From 05033536402fb9c182f28a7026935f1f19d62ad8 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Mon, 24 Jun 2024 11:22:38 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 8e243236ec2701a5b7b0cd4aa505785ee3310c80
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-06-24 11:22:24 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 5818e174a0a450a4a4c2682c998c8f391c3c929e
Branch  : main
Author  : Andree Valle Campos <avallecam@gmail.com>
Time    : 2024-06-24 11:20:32 +0000
Message : Apply suggestions from code review
---
 404.html                                      |  19 +-
 CODE_OF_CONDUCT.html                          |  15 +-
 LICENSE.html                                  |  15 +-
 aio.html                                      | 424 +++--------------
 clean-data.html                               |  21 +-
 config.yaml                                   |   2 +-
 describe-cases.html                           | 107 +++--
 ...cribe-cases-rendered-unnamed-chunk-7-1.png | Bin 9500 -> 9477 bytes
 ...cribe-cases-rendered-unnamed-chunk-8-1.png | Bin 21079 -> 6284 bytes
 images.html                                   |  33 +-
 index.html                                    |  25 +-
 instructor-notes.html                         |  20 +-
 instructor/404.html                           |  19 +-
 instructor/CODE_OF_CONDUCT.html               |  15 +-
 instructor/LICENSE.html                       |  15 +-
 instructor/aio.html                           | 425 +++---------------
 instructor/clean-data.html                    |  21 +-
 instructor/describe-cases.html                | 107 +++--
 instructor/images.html                        |  33 +-
 instructor/index.html                         |  35 +-
 instructor/instructor-notes.html              |  21 +-
 instructor/key-points.html                    |  33 +-
 instructor/profiles.html                      |  17 +-
 instructor/read-cases.html                    |  19 +-
 instructor/reference.html                     |  15 +-
 key-points.html                               |  33 +-
 md5sum.txt                                    |   5 +-
 pkgdown.yml                                   |   2 +-
 profiles.html                                 |  17 +-
 read-cases.html                               |  19 +-
 reference.html                                |  15 +-
 31 files changed, 408 insertions(+), 1139 deletions(-)

diff --git a/404.html b/404.html
index c6885bef..88aad3e3 100644
--- a/404.html
+++ b/404.html
@@ -189,17 +189,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         
   </div>
 <!--/div.accordion-item-->
-</div>
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="https://epiverse-trace.github.io/tutorials-early/simple-analysis.html" class="external-link">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
 </div>
 
                 </div>
@@ -286,7 +275,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -307,9 +296,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/404.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 31bfe7b9..d520a794 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -312,7 +303,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -333,9 +324,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/CODE_OF_CONDUCT.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index e6bf7570..778d4d8e 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -360,7 +351,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -381,9 +372,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/LICENSE.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/LICENSE.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index dfb4b80d..0913d527 100644
--- a/aio.html
+++ b/aio.html
@@ -222,18 +222,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
 </div>
-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -433,7 +421,7 @@ <h3 class="callout-title">Reading compressed data<a class="anchor" aria-label="a
 <div id="accordionHint1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Give me a hint</h4>
+  <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
 <div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
@@ -456,7 +444,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Show me the solution</h4>
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
 <div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
@@ -1224,7 +1212,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-describe-cases"><p>Content from <a href="describe-cases.html">Aggregate and visualize</a></p>
 <hr>
-<p>Last updated on 2024-06-18 |
+<p>Last updated on 2024-06-24 |
         
         <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/describe-cases.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1272,10 +1260,14 @@ <h3 class="card-title">Objectives</h3>
 between time and the number of reported cases, spanning various
 categories (confirmed, hospitalized, deaths, and recoveries), locations,
 and other demographic factors such as gender, age, etc.</p>
-<p>::::::::::::::::::: checklist</p>
-<div class="section level3">
-<h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
+<div id="the-double-colon" class="callout checklist">
+<div class="callout-square">
+<i class="callout-icon" data-feather="check-square"></i>
+</div>
+<div id="the-double-colon" class="callout-inner">
+<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
 </h3>
+<div class="callout-content">
 <p>The double-colon <code>::</code> in R let you call a specific
 function from a package without loading the entire package into the
 current environment.</p>
@@ -1283,7 +1275,8 @@ <h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor"
 <code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
 <p>This help us remember package functions and avoid namespace
 conflicts.</p>
-<p>:::::::::::::::::::</p>
+</div>
+</div>
 </div>
 </section><section id="synthetic-outbreak-data"><h2 class="section-heading">Synthetic outbreak data<a class="anchor" aria-label="anchor" href="#synthetic-outbreak-data"></a>
 </h2>
@@ -1560,352 +1553,81 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span></span>
 <span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">weekly_incidence_data</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
-<span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in weeks)"</span>,</span>
 <span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
 <span>  <span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-can-you-do-it" class="callout discussion">
-<div class="callout-square">
-<i class="callout-icon" data-feather="message-circle"></i>
-</div>
-<div id="challenge-1-can-you-do-it" class="callout-inner">
-<h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-label="anchor" href="#challenge-1-can-you-do-it"></a>
-</h3>
-<div class="callout-content">
-<ul>
-<li>Using suitable distributions for contacts, contact interval,
-infectious period, onset to hospitalized, and onset to death, generate a
-simulated linelist data for Marburg outbreak that has the probability of
-<span class="math inline">\(0.5\)</span> infection?</li>
-<li>Aggregate the generated linelist and produce some epidemic
-curves?</li>
-</ul>
-</div>
-</div>
-</div>
-<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>
-<div class="callout-content">
-<ul>
-<li>Use <code>{simulist}</code> package to generate synthetic outbreak
-data</li>
-<li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
-on a date event, and produce epidemic curves.</li>
-</ul>
-</div>
-</div>
-</div>
-<!-- 
-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><section id="aio-simple-analysis"><p>Content from <a href="simple-analysis.html">Simple analysis</a></p>
-<hr>
-<p>Last updated on 2024-06-18 |
-        
-        <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/simple-analysis.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-<div class="text-end">
-          <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
-        </div>
-<div class="overview card">
-<h2 class="card-header">Overview</h2>
-<div class="row g-0">
-<div class="col-md-4">
-<div class="card-body">
-<div class="inner">
-<h3 class="card-title">Questions</h3>
-<ul>
-<li>What is the growth rate of the epidemic?</li>
-<li>How to identify the peak time of an outbreak?</li>
-<li>How to compute moving average of cases?</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="col-md-8">
-<div class="card-body">
-<div class="inner bordered">
-<h3 class="card-title">Objectives</h3>
-<ul>
-<li>Perform an early analysis of outbreak data</li>
-<li>Identify trends, exponential, doubling, and peak time</li>
-</ul>
-</div>
-</div>
-</div>
-</div>
-</div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
-</h2>
-<hr class="half-width">
-<p>Understanding the trend in case data is crucial for various purposes,
-such as forecasting future case counts, implementing public health
-interventions, and assessing the effectiveness of control measures. By
-analyzing the trend, policymakers and public health experts can make
-informed decisions to mitigate the spread of diseases and protect public
-health. This episode focuses on how to perform a simple early analysis
-on incidence data. It uses the same dataset of <strong>Covid-19 case
-data from England</strong> that utilized it in <a href="describe-cases.html">Aggregate and visualize</a> episode.</p>
-<div id="the-double-colon" class="callout checklist">
-<div class="callout-square">
-<i class="callout-icon" data-feather="check-square"></i>
-</div>
-<div id="the-double-colon" class="callout-inner">
-<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
-</h3>
-<div class="callout-content">
-<p>The double-colon <code>::</code> in R let you call a specific
-function from a package without loading the entire package into the
-current environment.</p>
-<p>For example, <code>dplyr::filter(data, condition)</code> uses
-<code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
-<p>This help us remember package functions and avoid namespace
-conflicts.</p>
-</div>
-</div>
-</div>
-</section><section id="simple-model"><h2 class="section-heading">Simple model<a class="anchor" aria-label="anchor" href="#simple-model"></a>
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section id="curve-of-cumulative-cases"><h2 class="section-heading">Curve of cumulative cases<a class="anchor" aria-label="anchor" href="#curve-of-cumulative-cases"></a>
 </h2>
 <hr class="half-width">
-<p>Aggregated case data over a specific time unit, or incidence data,
-typically represent the number of cases occurring within that time
-frame. These data can often be assumed to follow either
-<code>Poisson distribution</code> or a
-<code>negative binomial (NB) distribution</code>, depending on the
-specific characteristics of the data and the underlying processes
-generating them. When analyzing such data, one common approach is to
-examine the trend over time by computing the rate of change, which can
-indicate whether there is exponential growth or decay in the number of
-cases. Exponential growth implies that the number of cases is increasing
-at an accelerating rate over time, while exponential decay suggests that
-the number of cases is decreasing at a decelerating rate.</p>
-<p>The <code>i2extras</code> package provides methods for modelling the
-trend in case data, calculating moving averages, and exponential growth
-or decay rate. The code chunk below computes the Covid-19 trend in UK
-within first 3 months using negative binomial distribution.</p>
-<div class="codewrapper sourceCode" id="cb1">
+<p>The cumulative number of cases can be calculated using the
+<code>cumulate()</code> function from an <code>incidence2</code> object
+and visualized, as in the example below.</p>
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="co"># load packages which provides methods for modeling</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"i2extras"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"incidence2"</span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># read data from {outbreaks} package</span></span>
-<span><span class="va">covid19_eng_case_data</span> <span class="op">&lt;-</span> <span class="fu">outbreaks</span><span class="fu">::</span><span class="va">covid19_england_nhscalls_2020</span></span>
-<span></span>
-<span><span class="co"># subset the covid19_eng_case_data to include only the first 3 months of data</span></span>
-<span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu">base</span><span class="fu">::</span><span class="fu">subset</span><span class="op">(</span></span>
-<span>  <span class="va">covid19_eng_case_data</span>,</span>
-<span>  <span class="va">covid19_eng_case_data</span><span class="op">$</span><span class="va">date</span> <span class="op">&lt;=</span> <span class="fu">min</span><span class="op">(</span><span class="va">covid19_eng_case_data</span><span class="op">$</span><span class="va">date</span><span class="op">)</span> <span class="op">+</span> <span class="fl">90</span></span>
-<span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># uses the incidence function from the incidence2 package to compute the</span></span>
-<span><span class="co"># incidence data</span></span>
-<span><span class="va">df_incid</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">incidence</span><span class="op">(</span></span>
-<span>  <span class="va">df</span>,</span>
-<span>  date_index <span class="op">=</span> <span class="st">"date"</span>,</span>
-<span>  groups <span class="op">=</span> <span class="st">"sex"</span></span>
-<span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># fit a curve to the incidence data. The model chosen is the negative binomial</span></span>
-<span><span class="co"># distribution with a significance level (alpha) of 0.05.</span></span>
-<span><span class="va">fitted_curve_nb</span> <span class="op">&lt;-</span></span>
-<span>  <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">fit_curve</span><span class="op">(</span></span>
-<span>    <span class="va">df_incid</span>,</span>
-<span>    model <span class="op">=</span> <span class="st">"negbin"</span>,</span>
-<span>    alpha <span class="op">=</span> <span class="fl">0.05</span></span>
-<span>  <span class="op">)</span></span>
-<span></span>
-<span><span class="co"># plot fitted curve</span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">fitted_curve_nb</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="fig/simple-analysis-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-poission-distribution" class="callout challenge">
-<div class="callout-square">
-<i class="callout-icon" data-feather="zap"></i>
-</div>
-<div id="challenge-1-poission-distribution" class="callout-inner">
-<h3 class="callout-title">Challenge 1: Poission distribution<a class="anchor" aria-label="anchor" href="#challenge-1-poission-distribution"></a>
-</h3>
-<div class="callout-content">
-<p>Repeat the above analysis using Poisson distribution?</p>
-</div>
-</div>
-</div>
-<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">Show me the solution</h4>
-</button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
-<div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb2">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">fitted_curve_poisson</span> <span class="op">&lt;-</span></span>
-<span>  <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">fit_curve</span><span class="op">(</span></span>
-<span>    x <span class="op">=</span> <span class="va">df_incid</span>,</span>
-<span>    model <span class="op">=</span> <span class="st">"poisson"</span>,</span>
-<span>    alpha <span class="op">=</span> <span class="fl">0.05</span></span>
-<span>  <span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">fitted_curve_poisson</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="fig/simple-analysis-rendered-unnamed-chunk-2-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure>
-</div>
-</div>
-</div>
+<code class="sourceCode R"><span><span class="va">cum_df</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">cumulate</span><span class="op">(</span><span class="va">dialy_incidence_data</span><span class="op">)</span></span>
+<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">cum_df</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
+<span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
+<span>  <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section id="exponential-growth-or-decay-rate"><h2 class="section-heading">Exponential growth or decay rate<a class="anchor" aria-label="anchor" href="#exponential-growth-or-decay-rate"></a>
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Note that this function preserves grouping, i.e., if the
+<code>incidence2</code> object contains groups, it will accumulate the
+cases accordingly. Give it a try with the
+<code>weekly_incidence_data</code> object!</p>
+</section><section id="peak-estimation"><h2 class="section-heading">Peak estimation<a class="anchor" aria-label="anchor" href="#peak-estimation"></a>
 </h2>
 <hr class="half-width">
-<p>The exponential growth or decay rate, denoted as <span class="math inline">\(r\)</span>, serves as an indicator for the trend
-in cases, indicating whether they are increasing (growth) or decreasing
-(decay) on an exponential scale. This rate is computed using the
-so-called <strong>renewal equation</strong> <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2006.3754" class="external-link">(Wallinga
-et al. 2006)</a>, which mechanistically links the reproductive number
-<span class="math inline">\(R\)</span> of new cases to the generation
-interval of the disease. This computational method is implemented in the
-<a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> package.</p>
-<p>Below is a code snippet demonstrating how to extract the growth/decay
-rate from the above <strong>NB</strong>-fitted curve using the
-<code>growth_rate()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb3">
+<p>One can estimate the peak –the time with the highest number of
+recorded cases– using the <code>estimate_peak()</code> function from the
+{incidence2} package. This function employs a bootstrapping method to
+determine the peak time.</p>
+<div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">rates_nb</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">growth_rate</span><span class="op">(</span><span class="va">fitted_curve_nb</span><span class="op">)</span></span>
-<span><span class="va">rates_nb</span> <span class="op">&lt;-</span> <span class="fu">base</span><span class="fu">::</span><span class="fu">as.data.frame</span><span class="op">(</span><span class="va">rates_nb</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">subset</span><span class="op">(</span>select <span class="op">=</span> <span class="fu">c</span><span class="op">(</span><span class="va">sex</span>, <span class="va">r</span>, <span class="va">r_lower</span>, <span class="va">r_upper</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">print</span><span class="op">(</span><span class="va">rates_nb</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">peak</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span></span>
+<span>  <span class="va">dialy_incidence_data</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  alpha <span class="op">=</span> <span class="fl">0.05</span>,</span>
+<span>  first_only <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  progress <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span><span class="fu">print</span><span class="op">(</span><span class="va">peak</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>      sex            r      r_lower      r_upper
-1  female -0.008241228 -0.009182635 -0.007300403
-2    male -0.008346783 -0.009316775 -0.007377392
-3 unknown -0.023703987 -0.028179436 -0.019299926</code></pre>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 7
+  count_variable observed_peak observed_count bootstrap_peaks lower_ci   median 
+  &lt;chr&gt;          &lt;period&gt;               &lt;int&gt; &lt;list&gt;          &lt;period&gt;   &lt;perio&gt;
+1 date_onset     2023-01-03              5478 &lt;df [100 × 1]&gt;  2023-01-03 2023-0…
+# ℹ 1 more variable: upper_ci &lt;period&gt;</code></pre>
 </div>
-<div id="challenge-2-growth-rates-from-a-poisson-fitted-curve" class="callout discussion">
+<p>This example demonstrates how to estimate the peak time using the
+<code>estimate_peak()</code> function at <span class="math inline">\(95%\)</span> confidence interval and using 100
+bootstrap samples.</p>
+<div id="challenge-1-can-you-do-it" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="challenge-2-growth-rates-from-a-poisson-fitted-curve" class="callout-inner">
-<h3 class="callout-title">Challenge 2: Growth rates from a<strong>Poisson</strong>-fitted curve<a class="anchor" aria-label="anchor" href="#challenge-2-growth-rates-from-a-poisson-fitted-curve"></a>
-</h3>
-<div class="callout-content">
-<p>Extract growth rates from the <strong>Poisson</strong>-fitted curve
-of <strong>Challenge 1</strong>?</p>
-</div>
-</div>
-</div>
-</section><section id="peak-time"><h2 class="section-heading">Peak time<a class="anchor" aria-label="anchor" href="#peak-time"></a>
-</h2>
-<hr class="half-width">
-<p>The <strong>Peak time </strong> is the time at which the highest
-number of cases is observed in the aggregated data. It can be estimated
-using the <code>i2extras::estimate_peak()</code> function as shown in
-the below code chunk, which identify peak time from the
-<code>incidenc2</code> object <code>df_incid</code>.</p>
-<div class="codewrapper sourceCode" id="cb5">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">peaks_nb</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span><span class="va">df_incid</span>, progress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">subset</span><span class="op">(</span>select <span class="op">=</span> <span class="op">-</span><span class="fu">c</span><span class="op">(</span><span class="va">count_variable</span>, <span class="va">bootstrap_peaks</span><span class="op">)</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">print</span><span class="op">(</span><span class="va">peaks_nb</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code># A data frame: 3 × 6
-  sex     observed_peak observed_count lower_ci   median     upper_ci  
-* &lt;chr&gt;   &lt;date&gt;                 &lt;int&gt; &lt;date&gt;     &lt;date&gt;     &lt;date&gt;    
-1 female  2020-03-26              1314 2020-03-19 2020-03-23 2020-03-30
-2 male    2020-03-27              1299 2020-03-18 2020-03-26 2020-03-30
-3 unknown 2020-04-10                32 2020-03-24 2020-04-10 2020-04-16</code></pre>
-</div>
-</section><section id="moving-average"><h2 class="section-heading">Moving average<a class="anchor" aria-label="anchor" href="#moving-average"></a>
-</h2>
-<hr class="half-width">
-<p>A moving or rolling average calculates the average number of cases
-within a specified time period. This can be achieved by utilizing the
-<code>add_rolling_average()</code> function from the
-<a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> package on an <code>incidence2 object</code>.
-The following code chunk demonstrates the computation of the weekly
-average number of cases from the <code>incidence2</code> object
-<code>df_incid</code>, followed by visualization.</p>
-<div class="codewrapper sourceCode" id="cb7">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">moving_Avg_week</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">add_rolling_average</span><span class="op">(</span><span class="va">df_incid</span>, n <span class="op">=</span> <span class="fl">7L</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">moving_Avg_week</span>, border_colour <span class="op">=</span> <span class="st">"white"</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">geom_line</span><span class="op">(</span></span>
-<span>    <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">aes</span><span class="op">(</span></span>
-<span>      x <span class="op">=</span> <span class="va">date_index</span>,</span>
-<span>      y <span class="op">=</span> <span class="va">rolling_average</span>,</span>
-<span>      color <span class="op">=</span> <span class="st">"red"</span></span>
-<span>    <span class="op">)</span></span>
-<span>  <span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="fig/simple-analysis-rendered-unnamed-chunk-5-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-3-monthly-moving-average" class="callout challenge">
-<div class="callout-square">
-<i class="callout-icon" data-feather="zap"></i>
-</div>
-<div id="challenge-3-monthly-moving-average" class="callout-inner">
-<h3 class="callout-title">Challenge 3: Monthly moving average<a class="anchor" aria-label="anchor" href="#challenge-3-monthly-moving-average"></a>
+<div id="challenge-1-can-you-do-it" class="callout-inner">
+<h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-label="anchor" href="#challenge-1-can-you-do-it"></a>
 </h3>
 <div class="callout-content">
-<p>Compute and visualize the monthly moving average of cases on
-<code>df_incid</code>?</p>
-</div>
-</div>
-</div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
-  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
-</button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
-<div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb8">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">moving_Avg_mont</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">add_rolling_average</span><span class="op">(</span><span class="va">df_incid</span>, n <span class="op">=</span> <span class="fl">30L</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span></span>
-<span>  <span class="va">moving_Avg_mont</span>,</span>
-<span>  border_colour <span class="op">=</span> <span class="st">"white"</span>,</span>
-<span>  angle <span class="op">=</span> <span class="fl">45</span></span>
-<span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">geom_line</span><span class="op">(</span></span>
-<span>    <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">aes</span><span class="op">(</span></span>
-<span>      x <span class="op">=</span> <span class="va">date_index</span>,</span>
-<span>      y <span class="op">=</span> <span class="va">rolling_average</span>,</span>
-<span>      color <span class="op">=</span> <span class="st">"red"</span></span>
-<span>    <span class="op">)</span></span>
-<span>  <span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="fig/simple-analysis-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure>
-</div>
+<ul>
+<li>Using suitable distributions for contacts, contact interval,
+infectious period, onset to hospitalized, and onset to death, generate a
+simulated linelist data for Marburg outbreak that has the probability of
+<span class="math inline">\(0.5\)</span> infection?</li>
+<li>Aggregate the generated linelist and produce some epidemic
+curves?</li>
+</ul>
 </div>
 </div>
 </div>
@@ -1918,16 +1640,10 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </h3>
 <div class="callout-content">
 <ul>
-<li>Use <a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> to:
-<ul>
-<li>fit epi-curve using either <strong>Poisson</strong> or
-<strong>NB</strong> distributions,<br>
-</li>
-<li>calculate exponential growth or decline of cases,</li>
-<li>find peak time, and</li>
-<li>computing moving average of cases in specified time window.</li>
-</ul>
-</li>
+<li>Use <code>{simulist}</code> package to generate synthetic outbreak
+data</li>
+<li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
+on a date event, and produce epidemic curves.</li>
 </ul>
 </div>
 </div>
@@ -1961,7 +1677,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -1983,9 +1699,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/aio.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/aio.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/clean-data.html b/clean-data.html
index 49108b77..d4779789 100644
--- a/clean-data.html
+++ b/clean-data.html
@@ -98,11 +98,11 @@
   Read and clean case data, and make linelist for outbreak analytics with R
 </div>
 
-<aside class="col-md-12 lesson-progress"><div style="width: 25%" class="percentage">
-    25%
+<aside class="col-md-12 lesson-progress"><div style="width: 33%" class="percentage">
+    33%
   </div>
   <div class="progress incubator">
-    <div class="progress-bar incubator" role="progressbar" style="width: 25%" aria-valuenow="25" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
+    <div class="progress-bar incubator" role="progressbar" style="width: 33%" aria-valuenow="33" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
     </div>
   </div>
 </aside><div class="container">
@@ -197,15 +197,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -920,7 +911,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -941,9 +932,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/clean-data.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/clean-data.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/config.yaml b/config.yaml
index 4c2427d2..21b1cdca 100644
--- a/config.yaml
+++ b/config.yaml
@@ -62,7 +62,7 @@ episodes:
 - read-cases.Rmd
 - clean-data.Rmd
 - describe-cases.Rmd
-- simple-analysis.Rmd
+#- simple-analysis.Rmd
 
 # Information for Learners
 learners:
diff --git a/describe-cases.html b/describe-cases.html
index fa8ace9b..0f5bfb11 100644
--- a/describe-cases.html
+++ b/describe-cases.html
@@ -98,11 +98,11 @@
   Read and clean case data, and make linelist for outbreak analytics with R
 </div>
 
-<aside class="col-md-12 lesson-progress"><div style="width: 50%" class="percentage">
-    50%
+<aside class="col-md-12 lesson-progress"><div style="width: 67%" class="percentage">
+    67%
   </div>
   <div class="progress incubator">
-    <div class="progress-bar incubator" role="progressbar" style="width: 50%" aria-valuenow="50" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
+    <div class="progress-bar incubator" role="progressbar" style="width: 67%" aria-valuenow="67" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
     </div>
   </div>
 </aside><div class="container">
@@ -191,18 +191,11 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#synthetic-outbreak-data">Synthetic outbreak data</a></li>
 <li><a href="#aggregating">Aggregating</a></li>
 <li><a href="#visualization">Visualization</a></li>
+<li><a href="#curve-of-cumulative-cases">Curve of cumulative cases</a></li>
+<li><a href="#peak-estimation">Peak estimation</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -249,7 +242,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   <div class="col-xl-8 col-lg-12 primary-content">
     <nav class="lesson-content mx-md-4" aria-label="Previous and Next Chapter"><!-- content for small screens --><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="clean-data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
-        <a class="chapter-link float-end" href="simple-analysis.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
+        <a class="chapter-link float-end" href="index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
       </div>
       <!-- content for large screens -->
       <div class="d-none d-sm-none d-md-block">
@@ -257,14 +250,14 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>
           Previous: Clean and validate
         </a>
-        <a class="chapter-link float-end" href="simple-analysis.html" rel="next">
-          Next: Simple analysis... 
+        <a class="chapter-link float-end" href="index.html" rel="next">
+          Home
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Aggregate and visualize</h1>
-        <p>Last updated on 2024-06-18 |
+        <p>Last updated on 2024-06-24 |
         
         <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/describe-cases.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -313,9 +306,14 @@ <h3 class="card-title">Objectives</h3>
 between time and the number of reported cases, spanning various
 categories (confirmed, hospitalized, deaths, and recoveries), locations,
 and other demographic factors such as gender, age, etc.</p>
-<p>::::::::::::::::::: checklist</p>
-<div class="section level3">
-<h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a></h3>
+<div id="the-double-colon" class="callout checklist">
+<div class="callout-square">
+<i class="callout-icon" data-feather="check-square"></i>
+</div>
+<div id="the-double-colon" class="callout-inner">
+<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
+</h3>
+<div class="callout-content">
 <p>The double-colon <code>::</code> in R let you call a specific
 function from a package without loading the entire package into the
 current environment.</p>
@@ -323,7 +321,8 @@ <h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor"
 <code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
 <p>This help us remember package functions and avoid namespace
 conflicts.</p>
-<p>:::::::::::::::::::</p>
+</div>
+</div>
 </div>
 </section><section id="synthetic-outbreak-data"><h2 class="section-heading">Synthetic outbreak data<a class="anchor" aria-label="anchor" href="#synthetic-outbreak-data"></a>
 </h2>
@@ -597,12 +596,64 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span></span>
 <span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">weekly_incidence_data</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in weeks)"</span>,</span>
+<span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
+<span>  <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
+</div>
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section id="curve-of-cumulative-cases"><h2 class="section-heading">Curve of cumulative cases<a class="anchor" aria-label="anchor" href="#curve-of-cumulative-cases"></a>
+</h2>
+<hr class="half-width"><p>The cumulative number of cases can be calculated using the
+<code>cumulate()</code> function from an <code>incidence2</code> object
+and visualized, as in the example below.</p>
+<div class="codewrapper sourceCode" id="cb12">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">cum_df</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">cumulate</span><span class="op">(</span><span class="va">dialy_incidence_data</span><span class="op">)</span></span>
+<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">cum_df</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
 <span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
 <span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
 <span>  <span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-can-you-do-it" class="callout discussion">
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Note that this function preserves grouping, i.e., if the
+<code>incidence2</code> object contains groups, it will accumulate the
+cases accordingly. Give it a try with the
+<code>weekly_incidence_data</code> object!</p>
+</section><section id="peak-estimation"><h2 class="section-heading">Peak estimation<a class="anchor" aria-label="anchor" href="#peak-estimation"></a>
+</h2>
+<hr class="half-width"><p>One can estimate the peak –the time with the highest number of
+recorded cases– using the <code>estimate_peak()</code> function from the
+{incidence2} package. This function employs a bootstrapping method to
+determine the peak time.</p>
+<div class="codewrapper sourceCode" id="cb13">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">peak</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span></span>
+<span>  <span class="va">dialy_incidence_data</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  alpha <span class="op">=</span> <span class="fl">0.05</span>,</span>
+<span>  first_only <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  progress <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span><span class="fu">print</span><span class="op">(</span><span class="va">peak</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 7
+  count_variable observed_peak observed_count bootstrap_peaks lower_ci   median 
+  &lt;chr&gt;          &lt;period&gt;               &lt;int&gt; &lt;list&gt;          &lt;period&gt;   &lt;perio&gt;
+1 date_onset     2023-01-03              5478 &lt;df [100 × 1]&gt;  2023-01-03 2023-0…
+# ℹ 1 more variable: upper_ci &lt;period&gt;</code></pre>
+</div>
+<p>This example demonstrates how to estimate the peak time using the
+<code>estimate_peak()</code> function at <span class="math inline">\(95%\)</span> confidence interval and using 100
+bootstrap samples.</p>
+<div id="challenge-1-can-you-do-it" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
@@ -641,7 +692,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="clean-data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
-        <a class="chapter-link float-end" href="simple-analysis.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
+        <a class="chapter-link float-end" href="index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
       </div>
       <!-- content for large screens -->
       <div class="d-none d-sm-none d-md-block">
@@ -649,8 +700,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>
           Previous: Clean and validate
         </a>
-        <a class="chapter-link float-end" href="simple-analysis.html" rel="next">
-          Next: Simple analysis... 
+        <a class="chapter-link float-end" href="index.html" rel="next">
+          Home
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -674,7 +725,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -695,9 +746,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/describe-cases.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/describe-cases.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/fig/describe-cases-rendered-unnamed-chunk-7-1.png b/fig/describe-cases-rendered-unnamed-chunk-7-1.png
index 222558d7f28ead0e89724ed70a2c6721ea27324b..bdefa18e5ec5db1979a3904d35e5ca3bbc386659 100644
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-<figure><img src="fig/simple-analysis-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="describe-cases-figure-3">Figure 3</h3>
+<figure><img src="fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
 </div>
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+        <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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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@@ -359,9 +340,9 @@ <h3 id="simple-analysis-figure-4">Figure 4</h3>
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-  "dateModified": "2024-06-19",
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 }
 
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diff --git a/index.html b/index.html
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-<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>do you get an error with epiverse-trace packages?</h3>
+  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>
+  do you get an error with epiverse-trace packages?
+  </h3>
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-<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>What to do if an Error persist?</h3>
+  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>
+  What to do if an Error persist?
+  </h3>
 </button>
 <div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
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+        <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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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   "url": "https://epiverse-trace.github.io/tutorials-early/index.html",
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-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
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 }
 
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diff --git a/instructor-notes.html b/instructor-notes.html
index 2ad925af..9c7559de 100644
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-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
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-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
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@@ -323,7 +311,7 @@ <h1>Instructor Notes</h1>
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         <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>
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+        <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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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@@ -345,9 +333,9 @@ <h1>Instructor Notes</h1>
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   "url": "https://epiverse-trace.github.io/tutorials-early/instructor-notes.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor-notes.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
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 }
 
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diff --git a/instructor/404.html b/instructor/404.html
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         <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -307,9 +296,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/404.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/404.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index e850ec3b..a88e3fbb 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -314,7 +305,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -335,9 +326,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 4bbe4de1..74169a8a 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -362,7 +353,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -383,9 +374,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/LICENSE.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/LICENSE.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 0cf476a9..f8d939d7 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -223,18 +223,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
 </div>
-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -436,7 +424,7 @@ <h3 class="callout-title">Reading compressed data<a class="anchor" aria-label="a
 <div id="accordionHint1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Give me a hint</h4>
+  <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
 <div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
@@ -459,7 +447,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Show me the solution</h4>
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
 <div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
@@ -1228,7 +1216,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-describe-cases"><p>Content from <a href="describe-cases.html">Aggregate and visualize</a></p>
 <hr>
-<p>Last updated on 2024-06-18 |
+<p>Last updated on 2024-06-24 |
         
         <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/describe-cases.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -1277,10 +1265,14 @@ <h3 class="card-title">Objectives</h3>
 between time and the number of reported cases, spanning various
 categories (confirmed, hospitalized, deaths, and recoveries), locations,
 and other demographic factors such as gender, age, etc.</p>
-<p>::::::::::::::::::: checklist</p>
-<div class="section level3">
-<h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
+<div id="the-double-colon" class="callout checklist">
+<div class="callout-square">
+<i class="callout-icon" data-feather="check-square"></i>
+</div>
+<div id="the-double-colon" class="callout-inner">
+<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
 </h3>
+<div class="callout-content">
 <p>The double-colon <code>::</code> in R let you call a specific
 function from a package without loading the entire package into the
 current environment.</p>
@@ -1288,7 +1280,8 @@ <h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor"
 <code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
 <p>This help us remember package functions and avoid namespace
 conflicts.</p>
-<p>:::::::::::::::::::</p>
+</div>
+</div>
 </div>
 </section><section id="synthetic-outbreak-data"><h2 class="section-heading">Synthetic outbreak data<a class="anchor" aria-label="anchor" href="#synthetic-outbreak-data"></a>
 </h2>
@@ -1565,353 +1558,81 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span></span>
 <span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">weekly_incidence_data</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
-<span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in weeks)"</span>,</span>
 <span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
 <span>  <span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-can-you-do-it" class="callout discussion">
-<div class="callout-square">
-<i class="callout-icon" data-feather="message-circle"></i>
-</div>
-<div id="challenge-1-can-you-do-it" class="callout-inner">
-<h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-label="anchor" href="#challenge-1-can-you-do-it"></a>
-</h3>
-<div class="callout-content">
-<ul>
-<li>Using suitable distributions for contacts, contact interval,
-infectious period, onset to hospitalized, and onset to death, generate a
-simulated linelist data for Marburg outbreak that has the probability of
-<span class="math inline">\(0.5\)</span> infection?</li>
-<li>Aggregate the generated linelist and produce some epidemic
-curves?</li>
-</ul>
-</div>
-</div>
-</div>
-<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>
-<div class="callout-content">
-<ul>
-<li>Use <code>{simulist}</code> package to generate synthetic outbreak
-data</li>
-<li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
-on a date event, and produce epidemic curves.</li>
-</ul>
-</div>
-</div>
-</div>
-<!-- 
-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><section id="aio-simple-analysis"><p>Content from <a href="simple-analysis.html">Simple analysis</a></p>
-<hr>
-<p>Last updated on 2024-06-18 |
-        
-        <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/simple-analysis.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-<p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
-<div class="text-end">
-          <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
-        </div>
-<div class="overview card">
-<h2 class="card-header">Overview</h2>
-<div class="row g-0">
-<div class="col-md-4">
-<div class="card-body">
-<div class="inner">
-<h3 class="card-title">Questions</h3>
-<ul>
-<li>What is the growth rate of the epidemic?</li>
-<li>How to identify the peak time of an outbreak?</li>
-<li>How to compute moving average of cases?</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="col-md-8">
-<div class="card-body">
-<div class="inner bordered">
-<h3 class="card-title">Objectives</h3>
-<ul>
-<li>Perform an early analysis of outbreak data</li>
-<li>Identify trends, exponential, doubling, and peak time</li>
-</ul>
-</div>
-</div>
-</div>
-</div>
-</div>
-<section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section id="curve-of-cumulative-cases"><h2 class="section-heading">Curve of cumulative cases<a class="anchor" aria-label="anchor" href="#curve-of-cumulative-cases"></a>
 </h2>
 <hr class="half-width">
-<p>Understanding the trend in case data is crucial for various purposes,
-such as forecasting future case counts, implementing public health
-interventions, and assessing the effectiveness of control measures. By
-analyzing the trend, policymakers and public health experts can make
-informed decisions to mitigate the spread of diseases and protect public
-health. This episode focuses on how to perform a simple early analysis
-on incidence data. It uses the same dataset of <strong>Covid-19 case
-data from England</strong> that utilized it in <a href="describe-cases.html">Aggregate and visualize</a> episode.</p>
-<div id="the-double-colon" class="callout checklist">
-<div class="callout-square">
-<i class="callout-icon" data-feather="check-square"></i>
-</div>
-<div id="the-double-colon" class="callout-inner">
-<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
-</h3>
-<div class="callout-content">
-<p>The double-colon <code>::</code> in R let you call a specific
-function from a package without loading the entire package into the
-current environment.</p>
-<p>For example, <code>dplyr::filter(data, condition)</code> uses
-<code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
-<p>This help us remember package functions and avoid namespace
-conflicts.</p>
-</div>
-</div>
-</div>
-</section><section id="simple-model"><h2 class="section-heading">Simple model<a class="anchor" aria-label="anchor" href="#simple-model"></a>
-</h2>
-<hr class="half-width">
-<p>Aggregated case data over a specific time unit, or incidence data,
-typically represent the number of cases occurring within that time
-frame. These data can often be assumed to follow either
-<code>Poisson distribution</code> or a
-<code>negative binomial (NB) distribution</code>, depending on the
-specific characteristics of the data and the underlying processes
-generating them. When analyzing such data, one common approach is to
-examine the trend over time by computing the rate of change, which can
-indicate whether there is exponential growth or decay in the number of
-cases. Exponential growth implies that the number of cases is increasing
-at an accelerating rate over time, while exponential decay suggests that
-the number of cases is decreasing at a decelerating rate.</p>
-<p>The <code>i2extras</code> package provides methods for modelling the
-trend in case data, calculating moving averages, and exponential growth
-or decay rate. The code chunk below computes the Covid-19 trend in UK
-within first 3 months using negative binomial distribution.</p>
-<div class="codewrapper sourceCode" id="cb1">
+<p>The cumulative number of cases can be calculated using the
+<code>cumulate()</code> function from an <code>incidence2</code> object
+and visualized, as in the example below.</p>
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="co"># load packages which provides methods for modeling</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"i2extras"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"incidence2"</span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># read data from {outbreaks} package</span></span>
-<span><span class="va">covid19_eng_case_data</span> <span class="op">&lt;-</span> <span class="fu">outbreaks</span><span class="fu">::</span><span class="va">covid19_england_nhscalls_2020</span></span>
-<span></span>
-<span><span class="co"># subset the covid19_eng_case_data to include only the first 3 months of data</span></span>
-<span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu">base</span><span class="fu">::</span><span class="fu">subset</span><span class="op">(</span></span>
-<span>  <span class="va">covid19_eng_case_data</span>,</span>
-<span>  <span class="va">covid19_eng_case_data</span><span class="op">$</span><span class="va">date</span> <span class="op">&lt;=</span> <span class="fu">min</span><span class="op">(</span><span class="va">covid19_eng_case_data</span><span class="op">$</span><span class="va">date</span><span class="op">)</span> <span class="op">+</span> <span class="fl">90</span></span>
-<span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># uses the incidence function from the incidence2 package to compute the</span></span>
-<span><span class="co"># incidence data</span></span>
-<span><span class="va">df_incid</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">incidence</span><span class="op">(</span></span>
-<span>  <span class="va">df</span>,</span>
-<span>  date_index <span class="op">=</span> <span class="st">"date"</span>,</span>
-<span>  groups <span class="op">=</span> <span class="st">"sex"</span></span>
-<span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># fit a curve to the incidence data. The model chosen is the negative binomial</span></span>
-<span><span class="co"># distribution with a significance level (alpha) of 0.05.</span></span>
-<span><span class="va">fitted_curve_nb</span> <span class="op">&lt;-</span></span>
-<span>  <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">fit_curve</span><span class="op">(</span></span>
-<span>    <span class="va">df_incid</span>,</span>
-<span>    model <span class="op">=</span> <span class="st">"negbin"</span>,</span>
-<span>    alpha <span class="op">=</span> <span class="fl">0.05</span></span>
-<span>  <span class="op">)</span></span>
-<span></span>
-<span><span class="co"># plot fitted curve</span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">fitted_curve_nb</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-poission-distribution" class="callout challenge">
-<div class="callout-square">
-<i class="callout-icon" data-feather="zap"></i>
-</div>
-<div id="challenge-1-poission-distribution" class="callout-inner">
-<h3 class="callout-title">Challenge 1: Poission distribution<a class="anchor" aria-label="anchor" href="#challenge-1-poission-distribution"></a>
-</h3>
-<div class="callout-content">
-<p>Repeat the above analysis using Poisson distribution?</p>
-</div>
-</div>
-</div>
-<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">Show me the solution</h4>
-</button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
-<div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb2">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">fitted_curve_poisson</span> <span class="op">&lt;-</span></span>
-<span>  <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">fit_curve</span><span class="op">(</span></span>
-<span>    x <span class="op">=</span> <span class="va">df_incid</span>,</span>
-<span>    model <span class="op">=</span> <span class="st">"poisson"</span>,</span>
-<span>    alpha <span class="op">=</span> <span class="fl">0.05</span></span>
-<span>  <span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">fitted_curve_poisson</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-2-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure>
-</div>
-</div>
-</div>
+<code class="sourceCode R"><span><span class="va">cum_df</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">cumulate</span><span class="op">(</span><span class="va">dialy_incidence_data</span><span class="op">)</span></span>
+<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">cum_df</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
+<span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
+<span>  <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section id="exponential-growth-or-decay-rate"><h2 class="section-heading">Exponential growth or decay rate<a class="anchor" aria-label="anchor" href="#exponential-growth-or-decay-rate"></a>
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Note that this function preserves grouping, i.e., if the
+<code>incidence2</code> object contains groups, it will accumulate the
+cases accordingly. Give it a try with the
+<code>weekly_incidence_data</code> object!</p>
+</section><section id="peak-estimation"><h2 class="section-heading">Peak estimation<a class="anchor" aria-label="anchor" href="#peak-estimation"></a>
 </h2>
 <hr class="half-width">
-<p>The exponential growth or decay rate, denoted as <span class="math inline">\(r\)</span>, serves as an indicator for the trend
-in cases, indicating whether they are increasing (growth) or decreasing
-(decay) on an exponential scale. This rate is computed using the
-so-called <strong>renewal equation</strong> <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2006.3754" class="external-link">(Wallinga
-et al. 2006)</a>, which mechanistically links the reproductive number
-<span class="math inline">\(R\)</span> of new cases to the generation
-interval of the disease. This computational method is implemented in the
-<a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> package.</p>
-<p>Below is a code snippet demonstrating how to extract the growth/decay
-rate from the above <strong>NB</strong>-fitted curve using the
-<code>growth_rate()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb3">
+<p>One can estimate the peak –the time with the highest number of
+recorded cases– using the <code>estimate_peak()</code> function from the
+{incidence2} package. This function employs a bootstrapping method to
+determine the peak time.</p>
+<div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">rates_nb</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">growth_rate</span><span class="op">(</span><span class="va">fitted_curve_nb</span><span class="op">)</span></span>
-<span><span class="va">rates_nb</span> <span class="op">&lt;-</span> <span class="fu">base</span><span class="fu">::</span><span class="fu">as.data.frame</span><span class="op">(</span><span class="va">rates_nb</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">subset</span><span class="op">(</span>select <span class="op">=</span> <span class="fu">c</span><span class="op">(</span><span class="va">sex</span>, <span class="va">r</span>, <span class="va">r_lower</span>, <span class="va">r_upper</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">print</span><span class="op">(</span><span class="va">rates_nb</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">peak</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span></span>
+<span>  <span class="va">dialy_incidence_data</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  alpha <span class="op">=</span> <span class="fl">0.05</span>,</span>
+<span>  first_only <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  progress <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span><span class="fu">print</span><span class="op">(</span><span class="va">peak</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>      sex            r      r_lower      r_upper
-1  female -0.008241228 -0.009182635 -0.007300403
-2    male -0.008346783 -0.009316775 -0.007377392
-3 unknown -0.023703987 -0.028179436 -0.019299926</code></pre>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 7
+  count_variable observed_peak observed_count bootstrap_peaks lower_ci   median 
+  &lt;chr&gt;          &lt;period&gt;               &lt;int&gt; &lt;list&gt;          &lt;period&gt;   &lt;perio&gt;
+1 date_onset     2023-01-03              5478 &lt;df [100 × 1]&gt;  2023-01-03 2023-0…
+# ℹ 1 more variable: upper_ci &lt;period&gt;</code></pre>
 </div>
-<div id="challenge-2-growth-rates-from-a-poisson-fitted-curve" class="callout discussion">
+<p>This example demonstrates how to estimate the peak time using the
+<code>estimate_peak()</code> function at <span class="math inline">\(95%\)</span> confidence interval and using 100
+bootstrap samples.</p>
+<div id="challenge-1-can-you-do-it" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="challenge-2-growth-rates-from-a-poisson-fitted-curve" class="callout-inner">
-<h3 class="callout-title">Challenge 2: Growth rates from a<strong>Poisson</strong>-fitted curve<a class="anchor" aria-label="anchor" href="#challenge-2-growth-rates-from-a-poisson-fitted-curve"></a>
-</h3>
-<div class="callout-content">
-<p>Extract growth rates from the <strong>Poisson</strong>-fitted curve
-of <strong>Challenge 1</strong>?</p>
-</div>
-</div>
-</div>
-</section><section id="peak-time"><h2 class="section-heading">Peak time<a class="anchor" aria-label="anchor" href="#peak-time"></a>
-</h2>
-<hr class="half-width">
-<p>The <strong>Peak time </strong> is the time at which the highest
-number of cases is observed in the aggregated data. It can be estimated
-using the <code>i2extras::estimate_peak()</code> function as shown in
-the below code chunk, which identify peak time from the
-<code>incidenc2</code> object <code>df_incid</code>.</p>
-<div class="codewrapper sourceCode" id="cb5">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">peaks_nb</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span><span class="va">df_incid</span>, progress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>  <span class="fu">subset</span><span class="op">(</span>select <span class="op">=</span> <span class="op">-</span><span class="fu">c</span><span class="op">(</span><span class="va">count_variable</span>, <span class="va">bootstrap_peaks</span><span class="op">)</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">print</span><span class="op">(</span><span class="va">peaks_nb</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code># A data frame: 3 × 6
-  sex     observed_peak observed_count lower_ci   median     upper_ci  
-* &lt;chr&gt;   &lt;date&gt;                 &lt;int&gt; &lt;date&gt;     &lt;date&gt;     &lt;date&gt;    
-1 female  2020-03-26              1314 2020-03-19 2020-03-23 2020-03-30
-2 male    2020-03-27              1299 2020-03-18 2020-03-26 2020-03-30
-3 unknown 2020-04-10                32 2020-03-24 2020-04-10 2020-04-16</code></pre>
-</div>
-</section><section id="moving-average"><h2 class="section-heading">Moving average<a class="anchor" aria-label="anchor" href="#moving-average"></a>
-</h2>
-<hr class="half-width">
-<p>A moving or rolling average calculates the average number of cases
-within a specified time period. This can be achieved by utilizing the
-<code>add_rolling_average()</code> function from the
-<a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> package on an <code>incidence2 object</code>.
-The following code chunk demonstrates the computation of the weekly
-average number of cases from the <code>incidence2</code> object
-<code>df_incid</code>, followed by visualization.</p>
-<div class="codewrapper sourceCode" id="cb7">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">moving_Avg_week</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">add_rolling_average</span><span class="op">(</span><span class="va">df_incid</span>, n <span class="op">=</span> <span class="fl">7L</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">moving_Avg_week</span>, border_colour <span class="op">=</span> <span class="st">"white"</span>, angle <span class="op">=</span> <span class="fl">45</span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">geom_line</span><span class="op">(</span></span>
-<span>    <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">aes</span><span class="op">(</span></span>
-<span>      x <span class="op">=</span> <span class="va">date_index</span>,</span>
-<span>      y <span class="op">=</span> <span class="va">rolling_average</span>,</span>
-<span>      color <span class="op">=</span> <span class="st">"red"</span></span>
-<span>    <span class="op">)</span></span>
-<span>  <span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-5-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-3-monthly-moving-average" class="callout challenge">
-<div class="callout-square">
-<i class="callout-icon" data-feather="zap"></i>
-</div>
-<div id="challenge-3-monthly-moving-average" class="callout-inner">
-<h3 class="callout-title">Challenge 3: Monthly moving average<a class="anchor" aria-label="anchor" href="#challenge-3-monthly-moving-average"></a>
+<div id="challenge-1-can-you-do-it" class="callout-inner">
+<h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-label="anchor" href="#challenge-1-can-you-do-it"></a>
 </h3>
 <div class="callout-content">
-<p>Compute and visualize the monthly moving average of cases on
-<code>df_incid</code>?</p>
-</div>
-</div>
-</div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
-  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
-</button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
-<div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb8">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">moving_Avg_mont</span> <span class="op">&lt;-</span> <span class="fu">i2extras</span><span class="fu">::</span><span class="fu">add_rolling_average</span><span class="op">(</span><span class="va">df_incid</span>, n <span class="op">=</span> <span class="fl">30L</span><span class="op">)</span></span>
-<span></span>
-<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span></span>
-<span>  <span class="va">moving_Avg_mont</span>,</span>
-<span>  border_colour <span class="op">=</span> <span class="st">"white"</span>,</span>
-<span>  angle <span class="op">=</span> <span class="fl">45</span></span>
-<span><span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">geom_line</span><span class="op">(</span></span>
-<span>    <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">aes</span><span class="op">(</span></span>
-<span>      x <span class="op">=</span> <span class="va">date_index</span>,</span>
-<span>      y <span class="op">=</span> <span class="va">rolling_average</span>,</span>
-<span>      color <span class="op">=</span> <span class="st">"red"</span></span>
-<span>    <span class="op">)</span></span>
-<span>  <span class="op">)</span> <span class="op">+</span></span>
-<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"Date"</span>, y <span class="op">=</span> <span class="st">"Cases"</span><span class="op">)</span></span></code></pre>
-</div>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure>
-</div>
+<ul>
+<li>Using suitable distributions for contacts, contact interval,
+infectious period, onset to hospitalized, and onset to death, generate a
+simulated linelist data for Marburg outbreak that has the probability of
+<span class="math inline">\(0.5\)</span> infection?</li>
+<li>Aggregate the generated linelist and produce some epidemic
+curves?</li>
+</ul>
 </div>
 </div>
 </div>
@@ -1924,16 +1645,10 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </h3>
 <div class="callout-content">
 <ul>
-<li>Use <a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> to:
-<ul>
-<li>fit epi-curve using either <strong>Poisson</strong> or
-<strong>NB</strong> distributions,<br>
-</li>
-<li>calculate exponential growth or decline of cases,</li>
-<li>find peak time, and</li>
-<li>computing moving average of cases in specified time window.</li>
-</ul>
-</li>
+<li>Use <code>{simulist}</code> package to generate synthetic outbreak
+data</li>
+<li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
+on a date event, and produce epidemic curves.</li>
 </ul>
 </div>
 </div>
@@ -1967,7 +1682,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -1989,9 +1704,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/aio.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/aio.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/clean-data.html b/instructor/clean-data.html
index 927bc3fa..2edafeb2 100644
--- a/instructor/clean-data.html
+++ b/instructor/clean-data.html
@@ -98,11 +98,11 @@
   Read and clean case data, and make linelist for outbreak analytics with R
 </div>
 
-<aside class="col-md-12 lesson-progress"><div style="width: 25%" class="percentage">
-    25%
+<aside class="col-md-12 lesson-progress"><div style="width: 33%" class="percentage">
+    33%
   </div>
   <div class="progress incubator">
-    <div class="progress-bar incubator" role="progressbar" style="width: 25%" aria-valuenow="25" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
+    <div class="progress-bar incubator" role="progressbar" style="width: 33%" aria-valuenow="33" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
     </div>
   </div>
 </aside><div class="container">
@@ -197,15 +197,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -922,7 +913,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -943,9 +934,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/clean-data.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/clean-data.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/describe-cases.html b/instructor/describe-cases.html
index f0e78421..ad9bff18 100644
--- a/instructor/describe-cases.html
+++ b/instructor/describe-cases.html
@@ -98,11 +98,11 @@
   Read and clean case data, and make linelist for outbreak analytics with R
 </div>
 
-<aside class="col-md-12 lesson-progress"><div style="width: 50%" class="percentage">
-    50%
+<aside class="col-md-12 lesson-progress"><div style="width: 67%" class="percentage">
+    67%
   </div>
   <div class="progress incubator">
-    <div class="progress-bar incubator" role="progressbar" style="width: 50%" aria-valuenow="50" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
+    <div class="progress-bar incubator" role="progressbar" style="width: 67%" aria-valuenow="67" aria-label="Lesson Progress" aria-valuemin="0" aria-valuemax="100">
     </div>
   </div>
 </aside><div class="container">
@@ -191,18 +191,11 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#synthetic-outbreak-data">Synthetic outbreak data</a></li>
 <li><a href="#aggregating">Aggregating</a></li>
 <li><a href="#visualization">Visualization</a></li>
+<li><a href="#curve-of-cumulative-cases">Curve of cumulative cases</a></li>
+<li><a href="#peak-estimation">Peak estimation</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -249,7 +242,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   <div class="col-xl-8 col-lg-12 primary-content">
     <nav class="lesson-content mx-md-4" aria-label="Previous and Next Chapter"><!-- content for small screens --><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/clean-data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
-        <a class="chapter-link float-end" href="../instructor/simple-analysis.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
+        <a class="chapter-link float-end" href="../instructor/index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
       </div>
       <!-- content for large screens -->
       <div class="d-none d-sm-none d-md-block">
@@ -257,14 +250,14 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>
           Previous: Clean and validate
         </a>
-        <a class="chapter-link float-end" href="../instructor/simple-analysis.html" rel="next">
-          Next: Simple analysis... 
+        <a class="chapter-link float-end" href="../instructor/index.html" rel="next">
+          Home
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Aggregate and visualize</h1>
-        <p>Last updated on 2024-06-18 |
+        <p>Last updated on 2024-06-24 |
         
         <a href="https://github.com/epiverse-trace/tutorials-early/edit/main/episodes/describe-cases.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -315,9 +308,14 @@ <h3 class="card-title">Objectives</h3>
 between time and the number of reported cases, spanning various
 categories (confirmed, hospitalized, deaths, and recoveries), locations,
 and other demographic factors such as gender, age, etc.</p>
-<p>::::::::::::::::::: checklist</p>
-<div class="section level3">
-<h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a></h3>
+<div id="the-double-colon" class="callout checklist">
+<div class="callout-square">
+<i class="callout-icon" data-feather="check-square"></i>
+</div>
+<div id="the-double-colon" class="callout-inner">
+<h3 class="callout-title">The double-colon<a class="anchor" aria-label="anchor" href="#the-double-colon"></a>
+</h3>
+<div class="callout-content">
 <p>The double-colon <code>::</code> in R let you call a specific
 function from a package without loading the entire package into the
 current environment.</p>
@@ -325,7 +323,8 @@ <h3 id="the-double-colon">The double-colon<a class="anchor" aria-label="anchor"
 <code>filter()</code> from the <a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a> package.</p>
 <p>This help us remember package functions and avoid namespace
 conflicts.</p>
-<p>:::::::::::::::::::</p>
+</div>
+</div>
 </div>
 </section><section id="synthetic-outbreak-data"><h2 class="section-heading">Synthetic outbreak data<a class="anchor" aria-label="anchor" href="#synthetic-outbreak-data"></a>
 </h2>
@@ -599,12 +598,64 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span></span>
 <span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">weekly_incidence_data</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
+<span>    x <span class="op">=</span> <span class="st">"Time (in weeks)"</span>,</span>
+<span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
+<span>  <span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
+</div>
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section id="curve-of-cumulative-cases"><h2 class="section-heading">Curve of cumulative cases<a class="anchor" aria-label="anchor" href="#curve-of-cumulative-cases"></a>
+</h2>
+<hr class="half-width"><p>The cumulative number of cases can be calculated using the
+<code>cumulate()</code> function from an <code>incidence2</code> object
+and visualized, as in the example below.</p>
+<div class="codewrapper sourceCode" id="cb12">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">cum_df</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">cumulate</span><span class="op">(</span><span class="va">dialy_incidence_data</span><span class="op">)</span></span>
+<span><span class="fu">base</span><span class="fu">::</span><span class="fu">plot</span><span class="op">(</span><span class="va">cum_df</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu">labs</span><span class="op">(</span></span>
 <span>    x <span class="op">=</span> <span class="st">"Time (in days)"</span>,</span>
 <span>    y <span class="op">=</span> <span class="st">"weekly cases"</span></span>
 <span>  <span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">tracetheme</span><span class="fu">::</span><span class="fu">theme_trace</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="challenge-1-can-you-do-it" class="callout discussion">
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Note that this function preserves grouping, i.e., if the
+<code>incidence2</code> object contains groups, it will accumulate the
+cases accordingly. Give it a try with the
+<code>weekly_incidence_data</code> object!</p>
+</section><section id="peak-estimation"><h2 class="section-heading">Peak estimation<a class="anchor" aria-label="anchor" href="#peak-estimation"></a>
+</h2>
+<hr class="half-width"><p>One can estimate the peak –the time with the highest number of
+recorded cases– using the <code>estimate_peak()</code> function from the
+{incidence2} package. This function employs a bootstrapping method to
+determine the peak time.</p>
+<div class="codewrapper sourceCode" id="cb13">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">peak</span> <span class="op">&lt;-</span> <span class="fu">incidence2</span><span class="fu">::</span><span class="fu">estimate_peak</span><span class="op">(</span></span>
+<span>  <span class="va">dialy_incidence_data</span>,</span>
+<span>  n <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  alpha <span class="op">=</span> <span class="fl">0.05</span>,</span>
+<span>  first_only <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  progress <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span><span class="fu">print</span><span class="op">(</span><span class="va">peak</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 7
+  count_variable observed_peak observed_count bootstrap_peaks lower_ci   median 
+  &lt;chr&gt;          &lt;period&gt;               &lt;int&gt; &lt;list&gt;          &lt;period&gt;   &lt;perio&gt;
+1 date_onset     2023-01-03              5478 &lt;df [100 × 1]&gt;  2023-01-03 2023-0…
+# ℹ 1 more variable: upper_ci &lt;period&gt;</code></pre>
+</div>
+<p>This example demonstrates how to estimate the peak time using the
+<code>estimate_peak()</code> function at <span class="math inline">\(95%\)</span> confidence interval and using 100
+bootstrap samples.</p>
+<div id="challenge-1-can-you-do-it" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
@@ -643,7 +694,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/clean-data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
-        <a class="chapter-link float-end" href="../instructor/simple-analysis.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
+        <a class="chapter-link float-end" href="../instructor/index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
       </div>
       <!-- content for large screens -->
       <div class="d-none d-sm-none d-md-block">
@@ -651,8 +702,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>
           Previous: Clean and validate
         </a>
-        <a class="chapter-link float-end" href="../instructor/simple-analysis.html" rel="next">
-          Next: Simple analysis... 
+        <a class="chapter-link float-end" href="../instructor/index.html" rel="next">
+          Home
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -676,7 +727,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -697,9 +748,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/describe-cases.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/describe-cases.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index ef38e5c0..eb68dfff 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -223,18 +223,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
 </div>
-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -305,16 +293,9 @@ <h3 id="clean-data-figure-1">Figure 1</h3>
 <h3 id="describe-cases-figure-1">Figure 1</h3>
 <figure><img src="../fig/describe-cases-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
 <h3 id="describe-cases-figure-2">Figure 2</h3>
-<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section><section id="simple-analysis"><h2 class="section-heading"><a href="simple-analysis.html">Simple analysis</a></h2>
-<hr class="half-width">
-<h3 id="simple-analysis-figure-1">Figure 1</h3>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-1-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
-<h3 id="simple-analysis-figure-2">Figure 2</h3>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-2-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
-<h3 id="simple-analysis-figure-3">Figure 3</h3>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-5-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
-<h3 id="simple-analysis-figure-4">Figure 4</h3>
-<figure><img src="../fig/simple-analysis-rendered-unnamed-chunk-6-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="describe-cases-figure-3">Figure 3</h3>
+<figure><img src="../fig/describe-cases-rendered-unnamed-chunk-8-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
 </div>
     </main>
 </div>
@@ -339,7 +320,7 @@ <h3 id="simple-analysis-figure-4">Figure 4</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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -361,9 +342,9 @@ <h3 id="simple-analysis-figure-4">Figure 4</h3>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/images.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/images.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index b4e5f87a..170d2832 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -184,15 +184,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -293,16 +284,6 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <span class="visually-hidden">Duration: </span>01h 30m
 </td>
 <td>
- 4. <a href="simple-analysis.html">Simple analysis</a>
-</td>
-<td>
-What is the growth rate of the epidemic?<br>How to identify the peak
-time of an outbreak?<br>How to compute moving average of cases?
-</td>
-</tr><tr><td>
-<span class="visually-hidden">Duration: </span>02h 00m
-</td>
-<td>
 Finish
 </td>
 <td>
@@ -523,7 +504,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="accordion-item">
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">
-<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>do you get an error with epiverse-trace packages?</h3>
+  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>
+  do you get an error with epiverse-trace packages?
+  </h3>
 </button>
 <div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
@@ -547,7 +530,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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   <h3 class="accordion-header" id="headingSpoiler2">
-<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>What to do if an Error persist?</h3>
+  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>
+  What to do if an Error persist?
+  </h3>
 </button>
 <div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
@@ -721,7 +706,7 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
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         <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>
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+        <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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -742,9 +727,9 @@ <h3 id="download-the-data">Download the data<a class="anchor" aria-label="anchor
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   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/index.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/index.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 8e4d50d8..449245ee 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -223,18 +223,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
 </div>
-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -303,7 +291,6 @@ <h1>Instructor Notes</h1>
       <section id="aggregate-instructor-notes"><section id="read-cases"><h2 class="section-heading"><a href="read-cases.html">Read case data</a></h2>
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 <hr class="half-width"></section><section id="describe-cases"><h2 class="section-heading"><a href="describe-cases.html">Aggregate and visualize</a></h2>
-<hr class="half-width"></section><section id="simple-analysis"><h2 class="section-heading"><a href="simple-analysis.html">Simple analysis</a></h2>
 <hr class="half-width"></section></section>
 </div>
     </main>
@@ -329,7 +316,7 @@ <h1>Instructor Notes</h1>
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         <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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@@ -351,9 +338,9 @@ <h1>Instructor Notes</h1>
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   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/instructor-notes.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index b31b09ee..78e62709 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -223,18 +223,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
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-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -313,19 +301,6 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 data</li>
 <li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
 on a date event, and produce epidemic curves.</li>
-</ul></section><section id="simple-analysis"><h2 class="section-heading"><a href="simple-analysis.html">Simple analysis</a></h2>
-<hr class="half-width">
-<ul>
-<li>Use <a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> to:
-<ul>
-<li>fit epi-curve using either <strong>Poisson</strong> or
-<strong>NB</strong> distributions,<br>
-</li>
-<li>calculate exponential growth or decline of cases,</li>
-<li>find peak time, and</li>
-<li>computing moving average of cases in specified time window.</li>
-</ul>
-</li>
 </ul></section>
 </div>
     </main>
@@ -351,7 +326,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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-        <p>Built with <a href="https://github.com/epiverse-trace/sandpaper/tree/patch-renv-github-bug" class="external-link">sandpaper (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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@@ -373,9 +348,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/key-points.html",
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-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 1e9524a8..e5b70a37 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
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-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
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@@ -273,7 +264,7 @@ <h1>Learner Profiles</h1>
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         <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -294,9 +285,9 @@ <h1>Learner Profiles</h1>
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   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/profiles.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/read-cases.html b/instructor/read-cases.html
index 9005e557..34fca39c 100644
--- a/instructor/read-cases.html
+++ b/instructor/read-cases.html
@@ -194,15 +194,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -405,7 +396,7 @@ <h3 class="callout-title">Reading compressed data<a class="anchor" aria-label="a
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 <div class="accordion-item">
 <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">Give me a hint</h4>
+  <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
 <div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
@@ -428,7 +419,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Show me the solution</h4>
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
 <div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
@@ -587,7 +578,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -608,9 +599,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/read-cases.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/read-cases.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 721580e0..210bdda8 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -574,7 +565,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -595,9 +586,9 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/instructor/reference.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/instructor/reference.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index c4ebf8ec..559daffa 100644
--- a/key-points.html
+++ b/key-points.html
@@ -222,18 +222,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
   </div>
 <!--/div.accordion-item-->
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-<!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div>
-<!--/div.accordion-header-->
-        
-  </div>
-<!--/div.accordion-item-->
-</div>
 <!--/div.accordion-flush-->
 
                 </div>
@@ -311,19 +299,6 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 data</li>
 <li>Use <a href="https://www.reconverse.org/incidence2/" class="external-link">incidence2</a> package to aggregate case data based
 on a date event, and produce epidemic curves.</li>
-</ul></section><section id="simple-analysis"><h2 class="section-heading"><a href="simple-analysis.html">Simple analysis</a></h2>
-<hr class="half-width">
-<ul>
-<li>Use <a href="https://www.reconverse.org/i2extras/" class="external-link">i2extras</a> to:
-<ul>
-<li>fit epi-curve using either <strong>Poisson</strong> or
-<strong>NB</strong> distributions,<br>
-</li>
-<li>calculate exponential growth or decline of cases,</li>
-<li>find peak time, and</li>
-<li>computing moving average of cases in specified time window.</li>
-</ul>
-</li>
 </ul></section>
 </div>
     </main>
@@ -349,7 +324,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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         <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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@@ -371,9 +346,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "url": "https://epiverse-trace.github.io/tutorials-early/key-points.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/key-points.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index e13aefde..a2509282 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,13 +1,12 @@
 "file" "checksum" "built" "date"
 "CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2024-06-18"
 "LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2024-06-18"
-"config.yaml" "60b0e85c5dcc45ddae827cc982c4639c" "site/built/config.yaml" "2024-06-18"
+"config.yaml" "f43c2370a9787e81ec952f5606830b1a" "site/built/config.yaml" "2024-06-24"
 "index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2024-06-18"
 "links.md" "fe82d0a436c46f4b07b82684ed2cceaf" "site/built/links.md" "2024-06-18"
 "episodes/read-cases.Rmd" "b7aef81b60501065599814c0db15f512" "site/built/read-cases.md" "2024-06-18"
 "episodes/clean-data.Rmd" "a9fb677a718fe9cfcbf60478d9be76f7" "site/built/clean-data.md" "2024-06-18"
-"episodes/describe-cases.Rmd" "14f3557b325b58d520e62d312f666cc1" "site/built/describe-cases.md" "2024-06-18"
-"episodes/simple-analysis.Rmd" "3c8af5cb2583a828e175666dc681169e" "site/built/simple-analysis.md" "2024-06-18"
+"episodes/describe-cases.Rmd" "68e83c7c95baa11a58f151728efe96b6" "site/built/describe-cases.md" "2024-06-24"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-06-18"
 "learners/reference.md" "106717912e909a7c8d9e3e8fea48e17d" "site/built/reference.md" "2024-06-18"
 "learners/setup.md" "714df3f336160fae26af04ee7091c588" "site/built/setup.md" "2024-06-19"
diff --git a/pkgdown.yml b/pkgdown.yml
index 639f49e7..a0f588a8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-19T16:33Z
+last_built: 2024-06-24T11:22Z
 
diff --git a/profiles.html b/profiles.html
index d146e3d7..ed49942d 100644
--- a/profiles.html
+++ b/profiles.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -273,7 +264,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -294,9 +285,9 @@ <h1>Learner Profiles</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/profiles.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/profiles.html",
-  "dateCreated": "2024-06-19",
-  "dateModified": "2024-06-19",
-  "datePublished": "2024-06-19"
+  "dateCreated": "2024-06-24",
+  "dateModified": "2024-06-24",
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/read-cases.html b/read-cases.html
index 40ff0b4b..36b36360 100644
--- a/read-cases.html
+++ b/read-cases.html
@@ -194,15 +194,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -403,7 +394,7 @@ <h3 class="callout-title">Reading compressed data<a class="anchor" aria-label="a
 <div id="accordionHint1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Give me a hint</h4>
+  <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
 <div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
@@ -426,7 +417,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Show me the solution</h4>
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
 <div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
@@ -585,7 +576,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -606,9 +597,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/read-cases.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/read-cases.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 3dcf3151..8746e155 100644
--- a/reference.html
+++ b/reference.html
@@ -180,15 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="describe-cases.html">3. Aggregate and visualize</a>
     </div><!--/div.accordion-header-->
         
-  </div><!--/div.accordion-item-->
-</div><!--/div.accordion-flush-->
-
-<div class="accordion accordion-flush" id="accordionFlush5">
-  <div class="accordion-item">
-    <div class="accordion-header" id="flush-heading5">
-        <a href="simple-analysis.html">4. Simple analysis</a>
-    </div><!--/div.accordion-header-->
-        
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -572,7 +563,7 @@ <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 (0.16.4)</a>, <a href="https://github.com/carpentries/pegboard/tree/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</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/a32a7836d4455f407c3cafe8ab95edc636e5e919" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/epiverse-trace/varnish/tree/epiversetheme" class="external-link">varnish (1.0.2)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -593,9 +584,9 @@ <h1>Glossary of Terms: Epiverse-TRACE</h1>
   "creativeWorkStatus": "active",
   "url": "https://epiverse-trace.github.io/tutorials-early/reference.html",
   "identifier": "https://epiverse-trace.github.io/tutorials-early/reference.html",
-  "dateCreated": "2024-06-19",
+  "dateCreated": "2024-06-24",
   "dateModified": "2024-06-18",
-  "datePublished": "2024-06-19"
+  "datePublished": "2024-06-24"
 }
 
   </script><script>