parameter values </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>We can run the Vacamole model with <a href="https://epiverse-trace.github.io/epidemics/articles/vacamole.html#model-epidemic-using-vacamole" class="external-link">default
 parameter values</a> by just specifying the population object and number
@@ -6273,7 +6177,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> SOLUTION </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Run the model</li>
@@ -6410,12 +6314,10 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
-<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
 </h2>
 <hr class="half-width">
 <p><em>Coming soon</em></p>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <p><em>Coming soon</em></p>
@@ -6424,8 +6326,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The counter factual scenario must be defined to make
@@ -6463,7 +6364,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -6486,8 +6387,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://epiverse-trace.github.io/tutorials/aio.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/aio.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/compare-interventions.html b/compare-interventions.html
index 90089436..ad0b3110 100644
--- a/compare-interventions.html
+++ b/compare-interventions.html
@@ -391,8 +391,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorials <a href="simulating-transmission.html">Simulating
 transmission</a> and <a href="modelling-interventions.html">Modelling
@@ -405,8 +404,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>In this tutorial we will compare intervention scenarios against each
 other. To quantify the effect of the intervention we need to compare our
 intervention scenario to a counter factual scenario. The <em>counter
@@ -421,8 +419,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <ul><li>a model outcome, e.g. number of infections or hospitalisations,</li>
 <li>a metric such as the epidemic peak time or size,</li>
 <li>a measure that uses the model outcomes such as QALY/DALYs.</li>
-</ul></section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
-<a class="anchor" aria-label="anchor" href="#vacamole-model"></a></h2>
+</ul></section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a></h2>
 <hr class="half-width"><p>The Vacamole model is a deterministic model based on a system of ODEs
 in <a href="https://doi.org/10.2807/1560-7917.ES.2022.27.44.2101090" class="external-link">Ainslie
 et al. 2022</a> to describe the effect of vaccination on COVID-19
@@ -446,8 +443,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-a-counterfactual-scenario-using-the-vacamole-model" class="callout-inner">
-<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model<a class="anchor" aria-label="anchor" href="#running-a-counterfactual-scenario-using-the-vacamole-model"></a>
-</h3>
+<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model</h3>
 <div class="callout-content">
 <ol style="list-style-type: decimal"><li>Run the model with the default parameter values for the UK
 population assuming that :</li>
@@ -468,7 +464,7 @@ <h3 class="callout-title">Running a counterfactual scenario using the Vacamole m
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Vaccination code </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>To run the model with no vaccination in place we can <em>either</em>
 create two vaccination objects (one for each dose) using
@@ -491,7 +487,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> HINT : Running the model with default parameter values </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>We can run the Vacamole model with <a href="https://epiverse-trace.github.io/epidemics/articles/vacamole.html#model-epidemic-using-vacamole" class="external-link">default
 parameter values</a> by just specifying the population object and number
@@ -515,7 +511,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> SOLUTION </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Run the model</li>
 </ol><div class="codewrapper sourceCode" id="cb3">
@@ -647,19 +643,16 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
-<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a></h2>
+</section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a></h2>
 <hr class="half-width"><p><em>Coming soon</em></p>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><p><em>Coming soon</em></p>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The counter factual scenario must be defined to make
 comparisons</li>
@@ -706,7 +699,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -729,7 +722,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/compare-interventions.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/create-forecast.html b/create-forecast.html
index 6dee358a..a2c6a169 100644
--- a/create-forecast.html
+++ b/create-forecast.html
@@ -396,8 +396,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="quantify-transmissibility.html">Quantifying transmission</a>
 </li>
@@ -409,8 +408,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Given case data, we can create estimates of the current and future
 number of cases by accounting for both delays in reporting and under
 reporting. To make statements about the future, we need to make an
@@ -420,8 +418,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 last observed. In this tutorial we will create short-term forecasts by
 assuming the reproduction number will remain the same as it was
 estimated to be on the final date for which data was available.</p>
-</section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
-<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a></h2>
+</section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a></h2>
 <hr class="half-width"><p>The function <code>epinow()</code> described in the previous tutorial
 is a wrapper for the function <code>estimate_infections()</code> used to
 estimate cases by date of infection. Using the same code in the previous
@@ -467,7 +464,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="forecasting-with-estimates-of-r_t" class="callout-inner">
-<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#forecasting-with-estimates-of-r_t"></a>
+<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>By default, the short-term forecasts are created using the latest
@@ -571,8 +568,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 Poisson, remove the default week effect and more. See
 <code>?EpiNow2::obs_opts</code> for more detail.</p>
 </div>
-</section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
-<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a></h2>
+</section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> also has the ability to estimate and forecast
 secondary observations e.g. deaths, hospitalisations from a primary
 observation e.g. cases. Here we will illustrate how to forecast the
@@ -644,8 +640,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="be-cautious-of-timescale" class="callout-inner">
-<h3 class="callout-title">Be cautious of timescale<a class="anchor" aria-label="anchor" href="#be-cautious-of-timescale"></a>
-</h3>
+<h3 class="callout-title">Be cautious of timescale</h3>
 <div class="callout-content">
 <p>In the early stages of an outbreak there can be substantial changes
 in testing and reporting. If there are testing changes from one month to
@@ -700,15 +695,13 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 deaths using forecast cases, here you would specify <code>primary</code>
 as the <code>estimates</code> output from
 <code>estimate_infections()</code>.</p>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><div id="challenge1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Download the file <a href="data/ebola_cases.csv">ebola_cases.csv</a>
 and read it into R. The simulated data consists of the date of symptom
@@ -738,7 +731,7 @@ <h4 class="accordion-header" id="headingHint1">
   HINT : data format
   </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Ensure the data is in the correct format :</p>
 <ul><li>
@@ -757,7 +750,7 @@ <h4 class="accordion-header" id="headingSolution1">
   SOLUTION
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To estimate the effective reproduction number and growth rate, we
 will use the function <code>epinow()</code>.</p>
@@ -850,8 +843,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> can be used to create short term forecasts and
 to estimate the relationship between different outcomes. There are a
 range of model options that can be implemented for different analysis,
@@ -864,8 +856,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>We can create short-term forecasts by making assumptions about the
 future behaviour of the reproduction number</li>
@@ -913,7 +904,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -936,7 +927,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/create-forecast.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 93745f06..c41a46e5 100644
--- a/images.html
+++ b/images.html
@@ -567,7 +567,7 @@ <h3 id="compare-interventions-figure-1">Figure 1</h3>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -590,8 +590,8 @@ <h3 id="compare-interventions-figure-1">Figure 1</h3>
   "url": "https://epiverse-trace.github.io/tutorials/images.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/images.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 8aa25438..e7c5b83b 100644
--- a/index.html
+++ b/index.html
@@ -345,8 +345,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><h1 class="schedule-heading">Summary and Setup</h1>
       
 
-<section><h2 class="section-heading" id="epiverse-trace-tutorials">Epiverse-TRACE tutorials<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a>
-<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a></h2>
+<section><h2 class="section-heading" id="epiverse-trace-tutorials">Epiverse-TRACE tutorials<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a></h2>
 <hr class="half-width"><p>The Epiverse-TRACE tutorials are training materials for Outbreak
 Analysis tasks aimed at <a href="profiles.html">learners</a> who are
 willing to achieve basic competence in modelling and analytics.</p>
@@ -374,8 +373,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 mathematical and modelling concepts with the explainer boxes.</li>
 </ul><p>Also check out the <a href="reference.html">glossary</a> for any
 terms you may be unfamiliar with.</p>
-</section><section><h2 class="section-heading" id="related-projects">Related projects<a class="anchor" aria-label="anchor" href="#related-projects"></a>
-<a class="anchor" aria-label="anchor" href="#related-projects"></a></h2>
+</section><section><h2 class="section-heading" id="related-projects">Related projects<a class="anchor" aria-label="anchor" href="#related-projects"></a></h2>
 <hr class="half-width"><ul><li>R package vignettes : for R package <code>{package}</code> find the
 vignette located at
 <code>https://epiverse-trace.github.io/{package}/</code>. <a href="https://epiverse-trace.github.io/" class="external-link">Look at all Epiverse-TRACE
@@ -398,8 +396,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
  -->
-</section><section id="setup"><section><h2 class="section-heading" id="software-setup">Software Setup<a class="anchor" aria-label="anchor" href="#software-setup"></a>
-<a class="anchor" aria-label="anchor" href="#software-setup"></a></h2>
+</section><section id="setup"><section><h2 class="section-heading" id="software-setup">Software Setup<a class="anchor" aria-label="anchor" href="#software-setup"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="install-r-and-rstudio">Install R and RStudio<a class="anchor" aria-label="anchor" href="#install-r-and-rstudio"></a></h3>
 <p>R and RStudio are two separate pieces of software:</p>
@@ -439,8 +436,7 @@ <h3 id="update-r-and-rstudio">Update R and RStudio<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#callout1"></a>
-</h3>
+<h3 class="callout-title">Callout</h3>
 <div class="callout-content">
 <p>While this may sound scary, it is <strong>far more common</strong> to
 run into issues due to using out-of-date versions of R or R packages.
@@ -494,8 +490,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>there is no package called ‘...’</code> you are good to go! If you
 do, <a href="#your-questions">contact us</a>!</p>
 </div>
-</section><section><h2 class="section-heading" id="data-sets">Data sets<a class="anchor" aria-label="anchor" href="#data-sets"></a>
-<a class="anchor" aria-label="anchor" href="#data-sets"></a></h2>
+</section><section><h2 class="section-heading" id="data-sets">Data sets<a class="anchor" aria-label="anchor" href="#data-sets"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor" href="#download-the-data"></a></h3>
 <p>We will download the data directly from R during the tutorial.
@@ -504,8 +499,7 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
 <p>The data files for the tutorial can be downloaded manually here:</p>
 <ul><li><a href="https://epiverse-trace.github.io/tutorials/data/ebola_cases.csv" class="external-link uri">https://epiverse-trace.github.io/tutorials/data/ebola_cases.csv</a></li>
 </ul></div>
-</section><section><h2 class="section-heading" id="your-questions">Your Questions<a class="anchor" aria-label="anchor" href="#your-questions"></a>
-<a class="anchor" aria-label="anchor" href="#your-questions"></a></h2>
+</section><section><h2 class="section-heading" id="your-questions">Your Questions<a class="anchor" aria-label="anchor" href="#your-questions"></a></h2>
 <hr class="half-width"><p>If you need any assistance installing the software or have any other
 questions about this tutorial, please send an email to <a href="mailto:andree.valle-campos@lshtm.ac.uk" class="email">andree.valle-campos@lshtm.ac.uk</a></p>
 <!--
@@ -539,7 +533,7 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -561,8 +555,8 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
   "url": "https://epiverse-trace.github.io/tutorials/index.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/index.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 9032dcf9..071b8b96 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -429,7 +429,7 @@ <h1>Instructor Notes</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -452,8 +452,8 @@ <h1>Instructor Notes</h1>
   "url": "https://epiverse-trace.github.io/tutorials/instructor-notes.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor-notes.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 72acaded..7b6b3467 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -343,8 +343,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Page not found</h1>
         
-<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
 <hr class="half-width"><p>We cannot seem to find the page you are looking for. Here are some
 tips that may help:</p>
 <ol style="list-style-type: decimal"><li>try going back to the <a href="javascript:history.back()">previous
@@ -383,7 +382,7 @@ <h1>Page not found</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -405,8 +404,8 @@ <h1>Page not found</h1>
   "url": "https://epiverse-trace.github.io/tutorials/instructor/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/404.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 7c8308b7..9ed2d2f2 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -403,7 +403,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -426,7 +426,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 59253275..700ab35b 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -353,8 +353,7 @@ <h1>Licenses</h1>
 
         
 
-<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>The tutorials in this repository are developed by Epiverse-TRACE,
 based on the <a href="https://github.com/carpentries/workbench-template-rmd" class="external-link">lesson
 template from the Carpentries</a> (template under CC BY license).</p>
@@ -390,8 +389,7 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-<a class="anchor" aria-label="anchor" href="#software"></a></h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by Epiverse-TRACE are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -451,7 +449,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -474,7 +472,7 @@ <h1>Licenses</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/LICENSE.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index b52480d6..cd3fe1e2 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -444,8 +444,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -454,7 +453,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
-<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
 </h2>
 <hr class="half-width">
 <p>Outbreaks appear with different diseases and in different contexts,
@@ -493,8 +491,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="questions-to-think-about" class="callout-inner">
-<h3 class="callout-title">Questions to think about<a class="anchor" aria-label="anchor" href="#questions-to-think-about"></a>
-</h3>
+<h3 class="callout-title">Questions to think about</h3>
 <div class="callout-content">
 <p>Remember your last experience with outbreak data and reflect on these
 questions:</p>
@@ -509,7 +506,6 @@ <h3 class="callout-title">Questions to think about<a class="anchor" aria-label="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
-<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="https://epiforecasts.io/EpiNow2/" class="external-link">EpiNow2</a> package provides a three-step solution to
@@ -619,8 +615,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="is-this-rt-estimation-biased" class="callout-inner">
-<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?<a class="anchor" aria-label="anchor" href="#is-this-rt-estimation-biased"></a>
-</h3>
+<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?</h3>
 <div class="callout-content">
 <p>Review <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008409" class="external-link">Gostic
 et al., 2020</a> about what additional adjustments this estimation
@@ -630,7 +625,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 </div>
 </div>
 </section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a>
-<a class="anchor" aria-label="anchor" href="#the-problem"></a>
 </h2>
 <hr class="half-width">
 <p>However, <em>quantifying the transmissibility</em> during a real-life
@@ -658,7 +652,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <p>So, all these tasks can be interconnected in a pipeline:</p>
 <figure><img src="https://epiverse-trace.github.io/task_pipeline-minimal.svg" alt="The outbreak analytics pipeline." class="figure mx-auto d-block"><div class="figcaption">The outbreak analytics pipeline.</div>
 </figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
-<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
 </h2>
 <hr class="half-width">
 <p>Our strategy is gradually incorporating specialised R packages into
@@ -669,7 +662,6 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 existing ones interoperable for the user experience, and stimulate a
 community of practice.</p>
 <figure><img src="../fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
-<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
 </h2>
 <hr class="half-width">
 <p>Our plan for these tutorials is to introduce key solutions from
@@ -700,8 +692,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Our vision is to have pipelines of R packages for outbreak
@@ -765,8 +756,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -776,7 +766,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>The <a href="reference.html#naturalhistory">natural history</a> of an
@@ -791,8 +780,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="definitions" class="callout-inner">
-<h3 class="callout-title">Definitions<a class="anchor" aria-label="anchor" href="#definitions"></a>
-</h3>
+<h3 class="callout-title">Definitions</h3>
 <div class="callout-content">
 <p>Look at the <a href="reference.html">glossary</a> for the definitions
 of all the time periods of the figure above!</p>
@@ -857,7 +845,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="kw">library</span><span class="op">(</span><span class="va">tidyverse</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
-<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
 </h2>
 <hr class="half-width">
 <p>The generation time, jointly with the <span class="math inline">\(R\)</span>, can inform about the speed of spread
@@ -896,8 +883,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="from-time-periods-to-probability-distributions." class="callout-inner">
-<h3 class="callout-title">From time periods to probability distributions.<a class="anchor" aria-label="anchor" href="#from-time-periods-to-probability-distributions."></a>
-</h3>
+<h3 class="callout-title">From time periods to probability distributions.</h3>
 <div class="callout-content">
 <p>When we calculate the <em>serial interval</em>, we see that not all
 case pairs have the same time length. We will observe this variability
@@ -1001,8 +987,7 @@ <h3 class="callout-title">From time periods to probability distributions.<a clas
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="serial-interval" class="callout-inner">
-<h3 class="callout-title">Serial interval<a class="anchor" aria-label="anchor" href="#serial-interval"></a>
-</h3>
+<h3 class="callout-title">Serial interval</h3>
 <div class="callout-content">
 <p>Assume that COVID-19 and SARS have similar reproduction number values
 and that the serial interval approximates the generation time.</p>
@@ -1068,7 +1053,6 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
-<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
 </h2>
 <hr class="half-width">
 <p>First, let’s assume that the data set <code>example_confirmed</code>
@@ -1222,8 +1206,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="case-insensitive" class="callout-inner">
-<h3 class="callout-title">CASE-INSENSITIVE<a class="anchor" aria-label="anchor" href="#case-insensitive"></a>
-</h3>
+<h3 class="callout-title">CASE-INSENSITIVE</h3>
 <div class="callout-content">
 <p><code>epidist_db</code> is <a href="https://dillionmegida.com/p/case-sensitivity-vs-case-insensitivity/#case-insensitivity" class="external-link">case-insensitive</a>.
 This means that you can use strings with letters in upper or lower case
@@ -1266,8 +1249,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-periods" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation periods<a class="anchor" aria-label="anchor" href="#ebolas-incubation-periods"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation periods</h3>
 <div class="callout-content">
 <p>Take 5 minutes:</p>
 <ul>
@@ -1330,7 +1312,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
 </h2>
 <hr class="half-width">
 <p>The <code>epiparameter::epidist_db()</code> function works as a
@@ -1405,8 +1386,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-does-single_epidist-works" class="callout-inner">
 <h3 class="callout-title">How does <code>single_epidist</code>
-works?<a class="anchor" aria-label="anchor" href="#how-does-single_epidist-works"></a>
-</h3>
+works?</h3>
 <div class="callout-content">
 <p>Looking at the help documentation for
 <code>?epiparameter::epidist_db()</code>:</p>
@@ -1474,8 +1454,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-period" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation period<a class="anchor" aria-label="anchor" href="#ebolas-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation period</h3>
 <div class="callout-content">
 <p>Take 2 minutes:</p>
 <ul>
@@ -1543,7 +1522,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
-<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
 </h2>
 <hr class="half-width">
 <p>We can get the <code>mean</code> and standard deviation
@@ -1567,8 +1545,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-to-get-the-sd-and-other-nested-elements" class="callout-inner">
 <h3 class="callout-title">How to get the <code>sd</code> and other
-nested elements?<a class="anchor" aria-label="anchor" href="#how-to-get-the-sd-and-other-nested-elements"></a>
-</h3>
+nested elements?</h3>
 <div class="callout-content">
 <p>Take 1 minute to:</p>
 <ol style="list-style-type: decimal">
@@ -1656,8 +1633,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-severity-parameter" class="callout-inner">
-<h3 class="callout-title">Ebola’s severity parameter<a class="anchor" aria-label="anchor" href="#ebolas-severity-parameter"></a>
-</h3>
+<h3 class="callout-title">Ebola’s severity parameter</h3>
 <div class="callout-content">
 <p>A severity parameter like the duration of hospitalization could add
 to the information needed about the bed capacity in response to an
@@ -1718,7 +1694,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
-<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
 </h2>
 <hr class="half-width">
 <p>The following output has four entries with different content in the
@@ -1837,8 +1812,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="the-distribution-zoo" class="callout-inner">
-<h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anchor" href="#the-distribution-zoo"></a>
-</h3>
+<h3 class="callout-title">The distribution Zoo</h3>
 <div class="callout-content">
 <p>Explore this shinyapp called <strong>The Distribution
 Zoo</strong>!</p>
@@ -1870,7 +1844,6 @@ <h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anch
 </div>
 <!-- A slider, in the context of user interfaces and graphical user interfaces (GUIs), is a graphical control element that allows users to adjust a value by moving a handle along a track or bar. Conceptually, it provides a way to select a numeric value within a specified range by visually sliding or dragging a pointer (the handle) along a continuous axis. -->
 </section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
-<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
 </h2>
 <hr class="half-width">
 <p>In R, all the statistical distributions have functions to access
@@ -1989,8 +1962,7 @@ <h3 class="accordion-header" id="headingInstructor2">  <div class="note-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="window-for-contact-tracing-and-the-serial-interval" class="callout-inner">
-<h3 class="callout-title">Window for contact tracing and the Serial interval<a class="anchor" aria-label="anchor" href="#window-for-contact-tracing-and-the-serial-interval"></a>
-</h3>
+<h3 class="callout-title">Window for contact tracing and the Serial interval</h3>
 <div class="callout-content">
 <p>The <strong>serial interval</strong> is important in the optimization
 of contact tracing since it provides a time window for the containment
@@ -2085,7 +2057,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
 </h2>
 <hr class="half-width">
 <p>We are getting closer to the end! <code>EpiNow2::dist_spec()</code>
@@ -2159,8 +2130,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="lenght-of-quarantine-and-incubation-period" class="callout-inner">
-<h3 class="callout-title">Lenght of quarantine and Incubation period<a class="anchor" aria-label="anchor" href="#lenght-of-quarantine-and-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Lenght of quarantine and Incubation period</h3>
 <div class="callout-content">
 <p>The <strong>incubation period</strong> distribution is a useful delay
 to assess the length of active monitoring or quarantine (<a href="https://www.acpjournals.org/doi/10.7326/M20-0504" class="external-link">Lauer et al.,
@@ -2281,7 +2251,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code><a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
+</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code>
 <a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
 </h2>
 <hr class="half-width">
@@ -2312,8 +2282,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="warning" class="callout-inner">
-<h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#warning"></a>
-</h3>
+<h3 class="callout-title">Warning</h3>
 <div class="callout-content">
 <p>Using the serial interval instead of the generation time is an
 alternative that can propagate bias in your estimates, even more so in
@@ -2346,8 +2315,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number</h3>
 <div class="callout-content">
 <p>Download and read the <a href="../data/ebola_cases.csv">Ebola
 dataset</a>:</p>
@@ -2443,7 +2411,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
-<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
 </h2>
 <hr class="half-width">
 <p>Estimating <span class="math inline">\(R_t\)</span> requires data on
@@ -2474,8 +2441,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="reuse-an-incubation-period-for-covid-19" class="callout-inner">
-<h3 class="callout-title">Reuse an Incubation period for COVID-19<a class="anchor" aria-label="anchor" href="#reuse-an-incubation-period-for-covid-19"></a>
-</h3>
+<h3 class="callout-title">Reuse an Incubation period for COVID-19</h3>
 <div class="callout-content">
 <p>Use <code>{epiparameter}</code> to:</p>
 <ul>
@@ -2589,8 +2555,7 @@ <h4 class="accordion-header" id="headingSolution12"> How much has it changed? </
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays</h3>
 <div class="callout-content">
 <p>Using the same <a href="../data/ebola_cases.csv">Ebola dataset</a>:</p>
 <ul>
@@ -2694,8 +2659,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="extract-parameters" class="callout-inner">
-<h3 class="callout-title">Extract parameters<a class="anchor" aria-label="anchor" href="#extract-parameters"></a>
-</h3>
+<h3 class="callout-title">Extract parameters</h3>
 <div class="callout-content">
 <p>Use the <code>influenza_england_1978_school</code> from the
 <a href="https://github.com/reconhub/outbreaks" class="external-link">outbreaks</a> package to calculate the effective reproduction
@@ -2798,7 +2762,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
-<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
 </h2>
 <hr class="half-width">
 <p>In the early stage of an outbreak, we can rely on reusing parameters
@@ -2847,8 +2810,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="heart"></i>
 </div>
 <div id="how-to-estimate-delay-distributions-for-disease-x" class="callout-inner">
-<h3 class="callout-title">How to estimate delay distributions for Disease X?<a class="anchor" aria-label="anchor" href="#how-to-estimate-delay-distributions-for-disease-x"></a>
-</h3>
+<h3 class="callout-title">How to estimate delay distributions for Disease X?</h3>
 <div class="callout-content">
 <p>Refer to this excellent tutorial on estimating the serial interval
 and incubation period of Disease X accounting for <em>censoring</em>
@@ -2907,8 +2869,7 @@ <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-type-of-transmission" class="callout-inner">
-<h3 class="callout-title">What type of transmission?<a class="anchor" aria-label="anchor" href="#what-type-of-transmission"></a>
-</h3>
+<h3 class="callout-title">What type of transmission?</h3>
 <div class="callout-content">
 <p>Compare the serial interval and incubation period of Influenza and
 MERS:</p>
@@ -3040,8 +3001,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Use <code>{epiparameter}</code> to access the systematic review
@@ -3105,8 +3065,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -3122,7 +3081,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 <div id="reminder-the-effective-reproduction-number-r_t" class="callout-inner">
 <h3 class="callout-title">Reminder: the Effective Reproduction Number,
-<span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#reminder-the-effective-reproduction-number-r_t"></a>
+<span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>The <a href="reference.html#basic">basic reproduction number</a>,
@@ -3140,7 +3099,6 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Quantifying transmission metrics at the start of an outbreak can give
@@ -3163,8 +3121,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference" class="callout-inner">
-<h3 class="callout-title">Bayesian inference<a class="anchor" aria-label="anchor" href="#bayesian-inference"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference</h3>
 <div class="callout-content">
 <p>The R package <code>EpiNow2</code> uses a <a href="reference.html#bayesian">Bayesian inference</a> framework to
 estimate reproduction numbers and infection times based on reporting
@@ -3202,7 +3159,6 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
-<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -3293,8 +3249,7 @@ <h3 id="delay-distributions">Delay distributions<a class="anchor" aria-label="an
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="delays-and-data" class="callout-inner">
-<h3 class="callout-title">Delays and data<a class="anchor" aria-label="anchor" href="#delays-and-data"></a>
-</h3>
+<h3 class="callout-title">Delays and data</h3>
 <div class="callout-content">
 <p>The number of delays and type of delay is a flexible input that
 depends on the data. The examples below highlight how the delays can be
@@ -3361,8 +3316,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-a-gamma-distrubution" class="callout-inner">
-<h3 class="callout-title">Why a gamma distrubution?<a class="anchor" aria-label="anchor" href="#why-a-gamma-distrubution"></a>
-</h3>
+<h3 class="callout-title">Why a gamma distrubution?</h3>
 <div class="callout-content">
 <p>The incubation period has to be positive in value. Therefore we must
 specific a distribution in <code>dist_spec</code> which is for positive
@@ -3492,7 +3446,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
-<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
 </h2>
 <hr class="half-width">
 <p>The function <code>epinow()</code> is a wrapper for the function
@@ -3519,8 +3472,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference-using-stan" class="callout-inner">
-<h3 class="callout-title">Bayesian inference using Stan<a class="anchor" aria-label="anchor" href="#bayesian-inference-using-stan"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference using Stan</h3>
 <div class="callout-content">
 <p>The Bayesian inference is performed using MCMC methods with the
 program <a href="https://mc-stan.org/" class="external-link">Stan</a>. There are a number of
@@ -3631,9 +3583,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="expected-change-in-daily-cases" class="callout-inner">
-<h3 class="callout-title">
-<code>Expected change in daily cases</code><a class="anchor" aria-label="anchor" href="#expected-change-in-daily-cases"></a>
-</h3>
+<h3 class="callout-title"><code>Expected change in daily cases</code></h3>
 <div class="callout-content">
 <p>A factor describing expected change in daily cases based on the
 posterior probability that <span class="math inline">\(R_t &lt;
@@ -3673,7 +3623,6 @@ <h3 class="callout-title">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
-<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
 </h2>
 <hr class="half-width">
 <p>The outbreak data of the start of the COVID-19 pandemic from the
@@ -3806,7 +3755,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">estimates_regional</span><span class="op">$</span><span class="va">summary</span><span class="op">$</span><span class="va">plots</span><span class="op">$</span><span class="va">R</span></span></code></pre>
 </div>
 <figure><img src="../fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> can be used to estimate transmission metrics
@@ -3820,8 +3768,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Transmission metrics can be estimated from case data after
@@ -3878,8 +3825,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="quantify-transmissibility.html">Quantifying transmission</a>
@@ -3894,7 +3840,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Given case data, we can create estimates of the current and future
@@ -3907,7 +3852,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 assuming the reproduction number will remain the same as it was
 estimated to be on the final date for which data was available.</p>
 </section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
-<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
 </h2>
 <hr class="half-width">
 <p>The function <code>epinow()</code> described in the previous tutorial
@@ -3957,7 +3901,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="forecasting-with-estimates-of-r_t" class="callout-inner">
-<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#forecasting-with-estimates-of-r_t"></a>
+<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>By default, the short-term forecasts are created using the latest
@@ -4063,7 +4007,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <code>?EpiNow2::obs_opts</code> for more detail.</p>
 </div>
 </section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
-<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> also has the ability to estimate and forecast
@@ -4141,8 +4084,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="be-cautious-of-timescale" class="callout-inner">
-<h3 class="callout-title">Be cautious of timescale<a class="anchor" aria-label="anchor" href="#be-cautious-of-timescale"></a>
-</h3>
+<h3 class="callout-title">Be cautious of timescale</h3>
 <div class="callout-content">
 <p>In the early stages of an outbreak there can be substantial changes
 in testing and reporting. If there are testing changes from one month to
@@ -4198,7 +4140,6 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 as the <code>estimates</code> output from
 <code>estimate_infections()</code>.</p>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <div id="challenge1" class="callout challenge">
@@ -4206,8 +4147,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Download the file <a href="../data/ebola_cases.csv">ebola_cases.csv</a>
 and read it into R. The simulated data consists of the date of symptom
@@ -4241,7 +4181,7 @@ <h4 class="accordion-header" id="headingHint1">
   HINT : data format
   </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Ensure the data is in the correct format :</p>
 <ul>
@@ -4262,7 +4202,7 @@ <h4 class="accordion-header" id="headingSolution1">
   SOLUTION
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To estimate the effective reproduction number and growth rate, we
 will use the function <code>epinow()</code>.</p>
@@ -4356,7 +4296,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p><code>EpiNow2</code> can be used to create short term forecasts and
@@ -4371,8 +4310,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>We can create short-term forecasts by making assumptions about the
@@ -4435,8 +4373,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -4449,7 +4386,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Mathematical models are useful tools for generating future
@@ -4472,7 +4408,6 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
-<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
 </h2>
 <hr class="half-width">
 <p>To generate predictions of infectious disease trajectories, we must
@@ -4497,8 +4432,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="model-parameters-rates" class="callout-inner">
-<h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="anchor" href="#model-parameters-rates"></a>
-</h3>
+<h3 class="callout-title">Model parameters : rates</h3>
 <div class="callout-content">
 <p>In ODE models, model parameters are often (but not always) specified
 as rates. The rate at which an event occurs is the inverse of the
@@ -4546,8 +4480,7 @@ <h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="exposed-infected-infectious" class="callout-inner">
-<h3 class="callout-title">Exposed, infected, infectious<a class="anchor" aria-label="anchor" href="#exposed-infected-infectious"></a>
-</h3>
+<h3 class="callout-title">Exposed, infected, infectious</h3>
 <div class="callout-content">
 <p>Confusion sometimes arises when referring to the terms ‘exposed’,
 ‘infected’ and ‘infectious’ in mathematical modelling. Infection occurs
@@ -4586,8 +4519,7 @@ <h3 id="contact-matrix">1. Contact matrix<a class="anchor" aria-label="anchor" h
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="load-contact-and-population-data" class="callout-inner">
-<h3 class="callout-title">Load contact and population data<a class="anchor" aria-label="anchor" href="#load-contact-and-population-data"></a>
-</h3>
+<h3 class="callout-title">Load contact and population data</h3>
 <div class="callout-content">
 <p>Using the R package <code>socialmixr</code>, run the following lines
 of R code to obtain the contact matrix for the United Kingdom for the
@@ -4643,8 +4575,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-would-a-contact-matrix-be-non-symmetric" class="callout-inner">
-<h3 class="callout-title">Why would a contact matrix be non-symmetric?<a class="anchor" aria-label="anchor" href="#why-would-a-contact-matrix-be-non-symmetric"></a>
-</h3>
+<h3 class="callout-title">Why would a contact matrix be non-symmetric?</h3>
 <div class="callout-content">
 <p>One of the arguments of the function <code>contact_matrix()</code> is
 <code>symmetric=TRUE</code>. This means that the total number of
@@ -4791,7 +4722,7 @@ <h3 id="model-parameters">4. Model parameters<a class="anchor" aria-label="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-basic-reproduction-number-r_0" class="callout-inner">
-<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span><a class="anchor" aria-label="anchor" href="#the-basic-reproduction-number-r_0"></a>
+<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span>
 </h3>
 <div class="callout-content">
 <p>The basic reproduction number, <span class="math inline">\(R_0\)</span>, for the SEIR model is:</p>
@@ -4804,7 +4735,6 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 </div>
 </div>
 </section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
 </h2>
 <hr class="half-width">
 <div id="running-solving-the-model" class="callout">
@@ -4812,8 +4742,7 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="running-solving-the-model" class="callout-inner">
-<h3 class="callout-title">Running (solving) the model<a class="anchor" aria-label="anchor" href="#running-solving-the-model"></a>
-</h3>
+<h3 class="callout-title">Running (solving) the model</h3>
 <div class="callout-content">
 <p>For models that are described by ODEs, running the model actually
 means to solve the system of ODEs. ODEs describe the rate of change in
@@ -4914,8 +4843,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="time-increments" class="callout-inner">
-<h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" href="#time-increments"></a>
-</h3>
+<h3 class="callout-title">Time increments</h3>
 <div class="callout-content">
 <p>Note that there is a default argument of <code>increment = 1</code>.
 This relates to the time step of the ODE solver. When the parameters are
@@ -4931,7 +4859,6 @@ <h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
-<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
 </h2>
 <hr class="half-width">
 <p>As the epidemic model is <a href="reference.html#deterministic">deterministic</a>, we have one
@@ -5024,7 +4951,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 al. 2021</a> to learn about different types of uncertainty in infectious
 disease modelling.</p>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>In this tutorial, we have learnt how to simulate disease spread using
@@ -5037,8 +4963,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Disease trajectories can be generated using the R package
@@ -5095,8 +5020,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="simulating-transmission.html">Simulating
@@ -5107,7 +5031,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>There are existing mathematical models for different infections,
@@ -5132,8 +5055,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="choosing-a-model" class="callout-inner">
-<h3 class="callout-title">Choosing a model<a class="anchor" aria-label="anchor" href="#choosing-a-model"></a>
-</h3>
+<h3 class="callout-title">Choosing a model</h3>
 <div class="callout-content">
 <p>When deciding which mathematical model to use, there are a number of
 questions we must consider :</p>
@@ -5235,7 +5157,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code><a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
+</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code>
 <a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
 </h2>
 <hr class="half-width">
@@ -5249,8 +5171,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-model" class="callout-inner">
-<h3 class="callout-title">What model?<a class="anchor" aria-label="anchor" href="#what-model"></a>
-</h3>
+<h3 class="callout-title">What model?</h3>
 <div class="callout-content">
 <p>You have been asked to explore the variation in numbers of infectious
 individuals in the early stages of an Ebola outbreak.</p>
@@ -5276,8 +5197,7 @@ <h4 class="accordion-header" id="headingHint1"> HINT </h4>
 <i class="callout-icon" data-feather="check-square"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#checklist1"></a>
-</h3>
+<h3 class="callout-title">Checklist</h3>
 <div class="callout-content">
 <ul>
 <li>What is the infection/disease of interest?</li>
@@ -5371,7 +5291,6 @@ <h4 id="model_ebola_r">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <div id="running-the-model" class="callout challenge">
@@ -5379,8 +5298,7 @@ <h4 id="model_ebola_r">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-the-model" class="callout-inner">
-<h3 class="callout-title">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-</h3>
+<h3 class="callout-title">Running the model</h3>
 <div class="callout-content">
 <p>You have been tasked to generate initial trajectories of an Ebola
 outbreak in Guinea. Using <code>model_ebola_r()</code> and the the
@@ -5578,8 +5496,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Existing mathematical models should be selected according to the
@@ -5635,8 +5552,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorial <a href="simulating-transmission.html">Simulating
@@ -5651,7 +5567,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>Mathematical models can be used to generate trajectories of disease
@@ -5671,7 +5586,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>In this tutorial different types of intervention and how they can be
 modelled are introduced. Learners should be able to understand the
@@ -5682,7 +5597,6 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
 </h2>
 <hr class="half-width">
 <p><a href="reference.html#NPIs">Non-pharmaceutical interventions</a>
@@ -5790,8 +5704,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="effect-of-interventions-on-contacts" class="callout-inner">
-<h3 class="callout-title">Effect of interventions on contacts<a class="anchor" aria-label="anchor" href="#effect-of-interventions-on-contacts"></a>
-</h3>
+<h3 class="callout-title">Effect of interventions on contacts</h3>
 <div class="callout-content">
 <p>In <code>epidemics</code>, the contact matrix is scaled down by
 proportions for the period in which the intervention is in place. To
@@ -6012,8 +5925,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="intervention-types" class="callout-inner">
-<h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor" href="#intervention-types"></a>
-</h3>
+<h3 class="callout-title">Intervention types</h3>
 <div class="callout-content">
 <p>There are two intervention types for
 <code>model_default_cpp()</code>. Rate interventions on model parameters
@@ -6032,7 +5944,6 @@ <h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor
 </div>
 </div>
 </section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
 </h2>
 <hr class="half-width">
 <p>Pharmaceutical interventions (PIs) are measures such as vaccination
@@ -6099,8 +6010,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="compare-interventions" class="callout-inner">
-<h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anchor" href="#compare-interventions"></a>
-</h3>
+<h3 class="callout-title">Compare interventions</h3>
 <div class="callout-content">
 <p>Plot the three interventions vaccination, school closure and mask
 mandate and the baseline simulation on one plot. Which intervention
@@ -6113,7 +6023,7 @@ <h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anc
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Output </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6154,7 +6064,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Different types of intervention can be implemented using mathematical
@@ -6170,8 +6079,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The effect of NPIs can be modelled as reducing contact rates between
@@ -6226,8 +6134,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul>
 <li>Complete tutorials <a href="simulating-transmission.html">Simulating
@@ -6243,7 +6150,6 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 <section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
 <p>In this tutorial we will compare intervention scenarios against each
@@ -6267,7 +6173,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>In this tutorial we introduce the concept of the counter factual and
 how to compare scenarios (counter factual versus intervention) against
@@ -6277,7 +6183,6 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
-<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
 </h2>
 <hr class="half-width">
 <p>The Vacamole model is a deterministic model based on a system of ODEs
@@ -6305,8 +6210,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-a-counterfactual-scenario-using-the-vacamole-model" class="callout-inner">
-<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model<a class="anchor" aria-label="anchor" href="#running-a-counterfactual-scenario-using-the-vacamole-model"></a>
-</h3>
+<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model</h3>
 <div class="callout-content">
 <ol style="list-style-type: decimal">
 <li>Run the model with the default parameter values for the UK
@@ -6335,7 +6239,7 @@ <h3 class="callout-title">Running a counterfactual scenario using the Vacamole m
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Vaccination code </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>To run the model with no vaccination in place we can <em>either</em>
 create two vaccination objects (one for each dose) using
@@ -6358,7 +6262,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> HINT : Running the model with default parameter values </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>We can run the Vacamole model with <a href="https://epiverse-trace.github.io/epidemics/articles/vacamole.html#model-epidemic-using-vacamole" class="external-link">default
 parameter values</a> by just specifying the population object and number
@@ -6382,7 +6286,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> SOLUTION </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>Run the model</li>
@@ -6519,12 +6423,10 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
-<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
 </h2>
 <hr class="half-width">
 <p><em>Coming soon</em></p>
 </section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
 </h2>
 <hr class="half-width">
 <p><em>Coming soon</em></p>
@@ -6533,8 +6435,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The counter factual scenario must be defined to make
@@ -6572,7 +6473,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -6595,8 +6496,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://epiverse-trace.github.io/tutorials/instructor/aio.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/aio.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/compare-interventions.html b/instructor/compare-interventions.html
index a6b4b202..a0d6c12e 100644
--- a/instructor/compare-interventions.html
+++ b/instructor/compare-interventions.html
@@ -393,8 +393,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorials <a href="simulating-transmission.html">Simulating
 transmission</a> and <a href="modelling-interventions.html">Modelling
@@ -407,8 +406,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>In this tutorial we will compare intervention scenarios against each
 other. To quantify the effect of the intervention we need to compare our
 intervention scenario to a counter factual scenario. The <em>counter
@@ -428,7 +426,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>In this tutorial we introduce the concept of the counter factual and
 how to compare scenarios (counter factual versus intervention) against
@@ -437,8 +435,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a>
-<a class="anchor" aria-label="anchor" href="#vacamole-model"></a></h2>
+</section><section><h2 class="section-heading" id="vacamole-model">Vacamole model<a class="anchor" aria-label="anchor" href="#vacamole-model"></a></h2>
 <hr class="half-width"><p>The Vacamole model is a deterministic model based on a system of ODEs
 in <a href="https://doi.org/10.2807/1560-7917.ES.2022.27.44.2101090" class="external-link">Ainslie
 et al. 2022</a> to describe the effect of vaccination on COVID-19
@@ -462,8 +459,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-a-counterfactual-scenario-using-the-vacamole-model" class="callout-inner">
-<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model<a class="anchor" aria-label="anchor" href="#running-a-counterfactual-scenario-using-the-vacamole-model"></a>
-</h3>
+<h3 class="callout-title">Running a counterfactual scenario using the Vacamole model</h3>
 <div class="callout-content">
 <ol style="list-style-type: decimal"><li>Run the model with the default parameter values for the UK
 population assuming that :</li>
@@ -484,7 +480,7 @@ <h3 class="callout-title">Running a counterfactual scenario using the Vacamole m
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Vaccination code </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>To run the model with no vaccination in place we can <em>either</em>
 create two vaccination objects (one for each dose) using
@@ -507,7 +503,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> HINT : Running the model with default parameter values </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>We can run the Vacamole model with <a href="https://epiverse-trace.github.io/epidemics/articles/vacamole.html#model-epidemic-using-vacamole" class="external-link">default
 parameter values</a> by just specifying the population object and number
@@ -531,7 +527,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> SOLUTION </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>Run the model</li>
 </ol><div class="codewrapper sourceCode" id="cb3">
@@ -663,19 +659,16 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a>
-<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a></h2>
+</section><section><h2 class="section-heading" id="comparing-scenarios">Comparing scenarios<a class="anchor" aria-label="anchor" href="#comparing-scenarios"></a></h2>
 <hr class="half-width"><p><em>Coming soon</em></p>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><p><em>Coming soon</em></p>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The counter factual scenario must be defined to make
 comparisons</li>
@@ -722,7 +715,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -745,7 +738,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/compare-interventions.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/create-forecast.html b/instructor/create-forecast.html
index 21e1cacc..9dacde5d 100644
--- a/instructor/create-forecast.html
+++ b/instructor/create-forecast.html
@@ -398,8 +398,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="quantify-transmissibility.html">Quantifying transmission</a>
 </li>
@@ -411,8 +410,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Given case data, we can create estimates of the current and future
 number of cases by accounting for both delays in reporting and under
 reporting. To make statements about the future, we need to make an
@@ -422,8 +420,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 last observed. In this tutorial we will create short-term forecasts by
 assuming the reproduction number will remain the same as it was
 estimated to be on the final date for which data was available.</p>
-</section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a>
-<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a></h2>
+</section><section><h2 class="section-heading" id="create-a-short-term-forecast">Create a short-term forecast<a class="anchor" aria-label="anchor" href="#create-a-short-term-forecast"></a></h2>
 <hr class="half-width"><p>The function <code>epinow()</code> described in the previous tutorial
 is a wrapper for the function <code>estimate_infections()</code> used to
 estimate cases by date of infection. Using the same code in the previous
@@ -469,7 +466,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="forecasting-with-estimates-of-r_t" class="callout-inner">
-<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#forecasting-with-estimates-of-r_t"></a>
+<h3 class="callout-title">Forecasting with estimates of <span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>By default, the short-term forecasts are created using the latest
@@ -573,8 +570,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 Poisson, remove the default week effect and more. See
 <code>?EpiNow2::obs_opts</code> for more detail.</p>
 </div>
-</section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a>
-<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a></h2>
+</section><section><h2 class="section-heading" id="forecast-secondary-observations">Forecast secondary observations<a class="anchor" aria-label="anchor" href="#forecast-secondary-observations"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> also has the ability to estimate and forecast
 secondary observations e.g. deaths, hospitalisations from a primary
 observation e.g. cases. Here we will illustrate how to forecast the
@@ -646,8 +642,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="be-cautious-of-timescale" class="callout-inner">
-<h3 class="callout-title">Be cautious of timescale<a class="anchor" aria-label="anchor" href="#be-cautious-of-timescale"></a>
-</h3>
+<h3 class="callout-title">Be cautious of timescale</h3>
 <div class="callout-content">
 <p>In the early stages of an outbreak there can be substantial changes
 in testing and reporting. If there are testing changes from one month to
@@ -702,15 +697,13 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 deaths using forecast cases, here you would specify <code>primary</code>
 as the <code>estimates</code> output from
 <code>estimate_infections()</code>.</p>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><div id="challenge1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Download the file <a href="../data/ebola_cases.csv">ebola_cases.csv</a>
 and read it into R. The simulated data consists of the date of symptom
@@ -740,7 +733,7 @@ <h4 class="accordion-header" id="headingHint1">
   HINT : data format
   </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Ensure the data is in the correct format :</p>
 <ul><li>
@@ -759,7 +752,7 @@ <h4 class="accordion-header" id="headingSolution1">
   SOLUTION
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To estimate the effective reproduction number and growth rate, we
 will use the function <code>epinow()</code>.</p>
@@ -852,8 +845,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> can be used to create short term forecasts and
 to estimate the relationship between different outcomes. There are a
 range of model options that can be implemented for different analysis,
@@ -866,8 +858,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>We can create short-term forecasts by making assumptions about the
 future behaviour of the reproduction number</li>
@@ -915,7 +906,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -938,7 +929,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/create-forecast.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 3fd5fb64..df9bd7b6 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -569,7 +569,7 @@ <h3 id="compare-interventions-figure-1">Figure 1</h3>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -592,8 +592,8 @@ <h3 id="compare-interventions-figure-1">Figure 1</h3>
   "url": "https://epiverse-trace.github.io/tutorials/instructor/images.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/images.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 94d9aa96..49b7bc7d 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -344,8 +344,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><h1 class="schedule-heading">Summary and Schedule</h1>
       
 
-<section><h2 class="section-heading" id="epiverse-trace-tutorials">Epiverse-TRACE tutorials<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a>
-<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a></h2>
+<section><h2 class="section-heading" id="epiverse-trace-tutorials">Epiverse-TRACE tutorials<a class="anchor" aria-label="anchor" href="#epiverse-trace-tutorials"></a></h2>
 <hr class="half-width"><p>The Epiverse-TRACE tutorials are training materials for Outbreak
 Analysis tasks aimed at <a href="profiles.html">learners</a> who are
 willing to achieve basic competence in modelling and analytics.</p>
@@ -373,8 +372,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 mathematical and modelling concepts with the explainer boxes.</li>
 </ul><p>Also check out the <a href="reference.html">glossary</a> for any
 terms you may be unfamiliar with.</p>
-</section><section><h2 class="section-heading" id="related-projects">Related projects<a class="anchor" aria-label="anchor" href="#related-projects"></a>
-<a class="anchor" aria-label="anchor" href="#related-projects"></a></h2>
+</section><section><h2 class="section-heading" id="related-projects">Related projects<a class="anchor" aria-label="anchor" href="#related-projects"></a></h2>
 <hr class="half-width"><ul><li>R package vignettes : for R package <code>{package}</code> find the
 vignette located at
 <code>https://epiverse-trace.github.io/{package}/</code>. <a href="https://epiverse-trace.github.io/" class="external-link">Look at all Epiverse-TRACE
@@ -496,14 +494,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
  --></tbody></table><p>
       The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
       </p>
-      </section><section id="setup"><section><h2 class="section-heading" id="software-setup">Software Setup<a class="anchor" aria-label="anchor" href="#software-setup"></a>
-<a class="anchor" aria-label="anchor" href="#software-setup"></a></h2>
+      </section><section id="setup"><section><h2 class="section-heading" id="software-setup">Software Setup<a class="anchor" aria-label="anchor" href="#software-setup"></a></h2>
 <hr class="half-width"><div id="accordionInstructor1" class="accordion instructor-note accordion-flush">
 <div class="accordion-item">
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Setup instructions live in this document. Please specify the tools
 and the data sets the learner needs to have installed. If you want to
@@ -552,8 +549,7 @@ <h3 id="update-r-and-rstudio">Update R and RStudio<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#callout1"></a>
-</h3>
+<h3 class="callout-title">Callout</h3>
 <div class="callout-content">
 <p>While this may sound scary, it is <strong>far more common</strong> to
 run into issues due to using out-of-date versions of R or R packages.
@@ -607,8 +603,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>there is no package called ‘...’</code> you are good to go! If you
 do, <a href="#your-questions">contact us</a>!</p>
 </div>
-</section><section><h2 class="section-heading" id="data-sets">Data sets<a class="anchor" aria-label="anchor" href="#data-sets"></a>
-<a class="anchor" aria-label="anchor" href="#data-sets"></a></h2>
+</section><section><h2 class="section-heading" id="data-sets">Data sets<a class="anchor" aria-label="anchor" href="#data-sets"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor" href="#download-the-data"></a></h3>
 <p>We will download the data directly from R during the tutorial.
@@ -617,8 +612,7 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
 <p>The data files for the tutorial can be downloaded manually here:</p>
 <ul><li><a href="https://epiverse-trace.github.io/tutorials/data/ebola_cases.csv" class="external-link uri">https://epiverse-trace.github.io/tutorials/data/ebola_cases.csv</a></li>
 </ul></div>
-</section><section><h2 class="section-heading" id="your-questions">Your Questions<a class="anchor" aria-label="anchor" href="#your-questions"></a>
-<a class="anchor" aria-label="anchor" href="#your-questions"></a></h2>
+</section><section><h2 class="section-heading" id="your-questions">Your Questions<a class="anchor" aria-label="anchor" href="#your-questions"></a></h2>
 <hr class="half-width"><p>If you need any assistance installing the software or have any other
 questions about this tutorial, please send an email to <a href="mailto:andree.valle-campos@lshtm.ac.uk" class="email">andree.valle-campos@lshtm.ac.uk</a></p>
 <!--
@@ -652,7 +646,7 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -674,8 +668,8 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
   "url": "https://epiverse-trace.github.io/tutorials/instructor/index.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/index.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index ca889cef..31dec7f6 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -499,7 +499,7 @@ <h3 id="compare-interventions-headingInstructor1">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -522,8 +522,8 @@ <h3 id="compare-interventions-headingInstructor1">
   "url": "https://epiverse-trace.github.io/tutorials/instructor/instructor-notes.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/instructor-notes.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/introduction.html b/instructor/introduction.html
index 3a80b8c9..e56b548d 100644
--- a/instructor/introduction.html
+++ b/instructor/introduction.html
@@ -401,8 +401,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -410,8 +409,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
-<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a></h2>
+<section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a></h2>
 <hr class="half-width"><p>Outbreaks appear with different diseases and in different contexts,
 but what all of them have in common are the key public health questions
 (<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371#d1e605" class="external-link">Cori
@@ -446,8 +444,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="questions-to-think-about" class="callout-inner">
-<h3 class="callout-title">Questions to think about<a class="anchor" aria-label="anchor" href="#questions-to-think-about"></a>
-</h3>
+<h3 class="callout-title">Questions to think about</h3>
 <div class="callout-content">
 <p>Remember your last experience with outbreak data and reflect on these
 questions:</p>
@@ -459,8 +456,7 @@ <h3 class="callout-title">Questions to think about<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
-<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a></h2>
+</section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a></h2>
 <hr class="half-width"><p>The <a href="https://epiforecasts.io/EpiNow2/" class="external-link">EpiNow2</a> package provides a three-step solution to
 <em>quantify the transmissibility</em>. Let’s see how to do this with a
 minimal example. First, load the package:</p>
@@ -563,8 +559,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="is-this-rt-estimation-biased" class="callout-inner">
-<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?<a class="anchor" aria-label="anchor" href="#is-this-rt-estimation-biased"></a>
-</h3>
+<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?</h3>
 <div class="callout-content">
 <p>Review <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008409" class="external-link">Gostic
 et al., 2020</a> about what additional adjustments this estimation
@@ -573,8 +568,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a>
-<a class="anchor" aria-label="anchor" href="#the-problem"></a></h2>
+</section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a></h2>
 <hr class="half-width"><p>However, <em>quantifying the transmissibility</em> during a real-life
 outbreak response is more challenging than this example!</p>
 <p>Usually, we receive outbreak data in non-standard formats, requiring
@@ -595,8 +589,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <li>Compare interventions</li>
 </ul><p>So, all these tasks can be interconnected in a pipeline:</p>
 <figure><img src="https://epiverse-trace.github.io/task_pipeline-minimal.svg" alt="The outbreak analytics pipeline." class="figure mx-auto d-block"><div class="figcaption">The outbreak analytics pipeline.</div>
-</figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
-<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a></h2>
+</figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a></h2>
 <hr class="half-width"><p>Our strategy is gradually incorporating specialised R packages into
 our traditional analysis pipeline. These packages should fill the gaps
 in these epidemiology-specific tasks in response to outbreaks.</p>
@@ -604,8 +597,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 analytics. We support the development of software pieces, make the
 existing ones interoperable for the user experience, and stimulate a
 community of practice.</p>
-<figure><img src="../fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
-<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a></h2>
+<figure><img src="../fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a></h2>
 <hr class="half-width"><p>Our plan for these tutorials is to introduce key solutions from
 packages in all the tasks before and after the <em>Quantify
 transmission</em> task, plus the required theory concepts to interpret
@@ -632,8 +624,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Our vision is to have pipelines of R packages for outbreak
 analytics.</li>
@@ -684,7 +675,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -707,7 +698,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/introduction.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 3fffb03b..cd9152e6 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -485,7 +485,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -508,8 +508,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://epiverse-trace.github.io/tutorials/instructor/key-points.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/key-points.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/model-choices.html b/instructor/model-choices.html
index 3846eb53..31e5bcf8 100644
--- a/instructor/model-choices.html
+++ b/instructor/model-choices.html
@@ -394,8 +394,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="simulating-transmission.html">Simulating
 transmission</a>
@@ -403,8 +402,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </ul></div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>There are existing mathematical models for different infections,
 interventions and transmission patterns which can be used to answer new
 questions. In this tutorial, we will learn how to choose an existing
@@ -427,8 +425,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="choosing-a-model" class="callout-inner">
-<h3 class="callout-title">Choosing a model<a class="anchor" aria-label="anchor" href="#choosing-a-model"></a>
-</h3>
+<h3 class="callout-title">Choosing a model</h3>
 <div class="callout-content">
 <p>When deciding which mathematical model to use, there are a number of
 questions we must consider :</p>
@@ -530,7 +527,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code><a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
+</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code>
 <a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a></h2>
 <hr class="half-width"><p>The R package <code>epidemics</code> contains functions to run
 existing models. For details on the models that are available, see the
@@ -542,8 +539,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-model" class="callout-inner">
-<h3 class="callout-title">What model?<a class="anchor" aria-label="anchor" href="#what-model"></a>
-</h3>
+<h3 class="callout-title">What model?</h3>
 <div class="callout-content">
 <p>You have been asked to explore the variation in numbers of infectious
 individuals in the early stages of an Ebola outbreak.</p>
@@ -567,8 +563,7 @@ <h4 class="accordion-header" id="headingHint1"> HINT </h4>
 <i class="callout-icon" data-feather="check-square"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#checklist1"></a>
-</h3>
+<h3 class="callout-title">Checklist</h3>
 <div class="callout-content">
 <ul><li>What is the infection/disease of interest?</li>
 <li>Do we need a deterministic or stochastic model?</li>
@@ -649,15 +644,13 @@ <h4 id="model_ebola_r"><code>model_ebola_r()</code><a class="anchor" aria-label=
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><div id="running-the-model" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-the-model" class="callout-inner">
-<h3 class="callout-title">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-</h3>
+<h3 class="callout-title">Running the model</h3>
 <div class="callout-content">
 <p>You have been tasked to generate initial trajectories of an Ebola
 outbreak in Guinea. Using <code>model_ebola_r()</code> and the the
@@ -844,8 +837,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Existing mathematical models should be selected according to the
 research question</li>
@@ -894,7 +886,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -917,7 +909,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/model-choices.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/modelling-interventions.html b/instructor/modelling-interventions.html
index e6203b20..fffaf725 100644
--- a/instructor/modelling-interventions.html
+++ b/instructor/modelling-interventions.html
@@ -395,8 +395,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="simulating-transmission.html">Simulating
 transmission</a>
@@ -408,8 +407,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Mathematical models can be used to generate trajectories of disease
 spread under the implementation of interventions at different stages of
 an outbreak. These predictions can be used to make decisions on what
@@ -427,7 +425,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>In this tutorial different types of intervention and how they can be
 modelled are introduced. Learners should be able to understand the
@@ -437,8 +435,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a></h2>
+</section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a></h2>
 <hr class="half-width"><p><a href="reference.html#NPIs">Non-pharmaceutical interventions</a>
 (NPIs) are measures put in place to reduce transmission that do not
 include the administration of drugs or vaccinations. NPIs aim reduce
@@ -543,8 +540,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="effect-of-interventions-on-contacts" class="callout-inner">
-<h3 class="callout-title">Effect of interventions on contacts<a class="anchor" aria-label="anchor" href="#effect-of-interventions-on-contacts"></a>
-</h3>
+<h3 class="callout-title">Effect of interventions on contacts</h3>
 <div class="callout-content">
 <p>In <code>epidemics</code>, the contact matrix is scaled down by
 proportions for the period in which the intervention is in place. To
@@ -764,8 +760,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="intervention-types" class="callout-inner">
-<h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor" href="#intervention-types"></a>
-</h3>
+<h3 class="callout-title">Intervention types</h3>
 <div class="callout-content">
 <p>There are two intervention types for
 <code>model_default_cpp()</code>. Rate interventions on model parameters
@@ -783,8 +778,7 @@ <h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a></h2>
+</section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a></h2>
 <hr class="half-width"><p>Pharmaceutical interventions (PIs) are measures such as vaccination
 and mass treatment programs. In the previous section, we assumed that
 interventions reduced the value of parameter values while the
@@ -849,8 +843,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="compare-interventions" class="callout-inner">
-<h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anchor" href="#compare-interventions"></a>
-</h3>
+<h3 class="callout-title">Compare interventions</h3>
 <div class="callout-content">
 <p>Plot the three interventions vaccination, school closure and mask
 mandate and the baseline simulation on one plot. Which intervention
@@ -863,7 +856,7 @@ <h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anc
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Output </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -903,8 +896,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Different types of intervention can be implemented using mathematical
 modelling. Modelling interventions requires assumptions of which model
 parameters are affected (e.g. contact matrices, transmissibility), by
@@ -918,8 +910,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The effect of NPIs can be modelled as reducing contact rates between
 age groups or reducing the transmissibility of infection</li>
@@ -969,7 +960,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -992,7 +983,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/modelling-interventions.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 5fbb1efa..2669d4c1 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -325,8 +325,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Learner Profiles</h1>
         
-<section><h2 class="section-heading" id="who-are-these-tutorials-for">Who are these tutorials for?<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a>
-<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a></h2>
+<section><h2 class="section-heading" id="who-are-these-tutorials-for">Who are these tutorials for?<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a></h2>
 <hr class="half-width"><p>We thought about Lucia, Patricia, and Vania as learner personas in
 designing the contents of this training:</p>
 <ul><li><p><a href="https://epiverse-trace.github.io/personas/lucia-outbreaks.html" class="external-link">Lucia</a>,
@@ -362,7 +361,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -384,8 +383,8 @@ <h1>Learner Profiles</h1>
   "url": "https://epiverse-trace.github.io/tutorials/instructor/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/profiles.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/quantify-transmissibility.html b/instructor/quantify-transmissibility.html
index e70b4d6a..115cf636 100644
--- a/instructor/quantify-transmissibility.html
+++ b/instructor/quantify-transmissibility.html
@@ -398,8 +398,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -415,7 +414,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 <div id="reminder-the-effective-reproduction-number-r_t" class="callout-inner">
 <h3 class="callout-title">Reminder: the Effective Reproduction Number,
-<span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#reminder-the-effective-reproduction-number-r_t"></a>
+<span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>The <a href="reference.html#basic">basic reproduction number</a>,
@@ -432,8 +431,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Quantifying transmission metrics at the start of an outbreak can give
 important information on the strength of transmission (reproduction
 number) and the speed of transmission (<a href="reference.html#growth">growth rate</a>, doubling/halving time). To
@@ -454,8 +452,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference" class="callout-inner">
-<h3 class="callout-title">Bayesian inference<a class="anchor" aria-label="anchor" href="#bayesian-inference"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference</h3>
 <div class="callout-content">
 <p>The R package <code>EpiNow2</code> uses a <a href="reference.html#bayesian">Bayesian inference</a> framework to
 estimate reproduction numbers and infection times based on reporting
@@ -492,8 +489,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
-<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a></h2>
+</section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="case-data">Case data<a class="anchor" aria-label="anchor" href="#case-data"></a></h3>
 <p>To illustrate the functions of <code>EpiNow2</code> we will use
@@ -577,8 +573,7 @@ <h3 id="delay-distributions">Delay distributions<a class="anchor" aria-label="an
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="delays-and-data" class="callout-inner">
-<h3 class="callout-title">Delays and data<a class="anchor" aria-label="anchor" href="#delays-and-data"></a>
-</h3>
+<h3 class="callout-title">Delays and data</h3>
 <div class="callout-content">
 <p>The number of delays and type of delay is a flexible input that
 depends on the data. The examples below highlight how the delays can be
@@ -628,8 +623,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-a-gamma-distrubution" class="callout-inner">
-<h3 class="callout-title">Why a gamma distrubution?<a class="anchor" aria-label="anchor" href="#why-a-gamma-distrubution"></a>
-</h3>
+<h3 class="callout-title">Why a gamma distrubution?</h3>
 <div class="callout-content">
 <p>The incubation period has to be positive in value. Therefore we must
 specific a distribution in <code>dist_spec</code> which is for positive
@@ -755,8 +749,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
-<a class="anchor" aria-label="anchor" href="#finding-estimates"></a></h2>
+</section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a></h2>
 <hr class="half-width"><p>The function <code>epinow()</code> is a wrapper for the function
 <code>estimate_infections()</code> used to estimate cases by date of
 infection. The generation time distribution and delay distributions must
@@ -781,8 +774,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference-using-stan" class="callout-inner">
-<h3 class="callout-title">Bayesian inference using Stan<a class="anchor" aria-label="anchor" href="#bayesian-inference-using-stan"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference using Stan</h3>
 <div class="callout-content">
 <p>The Bayesian inference is performed using MCMC methods with the
 program <a href="https://mc-stan.org/" class="external-link">Stan</a>. There are a number of
@@ -890,9 +882,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="expected-change-in-daily-cases" class="callout-inner">
-<h3 class="callout-title">
-<code>Expected change in daily cases</code><a class="anchor" aria-label="anchor" href="#expected-change-in-daily-cases"></a>
-</h3>
+<h3 class="callout-title"><code>Expected change in daily cases</code></h3>
 <div class="callout-content">
 <p>A factor describing expected change in daily cases based on the
 posterior probability that <span class="math inline">\(R_t &lt;
@@ -915,8 +905,7 @@ <h3 class="callout-title">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
-<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a></h2>
+</section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a></h2>
 <hr class="half-width"><p>The outbreak data of the start of the COVID-19 pandemic from the
 United Kingdom from the R package <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> includes the
 region in which the cases were recorded. To find regional estimates of
@@ -1044,8 +1033,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">estimates_regional</span><span class="op">$</span><span class="va">summary</span><span class="op">$</span><span class="va">plots</span><span class="op">$</span><span class="va">R</span></span></code></pre>
 </div>
-<figure><img src="../fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+<figure><img src="../fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> can be used to estimate transmission metrics
 from case data at the start of an outbreak. The reliability of these
 estimates depends on the quality of the data and appropriate choice of
@@ -1057,8 +1045,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Transmission metrics can be estimated from case data after
 accounting for delays</li>
@@ -1106,7 +1093,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1129,7 +1116,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/quantify-transmissibility.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/read-delays.html b/instructor/read-delays.html
index 75d4fd0e..e7db49ad 100644
--- a/instructor/read-delays.html
+++ b/instructor/read-delays.html
@@ -408,8 +408,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -418,8 +417,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>The <a href="reference.html#naturalhistory">natural history</a> of an
 infectious disease shows that its development has a regularity from
 stage to stage. The time periods from an infectious disease inform about
@@ -432,8 +430,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="definitions" class="callout-inner">
-<h3 class="callout-title">Definitions<a class="anchor" aria-label="anchor" href="#definitions"></a>
-</h3>
+<h3 class="callout-title">Definitions</h3>
 <div class="callout-content">
 <p>Look at the <a href="reference.html">glossary</a> for the definitions
 of all the time periods of the figure above!</p>
@@ -497,8 +494,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="kw">library</span><span class="op">(</span><span class="va">EpiNow2</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">tidyverse</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
-<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a></h2>
+</section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a></h2>
 <hr class="half-width"><p>The generation time, jointly with the <span class="math inline">\(R\)</span>, can inform about the speed of spread
 and its feasibility of control. Given a <span class="math inline">\(R&gt;1\)</span>, with a shorter generation time,
 cases can appear more quickly.</p>
@@ -535,8 +531,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="from-time-periods-to-probability-distributions." class="callout-inner">
-<h3 class="callout-title">From time periods to probability distributions.<a class="anchor" aria-label="anchor" href="#from-time-periods-to-probability-distributions."></a>
-</h3>
+<h3 class="callout-title">From time periods to probability distributions.</h3>
 <div class="callout-content">
 <p>When we calculate the <em>serial interval</em>, we see that not all
 case pairs have the same time length. We will observe this variability
@@ -610,8 +605,7 @@ <h3 class="callout-title">From time periods to probability distributions.<a clas
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="serial-interval" class="callout-inner">
-<h3 class="callout-title">Serial interval<a class="anchor" aria-label="anchor" href="#serial-interval"></a>
-</h3>
+<h3 class="callout-title">Serial interval</h3>
 <div class="callout-content">
 <p>Assume that COVID-19 and SARS have similar reproduction number values
 and that the serial interval approximates the generation time.</p>
@@ -669,8 +663,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
-<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a></h2>
+</section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a></h2>
 <hr class="half-width"><p>First, let’s assume that the data set <code>example_confirmed</code>
 has COVID-19 observed cases. So, we need to find a reported generation
 time for COVID-19 or any other useful parameter for this aim.</p>
@@ -822,8 +815,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="case-insensitive" class="callout-inner">
-<h3 class="callout-title">CASE-INSENSITIVE<a class="anchor" aria-label="anchor" href="#case-insensitive"></a>
-</h3>
+<h3 class="callout-title">CASE-INSENSITIVE</h3>
 <div class="callout-content">
 <p><code>epidist_db</code> is <a href="https://dillionmegida.com/p/case-sensitivity-vs-case-insensitivity/#case-insensitivity" class="external-link">case-insensitive</a>.
 This means that you can use strings with letters in upper or lower case
@@ -866,8 +858,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-periods" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation periods<a class="anchor" aria-label="anchor" href="#ebolas-incubation-periods"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation periods</h3>
 <div class="callout-content">
 <p>Take 5 minutes:</p>
 <ul><li><p>How many delay distributions are for the Ebola disease?</p></li>
@@ -925,8 +916,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a></h2>
+</section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a></h2>
 <hr class="half-width"><p>The <code>epiparameter::epidist_db()</code> function works as a
 filtering or subset function. Let’s use the <code>author</code> argument
 to filter <code>Hiroshi Nishiura</code> parameters:</p>
@@ -999,8 +989,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-does-single_epidist-works" class="callout-inner">
 <h3 class="callout-title">How does <code>single_epidist</code>
-works?<a class="anchor" aria-label="anchor" href="#how-does-single_epidist-works"></a>
-</h3>
+works?</h3>
 <div class="callout-content">
 <p>Looking at the help documentation for
 <code>?epiparameter::epidist_db()</code>:</p>
@@ -1066,8 +1055,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-period" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation period<a class="anchor" aria-label="anchor" href="#ebolas-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation period</h3>
 <div class="callout-content">
 <p>Take 2 minutes:</p>
 <ul><li>What type of distribution has the incubation period of Ebola with
@@ -1130,8 +1118,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
-<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a></h2>
+</section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a></h2>
 <hr class="half-width"><p>We can get the <code>mean</code> and standard deviation
 (<code>sd</code>) from this <code>&lt;epidist&gt;</code> diving into the
 <code>summary_stats</code> object:</p>
@@ -1153,8 +1140,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-to-get-the-sd-and-other-nested-elements" class="callout-inner">
 <h3 class="callout-title">How to get the <code>sd</code> and other
-nested elements?<a class="anchor" aria-label="anchor" href="#how-to-get-the-sd-and-other-nested-elements"></a>
-</h3>
+nested elements?</h3>
 <div class="callout-content">
 <p>Take 1 minute to:</p>
 <ol style="list-style-type: decimal"><li><p>Get the <code>sd</code> of the epidemiological
@@ -1238,8 +1224,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-severity-parameter" class="callout-inner">
-<h3 class="callout-title">Ebola’s severity parameter<a class="anchor" aria-label="anchor" href="#ebolas-severity-parameter"></a>
-</h3>
+<h3 class="callout-title">Ebola’s severity parameter</h3>
 <div class="callout-content">
 <p>A severity parameter like the duration of hospitalization could add
 to the information needed about the bed capacity in response to an
@@ -1297,8 +1282,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
-<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a></h2>
+</section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a></h2>
 <hr class="half-width"><p>The following output has four entries with different content in the
 <strong>probability distribution</strong>
 (<code>prob_distribution</code>) column:</p>
@@ -1413,8 +1397,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="the-distribution-zoo" class="callout-inner">
-<h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anchor" href="#the-distribution-zoo"></a>
-</h3>
+<h3 class="callout-title">The distribution Zoo</h3>
 <div class="callout-content">
 <p>Explore this shinyapp called <strong>The Distribution
 Zoo</strong>!</p>
@@ -1441,8 +1424,7 @@ <h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anch
 </div>
 </div>
 <!-- A slider, in the context of user interfaces and graphical user interfaces (GUIs), is a graphical control element that allows users to adjust a value by moving a handle along a track or bar. Conceptually, it provides a way to select a numeric value within a specified range by visually sliding or dragging a pointer (the handle) along a continuous axis. -->
-</section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
-<a class="anchor" aria-label="anchor" href="#distribution-functions"></a></h2>
+</section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a></h2>
 <hr class="half-width"><p>In R, all the statistical distributions have functions to access
 the:</p>
 <ul><li>Probability <strong>Density</strong> function (PDF),</li>
@@ -1554,8 +1536,7 @@ <h3 class="accordion-header" id="headingInstructor2">  <div class="note-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="window-for-contact-tracing-and-the-serial-interval" class="callout-inner">
-<h3 class="callout-title">Window for contact tracing and the Serial interval<a class="anchor" aria-label="anchor" href="#window-for-contact-tracing-and-the-serial-interval"></a>
-</h3>
+<h3 class="callout-title">Window for contact tracing and the Serial interval</h3>
 <div class="callout-content">
 <p>The <strong>serial interval</strong> is important in the optimization
 of contact tracing since it provides a time window for the containment
@@ -1641,8 +1622,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a></h2>
+</section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a></h2>
 <hr class="half-width"><p>We are getting closer to the end! <code>EpiNow2::dist_spec()</code>
 still needs a maximum value (<code>max</code>).</p>
 <p>One way to do this is to get the quantile value for the
@@ -1714,8 +1694,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="lenght-of-quarantine-and-incubation-period" class="callout-inner">
-<h3 class="callout-title">Lenght of quarantine and Incubation period<a class="anchor" aria-label="anchor" href="#lenght-of-quarantine-and-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Lenght of quarantine and Incubation period</h3>
 <div class="callout-content">
 <p>The <strong>incubation period</strong> distribution is a useful delay
 to assess the length of active monitoring or quarantine (<a href="https://www.acpjournals.org/doi/10.7326/M20-0504" class="external-link">Lauer et al.,
@@ -1834,7 +1813,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code><a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
+</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code>
 <a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a></h2>
 <hr class="half-width"><p>Now we can plug everything into the <code>EpiNow2::dist_spec()</code>
 function!</p>
@@ -1863,8 +1842,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="warning" class="callout-inner">
-<h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#warning"></a>
-</h3>
+<h3 class="callout-title">Warning</h3>
 <div class="callout-content">
 <p>Using the serial interval instead of the generation time is an
 alternative that can propagate bias in your estimates, even more so in
@@ -1897,8 +1875,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number</h3>
 <div class="callout-content">
 <p>Download and read the <a href="../data/ebola_cases.csv">Ebola
 dataset</a>:</p>
@@ -1987,8 +1964,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
-<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a></h2>
+</section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a></h2>
 <hr class="half-width"><p>Estimating <span class="math inline">\(R_t\)</span> requires data on
 the daily number of new infections. Due to lags in the development of
 detectable viral loads, symptom onset, seeking care, and reporting,
@@ -2017,8 +1993,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="reuse-an-incubation-period-for-covid-19" class="callout-inner">
-<h3 class="callout-title">Reuse an Incubation period for COVID-19<a class="anchor" aria-label="anchor" href="#reuse-an-incubation-period-for-covid-19"></a>
-</h3>
+<h3 class="callout-title">Reuse an Incubation period for COVID-19</h3>
 <div class="callout-content">
 <p>Use <code>{epiparameter}</code> to:</p>
 <ul><li>Find an incubation period for COVID-19.</li>
@@ -2128,8 +2103,7 @@ <h4 class="accordion-header" id="headingSolution12"> How much has it changed? </
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays</h3>
 <div class="callout-content">
 <p>Using the same <a href="../data/ebola_cases.csv">Ebola dataset</a>:</p>
 <ul><li>Reuse one additional epidemiological parameter for the
@@ -2231,8 +2205,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="extract-parameters" class="callout-inner">
-<h3 class="callout-title">Extract parameters<a class="anchor" aria-label="anchor" href="#extract-parameters"></a>
-</h3>
+<h3 class="callout-title">Extract parameters</h3>
 <div class="callout-content">
 <p>Use the <code>influenza_england_1978_school</code> from the
 <a href="https://github.com/reconhub/outbreaks" class="external-link">outbreaks</a> package to calculate the effective reproduction
@@ -2332,8 +2305,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
-<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a></h2>
+</section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a></h2>
 <hr class="half-width"><p>In the early stage of an outbreak, we can rely on reusing parameters
 for known pathogens to unknown ones, like for the <a href="https://en.wikipedia.org/wiki/Disease_X" class="external-link">Disease X</a>, a pathogen
 currently unknown to cause human disease and potentially cause a serious
@@ -2378,8 +2350,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="heart"></i>
 </div>
 <div id="how-to-estimate-delay-distributions-for-disease-x" class="callout-inner">
-<h3 class="callout-title">How to estimate delay distributions for Disease X?<a class="anchor" aria-label="anchor" href="#how-to-estimate-delay-distributions-for-disease-x"></a>
-</h3>
+<h3 class="callout-title">How to estimate delay distributions for Disease X?</h3>
 <div class="callout-content">
 <p>Refer to this excellent tutorial on estimating the serial interval
 and incubation period of Disease X accounting for <em>censoring</em>
@@ -2436,8 +2407,7 @@ <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-type-of-transmission" class="callout-inner">
-<h3 class="callout-title">What type of transmission?<a class="anchor" aria-label="anchor" href="#what-type-of-transmission"></a>
-</h3>
+<h3 class="callout-title">What type of transmission?</h3>
 <div class="callout-content">
 <p>Compare the serial interval and incubation period of Influenza and
 MERS:</p>
@@ -2565,8 +2535,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Use <code>{epiparameter}</code> to access the systematic review
 catalogue of epidemiological delay distributions.</li>
@@ -2621,7 +2590,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -2644,7 +2613,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/read-delays.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index e375e61d..7187594b 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -353,8 +353,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 
         
 
-<section><h2 class="section-heading" id="a">A<a class="anchor" aria-label="anchor" href="#a"></a>
-<a class="anchor" aria-label="anchor" href="#a"></a></h2>
+<section><h2 class="section-heading" id="a">A<a class="anchor" aria-label="anchor" href="#a"></a></h2>
 <hr class="half-width"><dl><dt><span id="airborne">Airborne transmission</span></dt>
 <dd>
 Individuals become infected via contact with infectious particles in the
@@ -362,8 +361,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 discuss about <a href="https://www.ncbi.nlm.nih.gov/books/NBK531468/" class="external-link">factors and
 management procedures</a> of airborne transmission.
 </dd>
-</dl></section><section><h2 class="section-heading" id="b">B<a class="anchor" aria-label="anchor" href="#b"></a>
-<a class="anchor" aria-label="anchor" href="#b"></a></h2>
+</dl></section><section><h2 class="section-heading" id="b">B<a class="anchor" aria-label="anchor" href="#b"></a></h2>
 <hr class="half-width"><dl><dt><span id="basic">Basic reproduction number</span></dt>
 <dd>
 A measure of the transmissibility of a disease. Defined as the average
@@ -377,8 +375,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 observed data. <a href="https://en.wikipedia.org/wiki/Bayesian_inference" class="external-link">More information
 on Bayesian inference</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="c">C<a class="anchor" aria-label="anchor" href="#c"></a>
-<a class="anchor" aria-label="anchor" href="#c"></a></h2>
+</dl></section><section><h2 class="section-heading" id="c">C<a class="anchor" aria-label="anchor" href="#c"></a></h2>
 <hr class="half-width"><dl><dt><span id="contact">Contact matrix</span></dt>
 <dd>
 The contact matrix is a square matrix consisting of rows/columns equal
@@ -405,8 +402,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 can propagate bias to the estimation of the <a href="#incubation">incubation period</a> and generation time (<a href="https://www.nature.com/articles/s41467-022-35496-8/figures/2" class="external-link">Chen
 et al., 2022</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="d">D<a class="anchor" aria-label="anchor" href="#d"></a>
-<a class="anchor" aria-label="anchor" href="#d"></a></h2>
+</dl></section><section><h2 class="section-heading" id="d">D<a class="anchor" aria-label="anchor" href="#d"></a></h2>
 <hr class="half-width"><dl><dt><span id="deterministic">Deterministic model</span></dt>
 <dd>
 Models that will always have the same trajectory for given initial
@@ -420,8 +416,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 transmitted infections as they require close contact with infected
 individuals for successful transmission.
 </dd>
-</dl></section><section><h2 class="section-heading" id="e">E<a class="anchor" aria-label="anchor" href="#e"></a>
-<a class="anchor" aria-label="anchor" href="#e"></a></h2>
+</dl></section><section><h2 class="section-heading" id="e">E<a class="anchor" aria-label="anchor" href="#e"></a></h2>
 <hr class="half-width"><dl><dt><span id="effectiverepro">Effective reproduction number</span></dt>
 <dd>
 The time-varying or effective reproduction number (<span class="math inline">\(Rt\)</span>) is similar to the <a href="#basic">Basic reproductive number</a> (<span class="math inline">\(R0\)</span>), but <span class="math inline">\(Rt\)</span> measures the number of persons
@@ -429,8 +424,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 already been infected. Read more about the <a href="https://wwwnc.cdc.gov/eid/article/29/8/22-1445_article" class="external-link">etymology
 of Reproduction number by Sharma et al, 2023</a>.
 </dd>
-</dl><!-- ## F --></section><section><h2 class="section-heading" id="g">G<a class="anchor" aria-label="anchor" href="#g"></a>
-<a class="anchor" aria-label="anchor" href="#g"></a></h2>
+</dl><!-- ## F --></section><section><h2 class="section-heading" id="g">G<a class="anchor" aria-label="anchor" href="#g"></a></h2>
 <hr class="half-width"><dl><dt><span id="generationtime">Generation time</span></dt>
 <dd>
 Time between the onset of infectiousness of an index case and its
@@ -446,8 +440,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 of transmission, see <a href="https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.1556" class="external-link">Dushoff
 &amp; Park, 2021</a>.
 </dd>
-</dl><!-- ## H --></section><section><h2 class="section-heading" id="i">I<a class="anchor" aria-label="anchor" href="#i"></a>
-<a class="anchor" aria-label="anchor" href="#i"></a></h2>
+</dl><!-- ## H --></section><section><h2 class="section-heading" id="i">I<a class="anchor" aria-label="anchor" href="#i"></a></h2>
 <hr class="half-width"><dl><dt><span id="incubation">Incubation period</span></dt>
 <dd>
 The time between becoming infected and the onset of symptoms. <a href="https://en.wikipedia.org/wiki/Latent_period_(epidemiology)#Incubation_period" class="external-link">More
@@ -483,8 +476,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 2022</a> and <a href="https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(22)00226-0/fulltext" class="external-link">Hakki
 et al, 2022</a>](fig/infectiousness-covid19.jpg)).
 </dd>
-</dl><!-- ## J --><!-- ## K --></section><section><h2 class="section-heading" id="l">L<a class="anchor" aria-label="anchor" href="#l"></a>
-<a class="anchor" aria-label="anchor" href="#l"></a></h2>
+</dl><!-- ## J --><!-- ## K --></section><section><h2 class="section-heading" id="l">L<a class="anchor" aria-label="anchor" href="#l"></a></h2>
 <hr class="half-width"><dl><dt><span id="latent">Latent period</span></dt>
 <dd>
 The time between becoming infected and the onset of infectiousness. This
@@ -492,8 +484,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 shown in Figure 4 from (<a href="https://www.sciencedirect.com/science/article/pii/S2468042721000038#fig4" class="external-link">Xiang
 et al, 2021</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="m">M<a class="anchor" aria-label="anchor" href="#m"></a>
-<a class="anchor" aria-label="anchor" href="#m"></a></h2>
+</dl></section><section><h2 class="section-heading" id="m">M<a class="anchor" aria-label="anchor" href="#m"></a></h2>
 <hr class="half-width"><dl><dt><span id="parsode">Model parameters (ODEs)</span></dt>
 <dd>
 The model parameters are used in <a href="#ordinary">ordinary
@@ -501,8 +492,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 states. For example, a transmission rate <span class="math inline">\(\beta\)</span> is a model parameter that can be
 used to describe the flow between susceptible and infectious states.
 </dd>
-</dl></section><section><h2 class="section-heading" id="n">N<a class="anchor" aria-label="anchor" href="#n"></a>
-<a class="anchor" aria-label="anchor" href="#n"></a></h2>
+</dl></section><section><h2 class="section-heading" id="n">N<a class="anchor" aria-label="anchor" href="#n"></a></h2>
 <hr class="half-width"><dl><dt><span id="NPIs">Non-pharmaceutical interventions</span></dt>
 <dd>
 Non-pharmaceutical interventions (NPIs) are measures put in place to
@@ -510,8 +500,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 vaccinations. <a href="https://www.gov.uk/government/publications/technical-report-on-the-covid-19-pandemic-in-the-uk/chapter-8-non-pharmaceutical-interventions" class="external-link">More
 information on NPIs</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="o">O<a class="anchor" aria-label="anchor" href="#o"></a>
-<a class="anchor" aria-label="anchor" href="#o"></a></h2>
+</dl></section><section><h2 class="section-heading" id="o">O<a class="anchor" aria-label="anchor" href="#o"></a></h2>
 <hr class="half-width"><dl><dt><span id="ordinary">Ordinary differential equations</span></dt>
 <dd>
 Ordinary differential equations (ODEs) can be used to represent the rate
@@ -528,8 +517,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 the various coupling factors. (<a href="https://www.sciencedirect.com/science/article/pii/S2468042721000038" class="external-link">Xiang
 et al, 2021</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="o-1">O<a class="anchor" aria-label="anchor" href="#o-1"></a>
-<a class="anchor" aria-label="anchor" href="#o-1"></a></h2>
+</dl></section><section><h2 class="section-heading" id="o-1">O<a class="anchor" aria-label="anchor" href="#o-1"></a></h2>
 <hr class="half-width"><dl><dt><span id="offspringdist">Offspring distribution</span></dt>
 <dd>
 Distribution of the number of secondary cases caused by a particular
@@ -537,8 +525,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 2005</a>, <a href="https://wellcomeopenresearch.org/articles/5-67/v3" class="external-link">Endo et al.,
 2020</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="p">P<a class="anchor" aria-label="anchor" href="#p"></a>
-<a class="anchor" aria-label="anchor" href="#p"></a></h2>
+</dl></section><section><h2 class="section-heading" id="p">P<a class="anchor" aria-label="anchor" href="#p"></a></h2>
 <hr class="half-width"><dl><dt><span id="phasebias">(Dynamical or Epidemic) Phase bias</span></dt>
 <dd>
 Accounts for population susceptibility at the times transmission pairs
@@ -550,8 +537,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 and longer delay intervals, respectively. (<a href="https://github.com/parksw3/epidist-paper" class="external-link">Park et al., in
 progress</a>)
 </dd>
-</dl><!-- ## Q --></section><section><h2 class="section-heading" id="r">R<a class="anchor" aria-label="anchor" href="#r"></a>
-<a class="anchor" aria-label="anchor" href="#r"></a></h2>
+</dl><!-- ## Q --></section><section><h2 class="section-heading" id="r">R<a class="anchor" aria-label="anchor" href="#r"></a></h2>
 <hr class="half-width"><dl><dt><span id="reportingdelay">Reporting delay</span></dt>
 <dd>
 Delay or lag between the time an event occurs (e.g. symptom onset) and
@@ -560,8 +546,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 up-to-date reported aggregated case counts (<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371" class="external-link">Cori
 et al. 2017</a>).
 </dd>
-</dl></section><section><h2 class="section-heading" id="s">S<a class="anchor" aria-label="anchor" href="#s"></a>
-<a class="anchor" aria-label="anchor" href="#s"></a></h2>
+</dl></section><section><h2 class="section-heading" id="s">S<a class="anchor" aria-label="anchor" href="#s"></a></h2>
 <hr class="half-width"><dl><dt><span id="state">State variables</span></dt>
 <dd>
 The state variables in a model represented by <a href="#ordinary">ordinary differential equations</a> are the disease
@@ -589,8 +574,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 Examples include stochastic differential equations and branching process
 models. For more detail see <a href="https://doi.org/10.1016/j.idm.2017.03.001" class="external-link">Allen (2017)</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="t">T<a class="anchor" aria-label="anchor" href="#t"></a>
-<a class="anchor" aria-label="anchor" href="#t"></a></h2>
+</dl></section><section><h2 class="section-heading" id="t">T<a class="anchor" aria-label="anchor" href="#t"></a></h2>
 <hr class="half-width"><dl><dt><span id="truncation">(Right) Truncation</span></dt>
 <dd>
 Type of sampling bias related to the data collection process. It arises
@@ -599,8 +583,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 can lead to underestimation of the mean delay (<a href="https://github.com/parksw3/epidist-paper" class="external-link">Park et al., in
 progress</a>).
 </dd>
-</dl><!-- ## U --></section><section><h2 class="section-heading" id="v">V<a class="anchor" aria-label="anchor" href="#v"></a>
-<a class="anchor" aria-label="anchor" href="#v"></a></h2>
+</dl><!-- ## U --></section><section><h2 class="section-heading" id="v">V<a class="anchor" aria-label="anchor" href="#v"></a></h2>
 <hr class="half-width"><dl><dt><span id="vectorborne">Vector-borne transmission</span></dt>
 <dd>
 Vector-borne transmission means an infection can be passed from a vector
@@ -654,7 +637,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -677,7 +660,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/reference.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/simulating-transmission.html b/instructor/simulating-transmission.html
index 1f733f55..df7827a8 100644
--- a/instructor/simulating-transmission.html
+++ b/instructor/simulating-transmission.html
@@ -404,8 +404,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -417,8 +416,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Mathematical models are useful tools for generating future
 trajectories of disease spread. In this tutorial, we will use the R
 package <code>{epidemics}</code> to generate disease trajectories of an
@@ -438,8 +436,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
-<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a></h2>
+</section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a></h2>
 <hr class="half-width"><p>To generate predictions of infectious disease trajectories, we must
 first select a mathematical model to use. There is a library of models
 to choose from in <code>epidemics</code>. Models in
@@ -462,8 +459,7 @@ <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="model-parameters-rates" class="callout-inner">
-<h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="anchor" href="#model-parameters-rates"></a>
-</h3>
+<h3 class="callout-title">Model parameters : rates</h3>
 <div class="callout-content">
 <p>In ODE models, model parameters are often (but not always) specified
 as rates. The rate at which an event occurs is the inverse of the
@@ -509,8 +505,7 @@ <h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="exposed-infected-infectious" class="callout-inner">
-<h3 class="callout-title">Exposed, infected, infectious<a class="anchor" aria-label="anchor" href="#exposed-infected-infectious"></a>
-</h3>
+<h3 class="callout-title">Exposed, infected, infectious</h3>
 <div class="callout-content">
 <p>Confusion sometimes arises when referring to the terms ‘exposed’,
 ‘infected’ and ‘infectious’ in mathematical modelling. Infection occurs
@@ -544,8 +539,7 @@ <h3 id="contact-matrix">1. Contact matrix<a class="anchor" aria-label="anchor" h
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="load-contact-and-population-data" class="callout-inner">
-<h3 class="callout-title">Load contact and population data<a class="anchor" aria-label="anchor" href="#load-contact-and-population-data"></a>
-</h3>
+<h3 class="callout-title">Load contact and population data</h3>
 <div class="callout-content">
 <p>Using the R package <code>socialmixr</code>, run the following lines
 of R code to obtain the contact matrix for the United Kingdom for the
@@ -599,8 +593,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-would-a-contact-matrix-be-non-symmetric" class="callout-inner">
-<h3 class="callout-title">Why would a contact matrix be non-symmetric?<a class="anchor" aria-label="anchor" href="#why-would-a-contact-matrix-be-non-symmetric"></a>
-</h3>
+<h3 class="callout-title">Why would a contact matrix be non-symmetric?</h3>
 <div class="callout-content">
 <p>One of the arguments of the function <code>contact_matrix()</code> is
 <code>symmetric=TRUE</code>. This means that the total number of
@@ -738,7 +731,7 @@ <h3 id="model-parameters">4. Model parameters<a class="anchor" aria-label="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-basic-reproduction-number-r_0" class="callout-inner">
-<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span><a class="anchor" aria-label="anchor" href="#the-basic-reproduction-number-r_0"></a>
+<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span>
 </h3>
 <div class="callout-content">
 <p>The basic reproduction number, <span class="math inline">\(R_0\)</span>, for the SEIR model is:</p>
@@ -750,15 +743,13 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-<a class="anchor" aria-label="anchor" href="#running-the-model"></a></h2>
+</section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a></h2>
 <hr class="half-width"><div id="running-solving-the-model" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="running-solving-the-model" class="callout-inner">
-<h3 class="callout-title">Running (solving) the model<a class="anchor" aria-label="anchor" href="#running-solving-the-model"></a>
-</h3>
+<h3 class="callout-title">Running (solving) the model</h3>
 <div class="callout-content">
 <p>For models that are described by ODEs, running the model actually
 means to solve the system of ODEs. ODEs describe the rate of change in
@@ -859,8 +850,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="time-increments" class="callout-inner">
-<h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" href="#time-increments"></a>
-</h3>
+<h3 class="callout-title">Time increments</h3>
 <div class="callout-content">
 <p>Note that there is a default argument of <code>increment = 1</code>.
 This relates to the time step of the ODE solver. When the parameters are
@@ -875,8 +865,7 @@ <h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
-<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a></h2>
+</section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a></h2>
 <hr class="half-width"><p>As the epidemic model is <a href="reference.html#deterministic">deterministic</a>, we have one
 trajectory for our given parameter values. In practice, we have
 uncertainty in the value of our parameters. To account for this, we must
@@ -960,8 +949,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 parameter value changes; and the purpose of the modelling task. See <a href="https://doi.org/10.1016%2Fj.epidem.2021.100520" class="external-link">McCabe et
 al. 2021</a> to learn about different types of uncertainty in infectious
 disease modelling.</p>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>In this tutorial, we have learnt how to simulate disease spread using
 a mathematical model. Once a model has been chosen, the parameters and
 other inputs must be specified in the correct way to perform model
@@ -972,8 +960,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Disease trajectories can be generated using the R package
 <code>epidemics</code>
@@ -1023,7 +1010,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1046,7 +1033,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/instructor/simulating-transmission.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/introduction.html b/introduction.html
index 5d9d8468..6e234e08 100644
--- a/introduction.html
+++ b/introduction.html
@@ -399,8 +399,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -408,8 +407,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a>
-<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a></h2>
+<section><h2 class="section-heading" id="why-to-use-r-packages-for-outbreak-analytics">Why to use R packages for Outbreak analytics?<a class="anchor" aria-label="anchor" href="#why-to-use-r-packages-for-outbreak-analytics"></a></h2>
 <hr class="half-width"><p>Outbreaks appear with different diseases and in different contexts,
 but what all of them have in common are the key public health questions
 (<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371#d1e605" class="external-link">Cori
@@ -444,8 +442,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="questions-to-think-about" class="callout-inner">
-<h3 class="callout-title">Questions to think about<a class="anchor" aria-label="anchor" href="#questions-to-think-about"></a>
-</h3>
+<h3 class="callout-title">Questions to think about</h3>
 <div class="callout-content">
 <p>Remember your last experience with outbreak data and reflect on these
 questions:</p>
@@ -457,8 +454,7 @@ <h3 class="callout-title">Questions to think about<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a>
-<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a></h2>
+</section><section><h2 class="section-heading" id="example-quantify-transmission">Example: Quantify transmission<a class="anchor" aria-label="anchor" href="#example-quantify-transmission"></a></h2>
 <hr class="half-width"><p>The <a href="https://epiforecasts.io/EpiNow2/" class="external-link">EpiNow2</a> package provides a three-step solution to
 <em>quantify the transmissibility</em>. Let’s see how to do this with a
 minimal example. First, load the package:</p>
@@ -561,8 +557,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="is-this-rt-estimation-biased" class="callout-inner">
-<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?<a class="anchor" aria-label="anchor" href="#is-this-rt-estimation-biased"></a>
-</h3>
+<h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estimation biased?</h3>
 <div class="callout-content">
 <p>Review <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008409" class="external-link">Gostic
 et al., 2020</a> about what additional adjustments this estimation
@@ -571,8 +566,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a>
-<a class="anchor" aria-label="anchor" href="#the-problem"></a></h2>
+</section><section><h2 class="section-heading" id="the-problem">The problem!<a class="anchor" aria-label="anchor" href="#the-problem"></a></h2>
 <hr class="half-width"><p>However, <em>quantifying the transmissibility</em> during a real-life
 outbreak response is more challenging than this example!</p>
 <p>Usually, we receive outbreak data in non-standard formats, requiring
@@ -593,8 +587,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <li>Compare interventions</li>
 </ul><p>So, all these tasks can be interconnected in a pipeline:</p>
 <figure><img src="https://epiverse-trace.github.io/task_pipeline-minimal.svg" alt="The outbreak analytics pipeline." class="figure mx-auto d-block"><div class="figcaption">The outbreak analytics pipeline.</div>
-</figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a>
-<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a></h2>
+</figure></section><section><h2 class="section-heading" id="what-can-we-do">What can we do?<a class="anchor" aria-label="anchor" href="#what-can-we-do"></a></h2>
 <hr class="half-width"><p>Our strategy is gradually incorporating specialised R packages into
 our traditional analysis pipeline. These packages should fill the gaps
 in these epidemiology-specific tasks in response to outbreaks.</p>
@@ -602,8 +595,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 analytics. We support the development of software pieces, make the
 existing ones interoperable for the user experience, and stimulate a
 community of practice.</p>
-<figure><img src="fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a>
-<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a></h2>
+<figure><img src="fig/pkgs-hexlogos.png" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="how-can-i-start">How can I start?<a class="anchor" aria-label="anchor" href="#how-can-i-start"></a></h2>
 <hr class="half-width"><p>Our plan for these tutorials is to introduce key solutions from
 packages in all the tasks before and after the <em>Quantify
 transmission</em> task, plus the required theory concepts to interpret
@@ -630,8 +622,7 @@ <h3 class="callout-title">Is this <span class="math inline">\(Rt\)</span> estima
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Our vision is to have pipelines of R packages for outbreak
 analytics.</li>
@@ -682,7 +673,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -705,7 +696,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/introduction.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 42af2da3..a8905333 100644
--- a/key-points.html
+++ b/key-points.html
@@ -483,7 +483,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -506,8 +506,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://epiverse-trace.github.io/tutorials/key-points.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/key-points.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/model-choices.html b/model-choices.html
index b36637e1..a28aecc0 100644
--- a/model-choices.html
+++ b/model-choices.html
@@ -392,8 +392,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="simulating-transmission.html">Simulating
 transmission</a>
@@ -401,8 +400,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </ul></div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>There are existing mathematical models for different infections,
 interventions and transmission patterns which can be used to answer new
 questions. In this tutorial, we will learn how to choose an existing
@@ -413,8 +411,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="choosing-a-model" class="callout-inner">
-<h3 class="callout-title">Choosing a model<a class="anchor" aria-label="anchor" href="#choosing-a-model"></a>
-</h3>
+<h3 class="callout-title">Choosing a model</h3>
 <div class="callout-content">
 <p>When deciding which mathematical model to use, there are a number of
 questions we must consider :</p>
@@ -516,7 +513,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code><a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a>
+</section><section><h2 class="section-heading" id="available-models-in-epidemics">Available models in <code>epidemics</code>
 <a class="anchor" aria-label="anchor" href="#available-models-in-epidemics"></a></h2>
 <hr class="half-width"><p>The R package <code>epidemics</code> contains functions to run
 existing models. For details on the models that are available, see the
@@ -528,8 +525,7 @@ <h4 class="accordion-header" id="headingSolution6"> Will any interventions be mo
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-model" class="callout-inner">
-<h3 class="callout-title">What model?<a class="anchor" aria-label="anchor" href="#what-model"></a>
-</h3>
+<h3 class="callout-title">What model?</h3>
 <div class="callout-content">
 <p>You have been asked to explore the variation in numbers of infectious
 individuals in the early stages of an Ebola outbreak.</p>
@@ -553,8 +549,7 @@ <h4 class="accordion-header" id="headingHint1"> HINT </h4>
 <i class="callout-icon" data-feather="check-square"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Checklist<a class="anchor" aria-label="anchor" href="#checklist1"></a>
-</h3>
+<h3 class="callout-title">Checklist</h3>
 <div class="callout-content">
 <ul><li>What is the infection/disease of interest?</li>
 <li>Do we need a deterministic or stochastic model?</li>
@@ -635,15 +630,13 @@ <h4 id="model_ebola_r"><code>model_ebola_r()</code><a class="anchor" aria-label=
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a>
-<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
+</section><section><h2 class="section-heading" id="challenge-ebola-outbreak-analysis">Challenge : Ebola outbreak analysis<a class="anchor" aria-label="anchor" href="#challenge-ebola-outbreak-analysis"></a></h2>
 <hr class="half-width"><div id="running-the-model" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="running-the-model" class="callout-inner">
-<h3 class="callout-title">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-</h3>
+<h3 class="callout-title">Running the model</h3>
 <div class="callout-content">
 <p>You have been tasked to generate initial trajectories of an Ebola
 outbreak in Guinea. Using <code>model_ebola_r()</code> and the the
@@ -830,8 +823,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Existing mathematical models should be selected according to the
 research question</li>
@@ -880,7 +872,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -903,7 +895,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/model-choices.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/modelling-interventions.html b/modelling-interventions.html
index c1d5c520..61342a1d 100644
--- a/modelling-interventions.html
+++ b/modelling-interventions.html
@@ -393,8 +393,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>Complete tutorial <a href="simulating-transmission.html">Simulating
 transmission</a>
@@ -406,8 +405,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Mathematical models can be used to generate trajectories of disease
 spread under the implementation of interventions at different stages of
 an outbreak. These predictions can be used to make decisions on what
@@ -421,8 +419,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 this tutorial, we will introduce how to include three different
 interventions in model of COVID-19 transmission.</p>
 
-</section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a></h2>
+</section><section><h2 class="section-heading" id="non-pharmaceutical-interventions">Non-pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#non-pharmaceutical-interventions"></a></h2>
 <hr class="half-width"><p><a href="reference.html#NPIs">Non-pharmaceutical interventions</a>
 (NPIs) are measures put in place to reduce transmission that do not
 include the administration of drugs or vaccinations. NPIs aim reduce
@@ -527,8 +524,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="effect-of-interventions-on-contacts" class="callout-inner">
-<h3 class="callout-title">Effect of interventions on contacts<a class="anchor" aria-label="anchor" href="#effect-of-interventions-on-contacts"></a>
-</h3>
+<h3 class="callout-title">Effect of interventions on contacts</h3>
 <div class="callout-content">
 <p>In <code>epidemics</code>, the contact matrix is scaled down by
 proportions for the period in which the intervention is in place. To
@@ -748,8 +744,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="intervention-types" class="callout-inner">
-<h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor" href="#intervention-types"></a>
-</h3>
+<h3 class="callout-title">Intervention types</h3>
 <div class="callout-content">
 <p>There are two intervention types for
 <code>model_default_cpp()</code>. Rate interventions on model parameters
@@ -767,8 +762,7 @@ <h3 class="callout-title">Intervention types<a class="anchor" aria-label="anchor
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a>
-<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a></h2>
+</section><section><h2 class="section-heading" id="pharmaceutical-interventions">Pharmaceutical interventions<a class="anchor" aria-label="anchor" href="#pharmaceutical-interventions"></a></h2>
 <hr class="half-width"><p>Pharmaceutical interventions (PIs) are measures such as vaccination
 and mass treatment programs. In the previous section, we assumed that
 interventions reduced the value of parameter values while the
@@ -833,8 +827,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="compare-interventions" class="callout-inner">
-<h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anchor" href="#compare-interventions"></a>
-</h3>
+<h3 class="callout-title">Compare interventions</h3>
 <div class="callout-content">
 <p>Plot the three interventions vaccination, school closure and mask
 mandate and the baseline simulation on one plot. Which intervention
@@ -847,7 +840,7 @@ <h3 class="callout-title">Compare interventions<a class="anchor" aria-label="anc
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Output </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -887,8 +880,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Different types of intervention can be implemented using mathematical
 modelling. Modelling interventions requires assumptions of which model
 parameters are affected (e.g. contact matrices, transmissibility), by
@@ -902,8 +894,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The effect of NPIs can be modelled as reducing contact rates between
 age groups or reducing the transmissibility of infection</li>
@@ -953,7 +944,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -976,7 +967,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/modelling-interventions.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 67f65cf4..b99b5bba 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-27T00:40Z
+last_built: 2024-09-03T00:40Z
diff --git a/profiles.html b/profiles.html
index ed3ddf0a..79742e91 100644
--- a/profiles.html
+++ b/profiles.html
@@ -325,8 +325,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Learner Profiles</h1>
         
-<section><h2 class="section-heading" id="who-are-these-tutorials-for">Who are these tutorials for?<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a>
-<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a></h2>
+<section><h2 class="section-heading" id="who-are-these-tutorials-for">Who are these tutorials for?<a class="anchor" aria-label="anchor" href="#who-are-these-tutorials-for"></a></h2>
 <hr class="half-width"><p>We thought about Lucia, Patricia, and Vania as learner personas in
 designing the contents of this training:</p>
 <ul><li><p><a href="https://epiverse-trace.github.io/personas/lucia-outbreaks.html" class="external-link">Lucia</a>,
@@ -362,7 +361,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -384,8 +383,8 @@ <h1>Learner Profiles</h1>
   "url": "https://epiverse-trace.github.io/tutorials/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials/profiles.html",
   "dateCreated": "2024-02-06",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/quantify-transmissibility.html b/quantify-transmissibility.html
index 0b2c814c..d7bb66aa 100644
--- a/quantify-transmissibility.html
+++ b/quantify-transmissibility.html
@@ -396,8 +396,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -413,7 +412,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 <div id="reminder-the-effective-reproduction-number-r_t" class="callout-inner">
 <h3 class="callout-title">Reminder: the Effective Reproduction Number,
-<span class="math inline">\(R_t\)</span><a class="anchor" aria-label="anchor" href="#reminder-the-effective-reproduction-number-r_t"></a>
+<span class="math inline">\(R_t\)</span>
 </h3>
 <div class="callout-content">
 <p>The <a href="reference.html#basic">basic reproduction number</a>,
@@ -430,8 +429,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Quantifying transmission metrics at the start of an outbreak can give
 important information on the strength of transmission (reproduction
 number) and the speed of transmission (<a href="reference.html#growth">growth rate</a>, doubling/halving time). To
@@ -452,8 +450,7 @@ <h3 class="callout-title">Reminder: the Effective Reproduction Number,
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference" class="callout-inner">
-<h3 class="callout-title">Bayesian inference<a class="anchor" aria-label="anchor" href="#bayesian-inference"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference</h3>
 <div class="callout-content">
 <p>The R package <code>EpiNow2</code> uses a <a href="reference.html#bayesian">Bayesian inference</a> framework to
 estimate reproduction numbers and infection times based on reporting
@@ -476,8 +473,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="va">EpiNow2</span><span class="op">)</span></span></code></pre>
 </div>
 
-</section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a>
-<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a></h2>
+</section><section><h2 class="section-heading" id="delay-distributions-and-case-data">Delay distributions and case data<a class="anchor" aria-label="anchor" href="#delay-distributions-and-case-data"></a></h2>
 <hr class="half-width"><div class="section level3">
 <h3 id="case-data">Case data<a class="anchor" aria-label="anchor" href="#case-data"></a></h3>
 <p>To illustrate the functions of <code>EpiNow2</code> we will use
@@ -561,8 +557,7 @@ <h3 id="delay-distributions">Delay distributions<a class="anchor" aria-label="an
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="delays-and-data" class="callout-inner">
-<h3 class="callout-title">Delays and data<a class="anchor" aria-label="anchor" href="#delays-and-data"></a>
-</h3>
+<h3 class="callout-title">Delays and data</h3>
 <div class="callout-content">
 <p>The number of delays and type of delay is a flexible input that
 depends on the data. The examples below highlight how the delays can be
@@ -612,8 +607,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-a-gamma-distrubution" class="callout-inner">
-<h3 class="callout-title">Why a gamma distrubution?<a class="anchor" aria-label="anchor" href="#why-a-gamma-distrubution"></a>
-</h3>
+<h3 class="callout-title">Why a gamma distrubution?</h3>
 <div class="callout-content">
 <p>The incubation period has to be positive in value. Therefore we must
 specific a distribution in <code>dist_spec</code> which is for positive
@@ -739,8 +733,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a>
-<a class="anchor" aria-label="anchor" href="#finding-estimates"></a></h2>
+</section><section><h2 class="section-heading" id="finding-estimates">Finding estimates<a class="anchor" aria-label="anchor" href="#finding-estimates"></a></h2>
 <hr class="half-width"><p>The function <code>epinow()</code> is a wrapper for the function
 <code>estimate_infections()</code> used to estimate cases by date of
 infection. The generation time distribution and delay distributions must
@@ -765,8 +758,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="bayesian-inference-using-stan" class="callout-inner">
-<h3 class="callout-title">Bayesian inference using Stan<a class="anchor" aria-label="anchor" href="#bayesian-inference-using-stan"></a>
-</h3>
+<h3 class="callout-title">Bayesian inference using Stan</h3>
 <div class="callout-content">
 <p>The Bayesian inference is performed using MCMC methods with the
 program <a href="https://mc-stan.org/" class="external-link">Stan</a>. There are a number of
@@ -874,9 +866,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="expected-change-in-daily-cases" class="callout-inner">
-<h3 class="callout-title">
-<code>Expected change in daily cases</code><a class="anchor" aria-label="anchor" href="#expected-change-in-daily-cases"></a>
-</h3>
+<h3 class="callout-title"><code>Expected change in daily cases</code></h3>
 <div class="callout-content">
 <p>A factor describing expected change in daily cases based on the
 posterior probability that <span class="math inline">\(R_t &lt;
@@ -899,8 +889,7 @@ <h3 class="callout-title">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a>
-<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a></h2>
+</section><section><h2 class="section-heading" id="quantify-geographical-heterogeneity">Quantify geographical heterogeneity<a class="anchor" aria-label="anchor" href="#quantify-geographical-heterogeneity"></a></h2>
 <hr class="half-width"><p>The outbreak data of the start of the COVID-19 pandemic from the
 United Kingdom from the R package <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> includes the
 region in which the cases were recorded. To find regional estimates of
@@ -1028,8 +1017,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">estimates_regional</span><span class="op">$</span><span class="va">summary</span><span class="op">$</span><span class="va">plots</span><span class="op">$</span><span class="va">R</span></span></code></pre>
 </div>
-<figure><img src="fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+<figure><img src="fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p><code>EpiNow2</code> can be used to estimate transmission metrics
 from case data at the start of an outbreak. The reliability of these
 estimates depends on the quality of the data and appropriate choice of
@@ -1041,8 +1029,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Transmission metrics can be estimated from case data after
 accounting for delays</li>
@@ -1090,7 +1077,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1113,7 +1100,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/quantify-transmissibility.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/read-delays.html b/read-delays.html
index 81559ee5..3514d665 100644
--- a/read-delays.html
+++ b/read-delays.html
@@ -406,8 +406,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>This episode requires you to be familiar with:</p>
 <p><strong>Data science</strong> : Basic programming with R.</p>
@@ -416,8 +415,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>The <a href="reference.html#naturalhistory">natural history</a> of an
 infectious disease shows that its development has a regularity from
 stage to stage. The time periods from an infectious disease inform about
@@ -430,8 +428,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="definitions" class="callout-inner">
-<h3 class="callout-title">Definitions<a class="anchor" aria-label="anchor" href="#definitions"></a>
-</h3>
+<h3 class="callout-title">Definitions</h3>
 <div class="callout-content">
 <p>Look at the <a href="reference.html">glossary</a> for the definitions
 of all the time periods of the figure above!</p>
@@ -495,8 +492,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="kw">library</span><span class="op">(</span><span class="va">EpiNow2</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">tidyverse</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a>
-<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a></h2>
+</section><section><h2 class="section-heading" id="find-a-generation-time">Find a Generation time<a class="anchor" aria-label="anchor" href="#find-a-generation-time"></a></h2>
 <hr class="half-width"><p>The generation time, jointly with the <span class="math inline">\(R\)</span>, can inform about the speed of spread
 and its feasibility of control. Given a <span class="math inline">\(R&gt;1\)</span>, with a shorter generation time,
 cases can appear more quickly.</p>
@@ -533,8 +529,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="from-time-periods-to-probability-distributions." class="callout-inner">
-<h3 class="callout-title">From time periods to probability distributions.<a class="anchor" aria-label="anchor" href="#from-time-periods-to-probability-distributions."></a>
-</h3>
+<h3 class="callout-title">From time periods to probability distributions.</h3>
 <div class="callout-content">
 <p>When we calculate the <em>serial interval</em>, we see that not all
 case pairs have the same time length. We will observe this variability
@@ -608,8 +603,7 @@ <h3 class="callout-title">From time periods to probability distributions.<a clas
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="serial-interval" class="callout-inner">
-<h3 class="callout-title">Serial interval<a class="anchor" aria-label="anchor" href="#serial-interval"></a>
-</h3>
+<h3 class="callout-title">Serial interval</h3>
 <div class="callout-content">
 <p>Assume that COVID-19 and SARS have similar reproduction number values
 and that the serial interval approximates the generation time.</p>
@@ -655,8 +649,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 
-</section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a>
-<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a></h2>
+</section><section><h2 class="section-heading" id="extract-epidemiological-parameters">Extract epidemiological parameters<a class="anchor" aria-label="anchor" href="#extract-epidemiological-parameters"></a></h2>
 <hr class="half-width"><p>First, let’s assume that the data set <code>example_confirmed</code>
 has COVID-19 observed cases. So, we need to find a reported generation
 time for COVID-19 or any other useful parameter for this aim.</p>
@@ -808,8 +801,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="case-insensitive" class="callout-inner">
-<h3 class="callout-title">CASE-INSENSITIVE<a class="anchor" aria-label="anchor" href="#case-insensitive"></a>
-</h3>
+<h3 class="callout-title">CASE-INSENSITIVE</h3>
 <div class="callout-content">
 <p><code>epidist_db</code> is <a href="https://dillionmegida.com/p/case-sensitivity-vs-case-insensitivity/#case-insensitivity" class="external-link">case-insensitive</a>.
 This means that you can use strings with letters in upper or lower case
@@ -852,8 +844,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-periods" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation periods<a class="anchor" aria-label="anchor" href="#ebolas-incubation-periods"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation periods</h3>
 <div class="callout-content">
 <p>Take 5 minutes:</p>
 <ul><li><p>How many delay distributions are for the Ebola disease?</p></li>
@@ -911,8 +902,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a></h2>
+</section><section><h2 class="section-heading" id="select-a-single-distribution">Select a single distribution<a class="anchor" aria-label="anchor" href="#select-a-single-distribution"></a></h2>
 <hr class="half-width"><p>The <code>epiparameter::epidist_db()</code> function works as a
 filtering or subset function. Let’s use the <code>author</code> argument
 to filter <code>Hiroshi Nishiura</code> parameters:</p>
@@ -985,8 +975,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-does-single_epidist-works" class="callout-inner">
 <h3 class="callout-title">How does <code>single_epidist</code>
-works?<a class="anchor" aria-label="anchor" href="#how-does-single_epidist-works"></a>
-</h3>
+works?</h3>
 <div class="callout-content">
 <p>Looking at the help documentation for
 <code>?epiparameter::epidist_db()</code>:</p>
@@ -1052,8 +1041,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-incubation-period" class="callout-inner">
-<h3 class="callout-title">Ebola’s incubation period<a class="anchor" aria-label="anchor" href="#ebolas-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Ebola’s incubation period</h3>
 <div class="callout-content">
 <p>Take 2 minutes:</p>
 <ul><li>What type of distribution has the incubation period of Ebola with
@@ -1116,8 +1104,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a>
-<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a></h2>
+</section><section><h2 class="section-heading" id="extract-the-summary-statistics">Extract the summary statistics<a class="anchor" aria-label="anchor" href="#extract-the-summary-statistics"></a></h2>
 <hr class="half-width"><p>We can get the <code>mean</code> and standard deviation
 (<code>sd</code>) from this <code>&lt;epidist&gt;</code> diving into the
 <code>summary_stats</code> object:</p>
@@ -1139,8 +1126,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="how-to-get-the-sd-and-other-nested-elements" class="callout-inner">
 <h3 class="callout-title">How to get the <code>sd</code> and other
-nested elements?<a class="anchor" aria-label="anchor" href="#how-to-get-the-sd-and-other-nested-elements"></a>
-</h3>
+nested elements?</h3>
 <div class="callout-content">
 <p>Take 1 minute to:</p>
 <ol style="list-style-type: decimal"><li><p>Get the <code>sd</code> of the epidemiological
@@ -1224,8 +1210,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-severity-parameter" class="callout-inner">
-<h3 class="callout-title">Ebola’s severity parameter<a class="anchor" aria-label="anchor" href="#ebolas-severity-parameter"></a>
-</h3>
+<h3 class="callout-title">Ebola’s severity parameter</h3>
 <div class="callout-content">
 <p>A severity parameter like the duration of hospitalization could add
 to the information needed about the bed capacity in response to an
@@ -1283,8 +1268,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a>
-<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a></h2>
+</section><section><h2 class="section-heading" id="continuous-distributions">Continuous distributions<a class="anchor" aria-label="anchor" href="#continuous-distributions"></a></h2>
 <hr class="half-width"><p>The following output has four entries with different content in the
 <strong>probability distribution</strong>
 (<code>prob_distribution</code>) column:</p>
@@ -1399,8 +1383,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="the-distribution-zoo" class="callout-inner">
-<h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anchor" href="#the-distribution-zoo"></a>
-</h3>
+<h3 class="callout-title">The distribution Zoo</h3>
 <div class="callout-content">
 <p>Explore this shinyapp called <strong>The Distribution
 Zoo</strong>!</p>
@@ -1427,8 +1410,7 @@ <h3 class="callout-title">The distribution Zoo<a class="anchor" aria-label="anch
 </div>
 </div>
 <!-- A slider, in the context of user interfaces and graphical user interfaces (GUIs), is a graphical control element that allows users to adjust a value by moving a handle along a track or bar. Conceptually, it provides a way to select a numeric value within a specified range by visually sliding or dragging a pointer (the handle) along a continuous axis. -->
-</section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a>
-<a class="anchor" aria-label="anchor" href="#distribution-functions"></a></h2>
+</section><section><h2 class="section-heading" id="distribution-functions">Distribution functions<a class="anchor" aria-label="anchor" href="#distribution-functions"></a></h2>
 <hr class="half-width"><p>In R, all the statistical distributions have functions to access
 the:</p>
 <ul><li>Probability <strong>Density</strong> function (PDF),</li>
@@ -1523,8 +1505,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="window-for-contact-tracing-and-the-serial-interval" class="callout-inner">
-<h3 class="callout-title">Window for contact tracing and the Serial interval<a class="anchor" aria-label="anchor" href="#window-for-contact-tracing-and-the-serial-interval"></a>
-</h3>
+<h3 class="callout-title">Window for contact tracing and the Serial interval</h3>
 <div class="callout-content">
 <p>The <strong>serial interval</strong> is important in the optimization
 of contact tracing since it provides a time window for the containment
@@ -1610,8 +1591,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a>
-<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a></h2>
+</section><section><h2 class="section-heading" id="discretize-a-continuous-distribution">Discretize a continuous distribution<a class="anchor" aria-label="anchor" href="#discretize-a-continuous-distribution"></a></h2>
 <hr class="half-width"><p>We are getting closer to the end! <code>EpiNow2::dist_spec()</code>
 still needs a maximum value (<code>max</code>).</p>
 <p>One way to do this is to get the quantile value for the
@@ -1683,8 +1663,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="lenght-of-quarantine-and-incubation-period" class="callout-inner">
-<h3 class="callout-title">Lenght of quarantine and Incubation period<a class="anchor" aria-label="anchor" href="#lenght-of-quarantine-and-incubation-period"></a>
-</h3>
+<h3 class="callout-title">Lenght of quarantine and Incubation period</h3>
 <div class="callout-content">
 <p>The <strong>incubation period</strong> distribution is a useful delay
 to assess the length of active monitoring or quarantine (<a href="https://www.acpjournals.org/doi/10.7326/M20-0504" class="external-link">Lauer et al.,
@@ -1803,7 +1782,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code><a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a>
+</section><section><h2 class="section-heading" id="plug-in-epiparameter-to-epinow2">Plug-in <code>{epiparameter}</code> to <code>{EpiNow2}</code>
 <a class="anchor" aria-label="anchor" href="#plug-in-epiparameter-to-epinow2"></a></h2>
 <hr class="half-width"><p>Now we can plug everything into the <code>EpiNow2::dist_spec()</code>
 function!</p>
@@ -1832,8 +1811,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="warning" class="callout-inner">
-<h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#warning"></a>
-</h3>
+<h3 class="callout-title">Warning</h3>
 <div class="callout-content">
 <p>Using the serial interval instead of the generation time is an
 alternative that can propagate bias in your estimates, even more so in
@@ -1866,8 +1844,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number</h3>
 <div class="callout-content">
 <p>Download and read the <a href="data/ebola_cases.csv">Ebola
 dataset</a>:</p>
@@ -1956,8 +1933,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a>
-<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a></h2>
+</section><section><h2 class="section-heading" id="adjusting-for-reporting-delays">Adjusting for reporting delays<a class="anchor" aria-label="anchor" href="#adjusting-for-reporting-delays"></a></h2>
 <hr class="half-width"><p>Estimating <span class="math inline">\(R_t\)</span> requires data on
 the daily number of new infections. Due to lags in the development of
 detectable viral loads, symptom onset, seeking care, and reporting,
@@ -1986,8 +1962,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="reuse-an-incubation-period-for-covid-19" class="callout-inner">
-<h3 class="callout-title">Reuse an Incubation period for COVID-19<a class="anchor" aria-label="anchor" href="#reuse-an-incubation-period-for-covid-19"></a>
-</h3>
+<h3 class="callout-title">Reuse an Incubation period for COVID-19</h3>
 <div class="callout-content">
 <p>Use <code>{epiparameter}</code> to:</p>
 <ul><li>Find an incubation period for COVID-19.</li>
@@ -2097,8 +2072,7 @@ <h4 class="accordion-header" id="headingSolution12"> How much has it changed? </
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays" class="callout-inner">
-<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays<a class="anchor" aria-label="anchor" href="#ebolas-effective-reproduction-number-was-adjusted-by-reporting-delays"></a>
-</h3>
+<h3 class="callout-title">Ebola’s effective reproduction number was adjusted by reporting delays</h3>
 <div class="callout-content">
 <p>Using the same <a href="data/ebola_cases.csv">Ebola dataset</a>:</p>
 <ul><li>Reuse one additional epidemiological parameter for the
@@ -2200,8 +2174,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="extract-parameters" class="callout-inner">
-<h3 class="callout-title">Extract parameters<a class="anchor" aria-label="anchor" href="#extract-parameters"></a>
-</h3>
+<h3 class="callout-title">Extract parameters</h3>
 <div class="callout-content">
 <p>Use the <code>influenza_england_1978_school</code> from the
 <a href="https://github.com/reconhub/outbreaks" class="external-link">outbreaks</a> package to calculate the effective reproduction
@@ -2301,8 +2274,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a>
-<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a></h2>
+</section><section><h2 class="section-heading" id="when-to-reuse-when-to-estimate">When to reuse? When to estimate?<a class="anchor" aria-label="anchor" href="#when-to-reuse-when-to-estimate"></a></h2>
 <hr class="half-width"><p>In the early stage of an outbreak, we can rely on reusing parameters
 for known pathogens to unknown ones, like for the <a href="https://en.wikipedia.org/wiki/Disease_X" class="external-link">Disease X</a>, a pathogen
 currently unknown to cause human disease and potentially cause a serious
@@ -2347,8 +2319,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="heart"></i>
 </div>
 <div id="how-to-estimate-delay-distributions-for-disease-x" class="callout-inner">
-<h3 class="callout-title">How to estimate delay distributions for Disease X?<a class="anchor" aria-label="anchor" href="#how-to-estimate-delay-distributions-for-disease-x"></a>
-</h3>
+<h3 class="callout-title">How to estimate delay distributions for Disease X?</h3>
 <div class="callout-content">
 <p>Refer to this excellent tutorial on estimating the serial interval
 and incubation period of Disease X accounting for <em>censoring</em>
@@ -2405,8 +2376,7 @@ <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="what-type-of-transmission" class="callout-inner">
-<h3 class="callout-title">What type of transmission?<a class="anchor" aria-label="anchor" href="#what-type-of-transmission"></a>
-</h3>
+<h3 class="callout-title">What type of transmission?</h3>
 <div class="callout-content">
 <p>Compare the serial interval and incubation period of Influenza and
 MERS:</p>
@@ -2534,8 +2504,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Use <code>{epiparameter}</code> to access the systematic review
 catalogue of epidemiological delay distributions.</li>
@@ -2590,7 +2559,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -2613,7 +2582,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/read-delays.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 03b6eb4c..62c75c5f 100644
--- a/reference.html
+++ b/reference.html
@@ -351,8 +351,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 
         
 
-<section><h2 class="section-heading" id="a">A<a class="anchor" aria-label="anchor" href="#a"></a>
-<a class="anchor" aria-label="anchor" href="#a"></a></h2>
+<section><h2 class="section-heading" id="a">A<a class="anchor" aria-label="anchor" href="#a"></a></h2>
 <hr class="half-width"><dl><dt><span id="airborne">Airborne transmission</span></dt>
 <dd>
 Individuals become infected via contact with infectious particles in the
@@ -360,8 +359,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 discuss about <a href="https://www.ncbi.nlm.nih.gov/books/NBK531468/" class="external-link">factors and
 management procedures</a> of airborne transmission.
 </dd>
-</dl></section><section><h2 class="section-heading" id="b">B<a class="anchor" aria-label="anchor" href="#b"></a>
-<a class="anchor" aria-label="anchor" href="#b"></a></h2>
+</dl></section><section><h2 class="section-heading" id="b">B<a class="anchor" aria-label="anchor" href="#b"></a></h2>
 <hr class="half-width"><dl><dt><span id="basic">Basic reproduction number</span></dt>
 <dd>
 A measure of the transmissibility of a disease. Defined as the average
@@ -375,8 +373,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 observed data. <a href="https://en.wikipedia.org/wiki/Bayesian_inference" class="external-link">More information
 on Bayesian inference</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="c">C<a class="anchor" aria-label="anchor" href="#c"></a>
-<a class="anchor" aria-label="anchor" href="#c"></a></h2>
+</dl></section><section><h2 class="section-heading" id="c">C<a class="anchor" aria-label="anchor" href="#c"></a></h2>
 <hr class="half-width"><dl><dt><span id="contact">Contact matrix</span></dt>
 <dd>
 The contact matrix is a square matrix consisting of rows/columns equal
@@ -403,8 +400,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 can propagate bias to the estimation of the <a href="#incubation">incubation period</a> and generation time (<a href="https://www.nature.com/articles/s41467-022-35496-8/figures/2" class="external-link">Chen
 et al., 2022</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="d">D<a class="anchor" aria-label="anchor" href="#d"></a>
-<a class="anchor" aria-label="anchor" href="#d"></a></h2>
+</dl></section><section><h2 class="section-heading" id="d">D<a class="anchor" aria-label="anchor" href="#d"></a></h2>
 <hr class="half-width"><dl><dt><span id="deterministic">Deterministic model</span></dt>
 <dd>
 Models that will always have the same trajectory for given initial
@@ -418,8 +414,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 transmitted infections as they require close contact with infected
 individuals for successful transmission.
 </dd>
-</dl></section><section><h2 class="section-heading" id="e">E<a class="anchor" aria-label="anchor" href="#e"></a>
-<a class="anchor" aria-label="anchor" href="#e"></a></h2>
+</dl></section><section><h2 class="section-heading" id="e">E<a class="anchor" aria-label="anchor" href="#e"></a></h2>
 <hr class="half-width"><dl><dt><span id="effectiverepro">Effective reproduction number</span></dt>
 <dd>
 The time-varying or effective reproduction number (<span class="math inline">\(Rt\)</span>) is similar to the <a href="#basic">Basic reproductive number</a> (<span class="math inline">\(R0\)</span>), but <span class="math inline">\(Rt\)</span> measures the number of persons
@@ -427,8 +422,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 already been infected. Read more about the <a href="https://wwwnc.cdc.gov/eid/article/29/8/22-1445_article" class="external-link">etymology
 of Reproduction number by Sharma et al, 2023</a>.
 </dd>
-</dl><!-- ## F --></section><section><h2 class="section-heading" id="g">G<a class="anchor" aria-label="anchor" href="#g"></a>
-<a class="anchor" aria-label="anchor" href="#g"></a></h2>
+</dl><!-- ## F --></section><section><h2 class="section-heading" id="g">G<a class="anchor" aria-label="anchor" href="#g"></a></h2>
 <hr class="half-width"><dl><dt><span id="generationtime">Generation time</span></dt>
 <dd>
 Time between the onset of infectiousness of an index case and its
@@ -444,8 +438,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 of transmission, see <a href="https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.1556" class="external-link">Dushoff
 &amp; Park, 2021</a>.
 </dd>
-</dl><!-- ## H --></section><section><h2 class="section-heading" id="i">I<a class="anchor" aria-label="anchor" href="#i"></a>
-<a class="anchor" aria-label="anchor" href="#i"></a></h2>
+</dl><!-- ## H --></section><section><h2 class="section-heading" id="i">I<a class="anchor" aria-label="anchor" href="#i"></a></h2>
 <hr class="half-width"><dl><dt><span id="incubation">Incubation period</span></dt>
 <dd>
 The time between becoming infected and the onset of symptoms. <a href="https://en.wikipedia.org/wiki/Latent_period_(epidemiology)#Incubation_period" class="external-link">More
@@ -481,8 +474,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 2022</a> and <a href="https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(22)00226-0/fulltext" class="external-link">Hakki
 et al, 2022</a>](fig/infectiousness-covid19.jpg)).
 </dd>
-</dl><!-- ## J --><!-- ## K --></section><section><h2 class="section-heading" id="l">L<a class="anchor" aria-label="anchor" href="#l"></a>
-<a class="anchor" aria-label="anchor" href="#l"></a></h2>
+</dl><!-- ## J --><!-- ## K --></section><section><h2 class="section-heading" id="l">L<a class="anchor" aria-label="anchor" href="#l"></a></h2>
 <hr class="half-width"><dl><dt><span id="latent">Latent period</span></dt>
 <dd>
 The time between becoming infected and the onset of infectiousness. This
@@ -490,8 +482,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 shown in Figure 4 from (<a href="https://www.sciencedirect.com/science/article/pii/S2468042721000038#fig4" class="external-link">Xiang
 et al, 2021</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="m">M<a class="anchor" aria-label="anchor" href="#m"></a>
-<a class="anchor" aria-label="anchor" href="#m"></a></h2>
+</dl></section><section><h2 class="section-heading" id="m">M<a class="anchor" aria-label="anchor" href="#m"></a></h2>
 <hr class="half-width"><dl><dt><span id="parsode">Model parameters (ODEs)</span></dt>
 <dd>
 The model parameters are used in <a href="#ordinary">ordinary
@@ -499,8 +490,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 states. For example, a transmission rate <span class="math inline">\(\beta\)</span> is a model parameter that can be
 used to describe the flow between susceptible and infectious states.
 </dd>
-</dl></section><section><h2 class="section-heading" id="n">N<a class="anchor" aria-label="anchor" href="#n"></a>
-<a class="anchor" aria-label="anchor" href="#n"></a></h2>
+</dl></section><section><h2 class="section-heading" id="n">N<a class="anchor" aria-label="anchor" href="#n"></a></h2>
 <hr class="half-width"><dl><dt><span id="NPIs">Non-pharmaceutical interventions</span></dt>
 <dd>
 Non-pharmaceutical interventions (NPIs) are measures put in place to
@@ -508,8 +498,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 vaccinations. <a href="https://www.gov.uk/government/publications/technical-report-on-the-covid-19-pandemic-in-the-uk/chapter-8-non-pharmaceutical-interventions" class="external-link">More
 information on NPIs</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="o">O<a class="anchor" aria-label="anchor" href="#o"></a>
-<a class="anchor" aria-label="anchor" href="#o"></a></h2>
+</dl></section><section><h2 class="section-heading" id="o">O<a class="anchor" aria-label="anchor" href="#o"></a></h2>
 <hr class="half-width"><dl><dt><span id="ordinary">Ordinary differential equations</span></dt>
 <dd>
 Ordinary differential equations (ODEs) can be used to represent the rate
@@ -526,8 +515,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 the various coupling factors. (<a href="https://www.sciencedirect.com/science/article/pii/S2468042721000038" class="external-link">Xiang
 et al, 2021</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="o-1">O<a class="anchor" aria-label="anchor" href="#o-1"></a>
-<a class="anchor" aria-label="anchor" href="#o-1"></a></h2>
+</dl></section><section><h2 class="section-heading" id="o-1">O<a class="anchor" aria-label="anchor" href="#o-1"></a></h2>
 <hr class="half-width"><dl><dt><span id="offspringdist">Offspring distribution</span></dt>
 <dd>
 Distribution of the number of secondary cases caused by a particular
@@ -535,8 +523,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 2005</a>, <a href="https://wellcomeopenresearch.org/articles/5-67/v3" class="external-link">Endo et al.,
 2020</a>)
 </dd>
-</dl></section><section><h2 class="section-heading" id="p">P<a class="anchor" aria-label="anchor" href="#p"></a>
-<a class="anchor" aria-label="anchor" href="#p"></a></h2>
+</dl></section><section><h2 class="section-heading" id="p">P<a class="anchor" aria-label="anchor" href="#p"></a></h2>
 <hr class="half-width"><dl><dt><span id="phasebias">(Dynamical or Epidemic) Phase bias</span></dt>
 <dd>
 Accounts for population susceptibility at the times transmission pairs
@@ -548,8 +535,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 and longer delay intervals, respectively. (<a href="https://github.com/parksw3/epidist-paper" class="external-link">Park et al., in
 progress</a>)
 </dd>
-</dl><!-- ## Q --></section><section><h2 class="section-heading" id="r">R<a class="anchor" aria-label="anchor" href="#r"></a>
-<a class="anchor" aria-label="anchor" href="#r"></a></h2>
+</dl><!-- ## Q --></section><section><h2 class="section-heading" id="r">R<a class="anchor" aria-label="anchor" href="#r"></a></h2>
 <hr class="half-width"><dl><dt><span id="reportingdelay">Reporting delay</span></dt>
 <dd>
 Delay or lag between the time an event occurs (e.g. symptom onset) and
@@ -558,8 +544,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 up-to-date reported aggregated case counts (<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0371" class="external-link">Cori
 et al. 2017</a>).
 </dd>
-</dl></section><section><h2 class="section-heading" id="s">S<a class="anchor" aria-label="anchor" href="#s"></a>
-<a class="anchor" aria-label="anchor" href="#s"></a></h2>
+</dl></section><section><h2 class="section-heading" id="s">S<a class="anchor" aria-label="anchor" href="#s"></a></h2>
 <hr class="half-width"><dl><dt><span id="state">State variables</span></dt>
 <dd>
 The state variables in a model represented by <a href="#ordinary">ordinary differential equations</a> are the disease
@@ -587,8 +572,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 Examples include stochastic differential equations and branching process
 models. For more detail see <a href="https://doi.org/10.1016/j.idm.2017.03.001" class="external-link">Allen (2017)</a>.
 </dd>
-</dl></section><section><h2 class="section-heading" id="t">T<a class="anchor" aria-label="anchor" href="#t"></a>
-<a class="anchor" aria-label="anchor" href="#t"></a></h2>
+</dl></section><section><h2 class="section-heading" id="t">T<a class="anchor" aria-label="anchor" href="#t"></a></h2>
 <hr class="half-width"><dl><dt><span id="truncation">(Right) Truncation</span></dt>
 <dd>
 Type of sampling bias related to the data collection process. It arises
@@ -597,8 +581,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
 can lead to underestimation of the mean delay (<a href="https://github.com/parksw3/epidist-paper" class="external-link">Park et al., in
 progress</a>).
 </dd>
-</dl><!-- ## U --></section><section><h2 class="section-heading" id="v">V<a class="anchor" aria-label="anchor" href="#v"></a>
-<a class="anchor" aria-label="anchor" href="#v"></a></h2>
+</dl><!-- ## U --></section><section><h2 class="section-heading" id="v">V<a class="anchor" aria-label="anchor" href="#v"></a></h2>
 <hr class="half-width"><dl><dt><span id="vectorborne">Vector-borne transmission</span></dt>
 <dd>
 Vector-borne transmission means an infection can be passed from a vector
@@ -652,7 +635,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -675,7 +658,7 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "identifier": "https://epiverse-trace.github.io/tutorials/reference.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/simulating-transmission.html b/simulating-transmission.html
index 5b8c3235..931f3fca 100644
--- a/simulating-transmission.html
+++ b/simulating-transmission.html
@@ -402,8 +402,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <p>Learners should familiarise themselves with following concept
 dependencies before working through this tutorial:</p>
@@ -415,16 +414,14 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
+<section><h2 class="section-heading" id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a></h2>
 <hr class="half-width"><p>Mathematical models are useful tools for generating future
 trajectories of disease spread. In this tutorial, we will use the R
 package <code>{epidemics}</code> to generate disease trajectories of an
 influenza strain with pandemic potential. By the end of this tutorial,
 you will be able to generate the trajectory below showing the number of
 infectious individuals in different age categories over time.</p>
-<figure><img src="fig/simulating-transmission-rendered-traj-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a>
-<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a></h2>
+<figure><img src="fig/simulating-transmission-rendered-traj-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="simulating-disease-spread">Simulating disease spread<a class="anchor" aria-label="anchor" href="#simulating-disease-spread"></a></h2>
 <hr class="half-width"><p>To generate predictions of infectious disease trajectories, we must
 first select a mathematical model to use. There is a library of models
 to choose from in <code>epidemics</code>. Models in
@@ -447,8 +444,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="model-parameters-rates" class="callout-inner">
-<h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="anchor" href="#model-parameters-rates"></a>
-</h3>
+<h3 class="callout-title">Model parameters : rates</h3>
 <div class="callout-content">
 <p>In ODE models, model parameters are often (but not always) specified
 as rates. The rate at which an event occurs is the inverse of the
@@ -494,8 +490,7 @@ <h3 class="callout-title">Model parameters : rates<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="exposed-infected-infectious" class="callout-inner">
-<h3 class="callout-title">Exposed, infected, infectious<a class="anchor" aria-label="anchor" href="#exposed-infected-infectious"></a>
-</h3>
+<h3 class="callout-title">Exposed, infected, infectious</h3>
 <div class="callout-content">
 <p>Confusion sometimes arises when referring to the terms ‘exposed’,
 ‘infected’ and ‘infectious’ in mathematical modelling. Infection occurs
@@ -529,8 +524,7 @@ <h3 id="contact-matrix">1. Contact matrix<a class="anchor" aria-label="anchor" h
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="load-contact-and-population-data" class="callout-inner">
-<h3 class="callout-title">Load contact and population data<a class="anchor" aria-label="anchor" href="#load-contact-and-population-data"></a>
-</h3>
+<h3 class="callout-title">Load contact and population data</h3>
 <div class="callout-content">
 <p>Using the R package <code>socialmixr</code>, run the following lines
 of R code to obtain the contact matrix for the United Kingdom for the
@@ -584,8 +578,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="why-would-a-contact-matrix-be-non-symmetric" class="callout-inner">
-<h3 class="callout-title">Why would a contact matrix be non-symmetric?<a class="anchor" aria-label="anchor" href="#why-would-a-contact-matrix-be-non-symmetric"></a>
-</h3>
+<h3 class="callout-title">Why would a contact matrix be non-symmetric?</h3>
 <div class="callout-content">
 <p>One of the arguments of the function <code>contact_matrix()</code> is
 <code>symmetric=TRUE</code>. This means that the total number of
@@ -723,7 +716,7 @@ <h3 id="model-parameters">4. Model parameters<a class="anchor" aria-label="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-basic-reproduction-number-r_0" class="callout-inner">
-<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span><a class="anchor" aria-label="anchor" href="#the-basic-reproduction-number-r_0"></a>
+<h3 class="callout-title">The basic reproduction number <span class="math inline">\(R_0\)</span>
 </h3>
 <div class="callout-content">
 <p>The basic reproduction number, <span class="math inline">\(R_0\)</span>, for the SEIR model is:</p>
@@ -735,15 +728,13 @@ <h3 class="callout-title">The basic reproduction number <span class="math inline
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a>
-<a class="anchor" aria-label="anchor" href="#running-the-model"></a></h2>
+</section><section><h2 class="section-heading" id="running-the-model">Running the model<a class="anchor" aria-label="anchor" href="#running-the-model"></a></h2>
 <hr class="half-width"><div id="running-solving-the-model" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="running-solving-the-model" class="callout-inner">
-<h3 class="callout-title">Running (solving) the model<a class="anchor" aria-label="anchor" href="#running-solving-the-model"></a>
-</h3>
+<h3 class="callout-title">Running (solving) the model</h3>
 <div class="callout-content">
 <p>For models that are described by ODEs, running the model actually
 means to solve the system of ODEs. ODEs describe the rate of change in
@@ -844,8 +835,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="time-increments" class="callout-inner">
-<h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" href="#time-increments"></a>
-</h3>
+<h3 class="callout-title">Time increments</h3>
 <div class="callout-content">
 <p>Note that there is a default argument of <code>increment = 1</code>.
 This relates to the time step of the ODE solver. When the parameters are
@@ -860,8 +850,7 @@ <h3 class="callout-title">Time increments<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a>
-<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a></h2>
+</section><section><h2 class="section-heading" id="accounting-for-uncertainty">Accounting for uncertainty<a class="anchor" aria-label="anchor" href="#accounting-for-uncertainty"></a></h2>
 <hr class="half-width"><p>As the epidemic model is <a href="reference.html#deterministic">deterministic</a>, we have one
 trajectory for our given parameter values. In practice, we have
 uncertainty in the value of our parameters. To account for this, we must
@@ -945,8 +934,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 parameter value changes; and the purpose of the modelling task. See <a href="https://doi.org/10.1016%2Fj.epidem.2021.100520" class="external-link">McCabe et
 al. 2021</a> to learn about different types of uncertainty in infectious
 disease modelling.</p>
-</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>In this tutorial, we have learnt how to simulate disease spread using
 a mathematical model. Once a model has been chosen, the parameters and
 other inputs must be specified in the correct way to perform model
@@ -957,8 +945,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Disease trajectories can be generated using the R package
 <code>epidemics</code>
@@ -1008,7 +995,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/ad2542f7f7b9c3f90cc871b355ff81ec14a09ca9" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1031,7 +1018,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://epiverse-trace.github.io/tutorials/simulating-transmission.html",
   "dateCreated": "2024-02-06",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>