From 6bef70ee32725305a97ae843b47e0c50706448bd Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Wed, 10 Apr 2024 16:54:02 +0000
Subject: [PATCH] site deploy

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Source  : ba5df882b441076ee62682576ee1619674bc96e9
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-04-10 16:53:44 +0000
Message : markdown source builds

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Source  : 2202d7c6eb14a8b7905f11759650cb9767320b8a
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2024-04-10 16:52:17 +0000
Message : Merge pull request #273 from JasonJWilliamsNY/patch-for-#55

Add challenges and explanations on classes and modes for #55
---
 00-introduction.html                          |   6 +-
 01-r-basics.html                              | 275 +++++++---
 03-basics-factors-dataframes.html             | 192 ++++---
 06-data-visualization.html                    |   8 +-
 aio.html                                      | 479 ++++++++++++------
 ...dataframes-rendered-unnamed-chunk-12-1.png | Bin 0 -> 362 bytes
 ...dataframes-rendered-unnamed-chunk-16-1.png | Bin 3688 -> 3685 bytes
 ...dataframes-rendered-unnamed-chunk-18-1.png | Bin 0 -> 3688 bytes
 images.html                                   |   4 +-
 instructor/00-introduction.html               |   6 +-
 instructor/01-r-basics.html                   | 275 +++++++---
 instructor/03-basics-factors-dataframes.html  | 192 ++++---
 instructor/06-data-visualization.html         |   8 +-
 instructor/aio.html                           | 479 ++++++++++++------
 instructor/images.html                        |   4 +-
 md5sum.txt                                    |   4 +-
 pkgdown.yml                                   |   2 +-
 17 files changed, 1331 insertions(+), 603 deletions(-)
 create mode 100644 fig/03-basics-factors-dataframes-rendered-unnamed-chunk-12-1.png
 create mode 100644 fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png

diff --git a/00-introduction.html b/00-introduction.html
index 04f5b3010..b29e9c680 100644
--- a/00-introduction.html
+++ b/00-introduction.html
@@ -664,7 +664,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -905,7 +905,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
diff --git a/01-r-basics.html b/01-r-basics.html
index 392bbd15d..ec5d7637b 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
@@ -172,7 +172,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#creating-objects-in-r">Creating objects in R</a></li>
 <li><a href="#naming-objects-in-r">Naming objects in R</a></li>
 <li><a href="#reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects</a></li>
-<li><a href="#understanding-object-data-types-modes">Understanding object data types (modes)</a></li>
+<li><a href="#understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)</a></li>
 <li><a href="#mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects</a></li>
 <li><a href="#vectors">Vectors</a></li>
 <li><a href="#creating-and-subsetting-vectors">Creating and subsetting vectors</a></li>
@@ -297,7 +297,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics</h1>
-        <p>Last updated on 2024-04-04 |
+        <p>Last updated on 2024-04-10 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -497,7 +497,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <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 id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -603,19 +603,48 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section id="understanding-object-data-types-modes"><h2 class="section-heading">Understanding object data types (modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-modes"></a>
+</section><section id="understanding-object-data-types-classes-and-modes"><h2 class="section-heading">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
-<hr class="half-width"><p>In R, <strong>every object has two properties</strong>:</p>
+<hr class="half-width"><p>In R, <strong>every object has several properties</strong>:</p>
 <ul><li>
 <strong>Length</strong>: How many distinct values are held in that
 object</li>
 <li>
 <strong>Mode</strong>: What is the classification (type) of that
 object.</li>
+<li>
+<strong>Class</strong>: A property assigned to an object that
+determines how a function will operate on it.</li>
 </ul><p>We will get to the “length” property later in the lesson. The
 <strong>“mode” property</strong> <strong>corresponds to the type of data
-an object represents</strong>. The most common modes you will encounter
-in R are:</p>
+an object represents</strong> and the <strong>“class” property
+determines how functions will work with that object.</strong></p>
+<div id="tip-classess-vs.-modes" class="callout">
+<div class="callout-square">
+<i class="callout-icon" data-feather="bell"></i>
+</div>
+<div id="tip-classess-vs.-modes" class="callout-inner">
+<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
+</h3>
+<div class="callout-content">
+<p>The difference between modes and classes is a bit
+<strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
+discussions</a>. Often, these terms are used interchangeably. Do you
+really need to know the difference?</p>
+<p>Well, perhaps. This section is important for you to have a better
+understanding of how R works and how to write usable code. However, you
+might not come across a situation where the difference is crucial while
+you are taking your first steps in learning R. However, the overarching
+concept—<strong>that objects in R have these properties and that you can
+use functions to check or change them</strong>—is very important!</p>
+<p>In this lesson we will mostly stick to <strong>mode</strong> but we
+will throw in a few examples of the <code>class()</code> and
+<code>typeof()</code> so you can see some examples of where it may make
+a difference.</p>
+</div>
+</div>
+</div>
+<p>The most common modes you will encounter in R are:</p>
 <table class="table"><colgroup><col width="7%"><col width="92%"></colgroup><thead><tr class="header"><th>Mode (abbreviation)</th>
 <th>Type of data</th>
 </tr></thead><tbody><tr class="odd"><td>Numeric (num)</td>
@@ -633,9 +662,9 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 natural language where we refer to them as the parts of speech,
 e.g. nouns, verbs, adverbs, etc. Once you know if a word - perhaps an
 unfamiliar one - is a noun, you can probably guess you can count it and
-make it plural if there is more than one (e.g. 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
+make it plural if there is more than one (e.g., 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
 Tuataras). If something is a adjective, you can usually change it into
-an adverb by adding “-ly” (e.g. <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
+an adverb by adding “-ly” (e.g., <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
 jejunely). Depending on the context, you may need to decide if a word is
 in one category or another (e.g “cut” may be a noun when it’s on your
 finger, or a verb when you are preparing vegetables). These concepts
@@ -665,7 +694,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <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 id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <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>
@@ -726,6 +755,88 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
+<h3 class="callout-title">Exercise: Create objects and check their class
+using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
+</h3>
+<div class="callout-content">
+<p>Using the objects created in the previous challenge, use the
+<code>class()</code> function to check their classes.</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution3" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+</button>
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div class="accordion-body">
+<div class="codewrapper sourceCode" id="cb17">
+<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="fu">class</span><span class="op">(</span><span class="va">chromosome_name</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb19">
+<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="fu">class</span><span class="op">(</span><span class="va">od_600_value</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>[1] "numeric"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb21">
+<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="fu">class</span><span class="op">(</span><span class="va">chr_position</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb23">
+<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="fu">class</span><span class="op">(</span><span class="va">spock</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>[1] "logical"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb25">
+<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="fu">class</span><span class="op">(</span><span class="va">pilot</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'pilot' not found</code></pre>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p>Notice that in the two challenges, <code>mode()</code> and
+<code>class()</code> return the same results. This time…</p>
 <p>Notice from the solution that even if a series of numbers is given as
 a value R will consider them to be in the “character” mode if they are
 enclosed as single or double quotes. Also, notice that you cannot take a
@@ -737,7 +848,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 was originally. If we want to create an object called <code>pilot</code>
 that was the <strong>name</strong> “Earhart”, we need to enclose
 <code>Earhart</code> in quotation marks.</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb27">
 <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">
@@ -749,6 +860,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
+<div class="codewrapper sourceCode" id="cb29">
+<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">pilot</span> <span class="op">&lt;-</span> <span class="st">"Earhart"</span></span>
+<span><span class="fu">typeof</span><span class="op">(</span><span class="va">pilot</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>[1] "character"</code></pre>
+</div>
 </section><section id="mathematical-and-functional-operations-on-objects"><h2 class="section-heading">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width"><p>Once an object exists (which by definition also means it has a mode),
@@ -772,7 +895,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tr><tr class="odd"><td>a%%b</td>
 <td>modulus (returns the remainder after division)</td>
 </tr></tbody></table><p>These can be used with literal numbers:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb31">
 <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">
@@ -785,7 +908,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>and importantly, can be used on any object that evaluates to
 (i.e. interpreted by R) a numeric object:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb33">
 <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">
@@ -814,14 +937,14 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb35">
 <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">
@@ -846,7 +969,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 “concatenate” or “combine” function. Inside the function you may enter
 one or more values; for multiple values, separate each value with a
 comma:</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb37">
 <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">
@@ -859,7 +982,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>mode()</code> and <code>length()</code> functions respectively.
 Another useful function that gives both of these pieces of information
 is the <code>str()</code> (structure) function.</p>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -871,7 +994,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -882,7 +1005,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -900,7 +1023,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </section><section id="creating-and-subsetting-vectors"><h2 class="section-heading">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
 </h2>
 <hr class="half-width"><p>Let’s create a few more vectors to play around with:</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -916,7 +1039,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <strong>bracket notation</strong>. We type the name of the vector
 followed by square brackets. In those square brackets we place the index
 (e.g. a number) in that bracket as follows:</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb45">
 <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">
@@ -931,7 +1054,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In R, every item your vector is indexed, starting from the first item
 (1) through to the final number of items in your vector. You can also
 retrieve a range of numbers:</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb47">
 <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">
@@ -947,7 +1070,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>If you want to retrieve several (but not necessarily sequential)
 items from a vector, you pass a <strong>vector of indices</strong>; a
 vector that has the numbered positions you wish to retrieve.</p>
-<div class="codewrapper sourceCode" id="cb37">
+<div class="codewrapper sourceCode" id="cb49">
 <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">
@@ -964,7 +1087,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 subsetting a vector (see <a href="https://thomasleeper.com/Rcourse/Tutorials/vectorindexing.html" class="external-link">these
 examples</a>). Also, several of these subsetting expressions can be
 combined:</p>
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb51">
 <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">
@@ -982,7 +1105,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <hr class="half-width"><p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
-<div class="codewrapper sourceCode" id="cb41">
+<div class="codewrapper sourceCode" id="cb53">
 <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">
@@ -991,7 +1114,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">snp_genes</span> <span class="op">&lt;-</span> <span class="fu">c</span><span class="op">(</span><span class="va">snp_genes</span>, <span class="st">"CYP1A1"</span>, <span class="st">"APOA5"</span><span class="op">)</span></span></code></pre>
 </div>
 <p>We can verify that “snp_genes” contains the new gene entry</p>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb54">
 <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">
@@ -1004,7 +1127,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Using a negative index will return a version of a vector with that
 index’s value removed:</p>
-<div class="codewrapper sourceCode" id="cb44">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1017,7 +1140,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can remove that value from our vector by overwriting it with this
 expression:</p>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1031,7 +1154,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can also explicitly rename or add a value to our index using
 double bracket notation:</p>
-<div class="codewrapper sourceCode" id="cb48">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -1065,12 +1188,12 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li>False - Vectors have both of these properties<br></li>
 <li>True<br></li>
@@ -1092,7 +1215,7 @@ <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 we wanted get all of the SNPs in our vector of SNP positions that were
 greater than 100,000,000. We could index using the ‘&gt;’ (greater than)
 logical operator:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -1138,7 +1261,7 @@ <h3 class="callout-title">The magic of programming<a class="anchor" aria-label="
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
 better understood if you examine what the expression “snp_positions &gt;
 100000000” evaluates to:</p>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -1152,7 +1275,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>The output above is a logical vector, the 4th element of which is
 TRUE. When you pass a logical vector as an index, R will return the true
 values:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -1176,7 +1299,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 positions was the one that was greater than 100,000,000?</p>
 <p>We can use the <code>which()</code> function to return the indices of
 any item that evaluates as TRUE in our comparison:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -1192,7 +1315,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 used when our code is executed. Rather than put in a pre-determined
 value (e.g 100000000) we can use an object that can take on whatever
 value we need. So for example:</p>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -1217,7 +1340,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 for <code>not avaliable</code>). Missing data will get a more detailed
 treatment later, but the <code>is.NA()</code> function will return a
 logical vector, with TRUE for any NA value:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -1235,7 +1358,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 values) is present a vector. You can do this using the comparison
 operator <code>%in%</code>, which will return TRUE for any value in your
 collection that is in the vector you are searching:</p>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -1294,14 +1417,14 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution6" 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="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
-  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
+  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -1312,7 +1435,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -1323,7 +1446,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -1353,14 +1476,14 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution6" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution7" 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="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
-  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
+  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -1372,7 +1495,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971" "rs662799" </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -1384,7 +1507,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "3"  "11" "X"  "6"  "11"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -1420,14 +1543,14 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution7" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution8" 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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
-  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
+  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -1465,14 +1588,14 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 </ul></div>
 </div>
 </div>
-<div id="accordionSolution8" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution9" 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="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
-  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
+  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb90">
 <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">
@@ -1500,14 +1623,14 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution9" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution10" 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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
-  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
+  <h4 class="accordion-header" id="headingSolution10">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb92">
 <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">
@@ -1538,7 +1661,7 @@ <h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#list
 lists using this <a href="https://r4ds.had.co.nz/vectors.html#lists" class="external-link">nice tutorial</a>. In
 this one example, we will create a named list and show you how to
 retrieve items from the list.</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb94">
 <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">
@@ -1567,7 +1690,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get all the values for the <code>position</code> object in the
 list, we use the <code>$</code> notation:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb96">
 <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">
@@ -1582,7 +1705,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get the first value in the <code>position</code> object, use the
 <code>[]</code> notation to index:</p>
-<div class="codewrapper sourceCode" id="cb86">
+<div class="codewrapper sourceCode" id="cb98">
 <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">
@@ -1675,7 +1798,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-04-04",
+  "dateModified": "2024-04-10",
   "datePublished": "2024-04-10"
 }
 
diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index cce88b938..9dfc26e3f 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -618,13 +618,71 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  $ ALT      : chr  "G" "T" "T" "CTTTTTTTT" ...</code></pre>
 </div>
 <p>Ok, thats a lot up unpack! Some things to notice.</p>
-<ul><li>the object type <code>data.frame</code> is displayed in the first
+<ul><li><p>the object type <code>data.frame</code> is displayed in the first
 row along with its dimensions, in this case 801 observations (rows) and
-4 variables (columns)</li>
-<li>Each variable (column) has a name (e.g. <code>sample_id</code>).
+4 variables (columns)</p></li>
+<li>
+<p>Each variable (column) has a name (e.g. <code>sample_id</code>).
 This is followed by the object mode (e.g. chr, int, etc.). Notice that
 before each variable name there is a <code>$</code> - this will be
-important later.</li>
+important later.</p>
+<div id="challenge2" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
+</h3>
+<div class="callout-content">
+<p>Remeber when we said mode and class are sometimes different? If you
+do, here is a chance to check. What happens when you try the
+following?</p>
+<ol style="list-style-type: decimal"><li><code>mode(variants)</code></li>
+<li><code>class(variants)</code></li>
+</ol></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="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="fu">mode</span><span class="op">(</span><span class="va">variants</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>[1] "list"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb9">
+<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="fu">class</span><span class="op">(</span><span class="va">variants</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>[1] "data.frame"</code></pre>
+</div>
+<p>This result makes sense because <code>mode()</code> (which deals with
+how an object is stored) tells us that <code>variants</code> is treated
+as a <strong>list</strong> in R. A data frame is in some sense a “fancy”
+list. However, data fames do have some specific properties beyond that
+of a basic list, so they have their own class
+(<strong>data.frame</strong>), which is important for functions (and
+programmers) to know.</p>
+</div>
+</div>
+</div>
+</div>
+</li>
 </ul></section><section id="introducing-factors"><h2 class="section-heading">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width"><p>Factors are the final major data structure we will introduce in our R
@@ -638,7 +696,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 alleles. We can use the <code>$</code> operator to access or extract a
 column by its name in data frames (or to extract objects within named
 lists).</p>
-<div class="codewrapper sourceCode" id="cb7">
+<div class="codewrapper sourceCode" id="cb11">
 <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">
@@ -648,7 +706,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>Let’s look at the first few items in our factor using
 <code>head()</code>:</p>
-<div class="codewrapper sourceCode" id="cb8">
+<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">
@@ -662,7 +720,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>There are 801 alleles (one for each row). To simplify, lets look at
 just the single-nucleotide alleles (SNPs). We can use some of the vector
 indexing skills from the last episode.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -676,7 +734,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 but we could treat them as categories of SNP. Doing this will enable
 some nice features. For example, we can try to generate a plot of this
 character vector as it is right now:</p>
-<div class="codewrapper sourceCode" id="cb11">
+<div class="codewrapper sourceCode" id="cb15">
 <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">
@@ -707,14 +765,14 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 to tell R to treat the SNPs as categories (i.e. a factor vector); we
 will create a new object to avoid confusion using the
 <code>factor()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb16">
+<div class="codewrapper sourceCode" id="cb20">
 <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">factor_snps</span> <span class="op">&lt;-</span> <span class="fu">factor</span><span class="op">(</span><span class="va">snps</span><span class="op">)</span></span></code></pre>
 </div>
 <p>Let’s learn a little more about this new type of vector:</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb21">
 <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">
@@ -739,7 +797,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 1 1 1 1 1 1 1 …“), since”A” is the first level, and the first few items
 in our factor are all “A”s.</p>
 <p>We can see how many items in our vector fall into each category:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb23">
 <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">
@@ -776,13 +834,13 @@ <h3 class="callout-title">Tip: treating objects as categories without
 <hr class="half-width"><p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb25">
 <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="fu">plot</span><span class="op">(</span><span class="va">factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
+<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
 We’ll be learning much more about creating nice, publication-quality
 graphics later in this lesson.</p>
 <p>If you recall, factors are ordered alphabetically. That might make
@@ -790,7 +848,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 an intrinsic order. What if we wanted to order our plot according to the
 numerical value (i.e., in descending order of SNP frequency)? We can
 enforce an order on our factors:</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -813,13 +871,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 the <code>levels=</code> parameter to enforce the ordering of the
 levels.</li>
 </ol><p>Now we see our plot has be reordered:</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb27">
 <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="fu">plot</span><span class="op">(</span><span class="va">ordered_factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
+<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout">
@@ -842,7 +900,7 @@ <h3 class="callout-title">Tip: Packages in R – what are they and why do
 <a href="https://www.tidyverse.org" class="external-link">tidyverse</a> packages such as
 <code>dplyr</code> and <code>ggplot2</code> (which you’ll do in the next
 few lessons), you would use the following command:</p>
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -858,7 +916,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.5 milliseconds.</code></pre>
+Successfully installed 1 package in 5.4 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -898,15 +956,15 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution3" 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 class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb26">
+</li></ol><div class="codewrapper sourceCode" id="cb30">
 <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">
@@ -918,7 +976,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "SRR2584863"</code></pre>
 </div>
 <ol start="2" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb28">
+</li></ol><div class="codewrapper sourceCode" id="cb32">
 <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">
@@ -930,7 +988,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] NA</code></pre>
 </div>
 <ol start="3" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb30">
+</li></ol><div class="codewrapper sourceCode" id="cb34">
 <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">
@@ -942,7 +1000,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "T"</code></pre>
 </div>
 <ol start="4" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb32">
+</li></ol><div class="codewrapper sourceCode" id="cb36">
 <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">
@@ -961,7 +1019,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 2     1             T</code></pre>
 </div>
 <ol start="5" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb34">
+</li></ol><div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -1000,7 +1058,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 7     1             A</code></pre>
 </div>
 <ol start="6" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb36">
+</li></ol><div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -1012,7 +1070,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863"</code></pre>
 </div>
 <ol start="7" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb38">
+</li></ol><div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -1045,7 +1103,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 10                                                      ATT</code></pre>
 </div>
 <ol start="8" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb40">
+</li></ol><div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -1058,7 +1116,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [6] "SRR2584863"</code></pre>
 </div>
 <ol style="list-style-type: lower-roman"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb42">
+</li></ol><div class="codewrapper sourceCode" id="cb46">
 <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">
@@ -1097,7 +1155,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 6     1             T</code></pre>
 </div>
 <ol start="10" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb44">
+</li></ol><div class="codewrapper sourceCode" id="cb48">
 <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">
@@ -1136,7 +1194,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 801     1             T</code></pre>
 </div>
 <ol start="11" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb46">
+</li></ol><div class="codewrapper sourceCode" id="cb50">
 <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">
@@ -1149,7 +1207,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [6] "SRR2584863"</code></pre>
 </div>
 <ol start="12" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb48">
+</li></ol><div class="codewrapper sourceCode" id="cb52">
 <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">
@@ -1213,7 +1271,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </ul><p>Finally, in all of the subsetting exercises above, we printed values
 to the screen. You can create a new data frame object by assigning them
 to a new object name:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -1230,7 +1288,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 25 29</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1327,7 +1385,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <p>First, its very important to recognize that coercion happens in R all
 the time. This can be a good thing when R gets it right, or a bad thing
 when the result is not what you expect. Consider:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1343,7 +1401,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 quotes, so we have explicitly told R to consider them as characters.
 However, even if we removed the quotes from the numbers, R would coerce
 everything into a character:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -1355,7 +1413,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -1369,7 +1427,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can use the <code>as.</code> functions to explicitly coerce values
 from one form into another. Consider the following vector of characters,
 which all happen to be valid numbers:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -1381,7 +1439,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb62">
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 <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">
@@ -1394,7 +1452,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Now we can coerce <code>snp_positions_2</code> into a numeric type
 using <code>as.numeric()</code>:</p>
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb68">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -1406,7 +1464,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "double"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1420,7 +1478,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Sometimes coercion is straight forward, but what would happen if we
 tried using <code>as.numeric()</code> on
 <code>snp_chromosomes_2</code></p>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -1433,7 +1491,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 </div>
 <p>If we check, we will see that an <code>NA</code> value (R’s default
 value for missing data) has been introduced.</p>
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -1447,7 +1505,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Trouble can really start when we try to coerce a factor. For example,
 when we try to coerce the <code>factor_snps</code> vector into a numeric
 mode look at the result:</p>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -1485,7 +1543,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 notice a problem.</p>
 <p>If you need to coerce an entire column you can overwrite it using an
 expression like this one:</p>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -1551,7 +1609,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <code>max()</code> on an individual column. Let’s look at the “DP” or
 filtered depth. This value shows the number of filtered reads that
 support each of the reported variants.</p>
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -1564,7 +1622,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>You can sort a data frame using the <code>order()</code>
 function:</p>
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -1591,14 +1649,14 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -1615,7 +1673,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 <p>You can rename columns:</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -1641,7 +1699,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <hr class="half-width"><p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -1689,7 +1747,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to adjust. Click the <kbd>Import</kbd> button to import the data.</p>
 <p>Finally, let’s check the first few lines of the
 <code>Ecoli_metadata</code> data frame:</p>
-<div class="codewrapper sourceCode" id="cb85">
+<div class="codewrapper sourceCode" id="cb89">
 <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">
@@ -1741,14 +1799,14 @@ <h3 class="callout-title">Exercise: Putting it all together - data
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb87">
+<div class="codewrapper sourceCode" id="cb91">
 <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">
@@ -1759,7 +1817,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 30  7</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb89">
+<div class="codewrapper sourceCode" id="cb93">
 <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">
@@ -1770,7 +1828,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "minus"   "plus"    "unknown"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb91">
+<div class="codewrapper sourceCode" id="cb95">
 <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">
@@ -1783,7 +1841,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   minus    plus unknown 
       9       9      12 </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb93">
+<div class="codewrapper sourceCode" id="cb97">
 <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">
@@ -1797,7 +1855,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
         &lt;dbl&gt;
 1        4.62</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb95">
+<div class="codewrapper sourceCode" id="cb99">
 <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">
@@ -1808,7 +1866,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4.625</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb97">
+<div class="codewrapper sourceCode" id="cb101">
 <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">
diff --git a/06-data-visualization.html b/06-data-visualization.html
index bd0d86c25..614c55952 100644
--- a/06-data-visualization.html
+++ b/06-data-visualization.html
@@ -897,7 +897,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -994,7 +994,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1043,7 +1043,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1090,7 +1090,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/aio.html b/aio.html
index 3b304d3a3..3e3b587ac 100644
--- a/aio.html
+++ b/aio.html
@@ -717,7 +717,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -814,7 +814,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul>
 <li>
@@ -968,7 +968,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1020,7 +1020,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-01-r-basics"><p>Content from <a href="01-r-basics.html">R Basics</a></p>
 <hr>
-<p>Last updated on 2024-04-04 |
+<p>Last updated on 2024-04-10 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1241,7 +1241,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <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 id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1354,10 +1354,10 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section id="understanding-object-data-types-modes"><h2 class="section-heading">Understanding object data types (modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-modes"></a>
+</section><section id="understanding-object-data-types-classes-and-modes"><h2 class="section-heading">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
 <hr class="half-width">
-<p>In R, <strong>every object has two properties</strong>:</p>
+<p>In R, <strong>every object has several properties</strong>:</p>
 <ul>
 <li>
 <strong>Length</strong>: How many distinct values are held in that
@@ -1365,11 +1365,40 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <li>
 <strong>Mode</strong>: What is the classification (type) of that
 object.</li>
+<li>
+<strong>Class</strong>: A property assigned to an object that
+determines how a function will operate on it.</li>
 </ul>
 <p>We will get to the “length” property later in the lesson. The
 <strong>“mode” property</strong> <strong>corresponds to the type of data
-an object represents</strong>. The most common modes you will encounter
-in R are:</p>
+an object represents</strong> and the <strong>“class” property
+determines how functions will work with that object.</strong></p>
+<div id="tip-classess-vs.-modes" class="callout">
+<div class="callout-square">
+<i class="callout-icon" data-feather="bell"></i>
+</div>
+<div id="tip-classess-vs.-modes" class="callout-inner">
+<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
+</h3>
+<div class="callout-content">
+<p>The difference between modes and classes is a bit
+<strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
+discussions</a>. Often, these terms are used interchangeably. Do you
+really need to know the difference?</p>
+<p>Well, perhaps. This section is important for you to have a better
+understanding of how R works and how to write usable code. However, you
+might not come across a situation where the difference is crucial while
+you are taking your first steps in learning R. However, the overarching
+concept—<strong>that objects in R have these properties and that you can
+use functions to check or change them</strong>—is very important!</p>
+<p>In this lesson we will mostly stick to <strong>mode</strong> but we
+will throw in a few examples of the <code>class()</code> and
+<code>typeof()</code> so you can see some examples of where it may make
+a difference.</p>
+</div>
+</div>
+</div>
+<p>The most common modes you will encounter in R are:</p>
 <table class="table">
 <colgroup>
 <col width="7%">
@@ -1403,9 +1432,9 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 natural language where we refer to them as the parts of speech,
 e.g. nouns, verbs, adverbs, etc. Once you know if a word - perhaps an
 unfamiliar one - is a noun, you can probably guess you can count it and
-make it plural if there is more than one (e.g. 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
+make it plural if there is more than one (e.g., 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
 Tuataras). If something is a adjective, you can usually change it into
-an adverb by adding “-ly” (e.g. <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
+an adverb by adding “-ly” (e.g., <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
 jejunely). Depending on the context, you may need to decide if a word is
 in one category or another (e.g “cut” may be a noun when it’s on your
 finger, or a verb when you are preparing vegetables). These concepts
@@ -1437,7 +1466,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <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 id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <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>
@@ -1498,6 +1527,88 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
+<h3 class="callout-title">Exercise: Create objects and check their class
+using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
+</h3>
+<div class="callout-content">
+<p>Using the objects created in the previous challenge, use the
+<code>class()</code> function to check their classes.</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution3" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+</button>
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div class="accordion-body">
+<div class="codewrapper sourceCode" id="cb17">
+<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="fu">class</span><span class="op">(</span><span class="va">chromosome_name</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb19">
+<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="fu">class</span><span class="op">(</span><span class="va">od_600_value</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>[1] "numeric"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb21">
+<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="fu">class</span><span class="op">(</span><span class="va">chr_position</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb23">
+<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="fu">class</span><span class="op">(</span><span class="va">spock</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>[1] "logical"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb25">
+<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="fu">class</span><span class="op">(</span><span class="va">pilot</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'pilot' not found</code></pre>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p>Notice that in the two challenges, <code>mode()</code> and
+<code>class()</code> return the same results. This time…</p>
 <p>Notice from the solution that even if a series of numbers is given as
 a value R will consider them to be in the “character” mode if they are
 enclosed as single or double quotes. Also, notice that you cannot take a
@@ -1509,7 +1620,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 was originally. If we want to create an object called <code>pilot</code>
 that was the <strong>name</strong> “Earhart”, we need to enclose
 <code>Earhart</code> in quotation marks.</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb27">
 <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">
@@ -1521,6 +1632,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
+<div class="codewrapper sourceCode" id="cb29">
+<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">pilot</span> <span class="op">&lt;-</span> <span class="st">"Earhart"</span></span>
+<span><span class="fu">typeof</span><span class="op">(</span><span class="va">pilot</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>[1] "character"</code></pre>
+</div>
 </section><section id="mathematical-and-functional-operations-on-objects"><h2 class="section-heading">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width">
@@ -1569,7 +1692,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tbody>
 </table>
 <p>These can be used with literal numbers:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb31">
 <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">
@@ -1582,7 +1705,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>and importantly, can be used on any object that evaluates to
 (i.e. interpreted by R) a numeric object:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb33">
 <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">
@@ -1611,14 +1734,14 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb35">
 <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">
@@ -1644,7 +1767,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 “concatenate” or “combine” function. Inside the function you may enter
 one or more values; for multiple values, separate each value with a
 comma:</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb37">
 <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">
@@ -1657,7 +1780,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>mode()</code> and <code>length()</code> functions respectively.
 Another useful function that gives both of these pieces of information
 is the <code>str()</code> (structure) function.</p>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -1669,7 +1792,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -1680,7 +1803,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -1699,7 +1822,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h2>
 <hr class="half-width">
 <p>Let’s create a few more vectors to play around with:</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -1715,7 +1838,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <strong>bracket notation</strong>. We type the name of the vector
 followed by square brackets. In those square brackets we place the index
 (e.g. a number) in that bracket as follows:</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb45">
 <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">
@@ -1730,7 +1853,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In R, every item your vector is indexed, starting from the first item
 (1) through to the final number of items in your vector. You can also
 retrieve a range of numbers:</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb47">
 <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">
@@ -1746,7 +1869,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>If you want to retrieve several (but not necessarily sequential)
 items from a vector, you pass a <strong>vector of indices</strong>; a
 vector that has the numbered positions you wish to retrieve.</p>
-<div class="codewrapper sourceCode" id="cb37">
+<div class="codewrapper sourceCode" id="cb49">
 <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">
@@ -1763,7 +1886,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 subsetting a vector (see <a href="https://thomasleeper.com/Rcourse/Tutorials/vectorindexing.html" class="external-link">these
 examples</a>). Also, several of these subsetting expressions can be
 combined:</p>
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb51">
 <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">
@@ -1782,7 +1905,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
-<div class="codewrapper sourceCode" id="cb41">
+<div class="codewrapper sourceCode" id="cb53">
 <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">
@@ -1791,7 +1914,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">snp_genes</span> <span class="op">&lt;-</span> <span class="fu">c</span><span class="op">(</span><span class="va">snp_genes</span>, <span class="st">"CYP1A1"</span>, <span class="st">"APOA5"</span><span class="op">)</span></span></code></pre>
 </div>
 <p>We can verify that “snp_genes” contains the new gene entry</p>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb54">
 <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">
@@ -1804,7 +1927,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Using a negative index will return a version of a vector with that
 index’s value removed:</p>
-<div class="codewrapper sourceCode" id="cb44">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1817,7 +1940,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can remove that value from our vector by overwriting it with this
 expression:</p>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1831,7 +1954,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can also explicitly rename or add a value to our index using
 double bracket notation:</p>
-<div class="codewrapper sourceCode" id="cb48">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -1865,12 +1988,12 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li>False - Vectors have both of these properties<br>
@@ -1899,7 +2022,7 @@ <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 we wanted get all of the SNPs in our vector of SNP positions that were
 greater than 100,000,000. We could index using the ‘&gt;’ (greater than)
 logical operator:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -1973,7 +2096,7 @@ <h3 class="callout-title">The magic of programming<a class="anchor" aria-label="
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
 better understood if you examine what the expression “snp_positions &gt;
 100000000” evaluates to:</p>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -1987,7 +2110,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>The output above is a logical vector, the 4th element of which is
 TRUE. When you pass a logical vector as an index, R will return the true
 values:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -2011,7 +2134,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 positions was the one that was greater than 100,000,000?</p>
 <p>We can use the <code>which()</code> function to return the indices of
 any item that evaluates as TRUE in our comparison:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -2027,7 +2150,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 used when our code is executed. Rather than put in a pre-determined
 value (e.g 100000000) we can use an object that can take on whatever
 value we need. So for example:</p>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -2053,7 +2176,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 for <code>not avaliable</code>). Missing data will get a more detailed
 treatment later, but the <code>is.NA()</code> function will return a
 logical vector, with TRUE for any NA value:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -2071,7 +2194,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 values) is present a vector. You can do this using the comparison
 operator <code>%in%</code>, which will return TRUE for any value in your
 collection that is in the vector you are searching:</p>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -2130,14 +2253,14 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution6" 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="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
-  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
+  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -2148,7 +2271,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -2159,7 +2282,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb80">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -2189,14 +2312,14 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution6" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution7" 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="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
-  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
+  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -2208,7 +2331,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971" "rs662799" </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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@@ -2220,7 +2343,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "3"  "11" "X"  "6"  "11"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -2259,14 +2382,14 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution7" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution8" 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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
-  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
+  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -2306,14 +2429,14 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution8" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution9" 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="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
-  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
+  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb90">
 <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">
@@ -2341,14 +2464,14 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution9" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution10" 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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
-  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
+  <h4 class="accordion-header" id="headingSolution10">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb92">
 <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">
@@ -2379,7 +2502,7 @@ <h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#list
 lists using this <a href="https://r4ds.had.co.nz/vectors.html#lists" class="external-link">nice tutorial</a>. In
 this one example, we will create a named list and show you how to
 retrieve items from the list.</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb94">
 <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">
@@ -2408,7 +2531,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get all the values for the <code>position</code> object in the
 list, we use the <code>$</code> notation:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb96">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -2423,7 +2546,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get the first value in the <code>position</code> object, use the
 <code>[]</code> notation to index:</p>
-<div class="codewrapper sourceCode" id="cb86">
+<div class="codewrapper sourceCode" id="cb98">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -3132,13 +3255,73 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Ok, thats a lot up unpack! Some things to notice.</p>
 <ul>
-<li>the object type <code>data.frame</code> is displayed in the first
+<li><p>the object type <code>data.frame</code> is displayed in the first
 row along with its dimensions, in this case 801 observations (rows) and
-4 variables (columns)</li>
-<li>Each variable (column) has a name (e.g. <code>sample_id</code>).
+4 variables (columns)</p></li>
+<li>
+<p>Each variable (column) has a name (e.g. <code>sample_id</code>).
 This is followed by the object mode (e.g. chr, int, etc.). Notice that
 before each variable name there is a <code>$</code> - this will be
-important later.</li>
+important later.</p>
+<div id="challenge2" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
+</h3>
+<div class="callout-content">
+<p>Remeber when we said mode and class are sometimes different? If you
+do, here is a chance to check. What happens when you try the
+following?</p>
+<ol style="list-style-type: decimal">
+<li><code>mode(variants)</code></li>
+<li><code>class(variants)</code></li>
+</ol>
+</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="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="fu">mode</span><span class="op">(</span><span class="va">variants</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>[1] "list"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb9">
+<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="fu">class</span><span class="op">(</span><span class="va">variants</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>[1] "data.frame"</code></pre>
+</div>
+<p>This result makes sense because <code>mode()</code> (which deals with
+how an object is stored) tells us that <code>variants</code> is treated
+as a <strong>list</strong> in R. A data frame is in some sense a “fancy”
+list. However, data fames do have some specific properties beyond that
+of a basic list, so they have their own class
+(<strong>data.frame</strong>), which is important for functions (and
+programmers) to know.</p>
+</div>
+</div>
+</div>
+</div>
+</li>
 </ul></section><section id="introducing-factors"><h2 class="section-heading">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width">
@@ -3153,7 +3336,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 alleles. We can use the <code>$</code> operator to access or extract a
 column by its name in data frames (or to extract objects within named
 lists).</p>
-<div class="codewrapper sourceCode" id="cb7">
+<div class="codewrapper sourceCode" id="cb11">
 <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">
@@ -3163,7 +3346,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>Let’s look at the first few items in our factor using
 <code>head()</code>:</p>
-<div class="codewrapper sourceCode" id="cb8">
+<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">
@@ -3177,7 +3360,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>There are 801 alleles (one for each row). To simplify, lets look at
 just the single-nucleotide alleles (SNPs). We can use some of the vector
 indexing skills from the last episode.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -3191,7 +3374,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 but we could treat them as categories of SNP. Doing this will enable
 some nice features. For example, we can try to generate a plot of this
 character vector as it is right now:</p>
-<div class="codewrapper sourceCode" id="cb11">
+<div class="codewrapper sourceCode" id="cb15">
 <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">
@@ -3222,14 +3405,14 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 to tell R to treat the SNPs as categories (i.e. a factor vector); we
 will create a new object to avoid confusion using the
 <code>factor()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb16">
+<div class="codewrapper sourceCode" id="cb20">
 <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">factor_snps</span> <span class="op">&lt;-</span> <span class="fu">factor</span><span class="op">(</span><span class="va">snps</span><span class="op">)</span></span></code></pre>
 </div>
 <p>Let’s learn a little more about this new type of vector:</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb21">
 <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">
@@ -3254,7 +3437,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 1 1 1 1 1 1 1 …“), since”A” is the first level, and the first few items
 in our factor are all “A”s.</p>
 <p>We can see how many items in our vector fall into each category:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb23">
 <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">
@@ -3292,13 +3475,13 @@ <h3 class="callout-title">Tip: treating objects as categories without
 <p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb25">
 <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="fu">plot</span><span class="op">(</span><span class="va">factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
+<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
 We’ll be learning much more about creating nice, publication-quality
 graphics later in this lesson.</p>
 <p>If you recall, factors are ordered alphabetically. That might make
@@ -3306,7 +3489,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 an intrinsic order. What if we wanted to order our plot according to the
 numerical value (i.e., in descending order of SNP frequency)? We can
 enforce an order on our factors:</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -3331,13 +3514,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 levels.</li>
 </ol>
 <p>Now we see our plot has be reordered:</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb27">
 <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="fu">plot</span><span class="op">(</span><span class="va">ordered_factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
+<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout">
@@ -3360,7 +3543,7 @@ <h3 class="callout-title">Tip: Packages in R – what are they and why do
 <a href="https://www.tidyverse.org" class="external-link">tidyverse</a> packages such as
 <code>dplyr</code> and <code>ggplot2</code> (which you’ll do in the next
 few lessons), you would use the following command:</p>
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -3376,7 +3559,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.5 milliseconds.</code></pre>
+Successfully installed 1 package in 5.4 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -3419,16 +3602,16 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 </div>
 </div>
 </div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution3" 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 class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb30">
 <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">
@@ -3441,7 +3624,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="2" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -3454,7 +3637,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="3" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb34">
 <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">
@@ -3467,7 +3650,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="4" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb36">
 <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">
@@ -3487,7 +3670,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="5" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb34">
+<div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -3527,7 +3710,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="6" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb36">
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 <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">
@@ -3540,7 +3723,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="7" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb38">
+<div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -3574,7 +3757,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="8" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb40">
+<div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -3588,7 +3771,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol style="list-style-type: lower-roman"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb46">
 <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">
@@ -3628,7 +3811,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="10" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb44">
+<div class="codewrapper sourceCode" id="cb48">
 <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">
@@ -3668,7 +3851,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="11" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb50">
 <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">
@@ -3682,7 +3865,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="12" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb48">
+<div class="codewrapper sourceCode" id="cb52">
 <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">
@@ -3748,7 +3931,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Finally, in all of the subsetting exercises above, we printed values
 to the screen. You can create a new data frame object by assigning them
 to a new object name:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb54">
 <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">
@@ -3765,7 +3948,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 25 29</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -3863,7 +4046,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <p>First, its very important to recognize that coercion happens in R all
 the time. This can be a good thing when R gets it right, or a bad thing
 when the result is not what you expect. Consider:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -3879,7 +4062,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 quotes, so we have explicitly told R to consider them as characters.
 However, even if we removed the quotes from the numbers, R would coerce
 everything into a character:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -3891,7 +4074,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -3905,7 +4088,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can use the <code>as.</code> functions to explicitly coerce values
 from one form into another. Consider the following vector of characters,
 which all happen to be valid numbers:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -3917,7 +4100,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -3930,7 +4113,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Now we can coerce <code>snp_positions_2</code> into a numeric type
 using <code>as.numeric()</code>:</p>
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -3942,7 +4125,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "double"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -3956,7 +4139,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Sometimes coercion is straight forward, but what would happen if we
 tried using <code>as.numeric()</code> on
 <code>snp_chromosomes_2</code></p>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -3969,7 +4152,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 </div>
 <p>If we check, we will see that an <code>NA</code> value (R’s default
 value for missing data) has been introduced.</p>
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -3983,7 +4166,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Trouble can really start when we try to coerce a factor. For example,
 when we try to coerce the <code>factor_snps</code> vector into a numeric
 mode look at the result:</p>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -4021,7 +4204,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 notice a problem.</p>
 <p>If you need to coerce an entire column you can overwrite it using an
 expression like this one:</p>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -4091,7 +4274,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <code>max()</code> on an individual column. Let’s look at the “DP” or
 filtered depth. This value shows the number of filtered reads that
 support each of the reported variants.</p>
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -4104,7 +4287,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>You can sort a data frame using the <code>order()</code>
 function:</p>
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -4131,14 +4314,14 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -4155,7 +4338,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 <p>You can rename columns:</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -4182,7 +4365,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -4231,7 +4414,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to adjust. Click the <kbd>Import</kbd> button to import the data.</p>
 <p>Finally, let’s check the first few lines of the
 <code>Ecoli_metadata</code> data frame:</p>
-<div class="codewrapper sourceCode" id="cb85">
+<div class="codewrapper sourceCode" id="cb89">
 <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">
@@ -4285,14 +4468,14 @@ <h3 class="callout-title">Exercise: Putting it all together - data
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb87">
+<div class="codewrapper sourceCode" id="cb91">
 <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">
@@ -4303,7 +4486,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 30  7</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb89">
+<div class="codewrapper sourceCode" id="cb93">
 <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">
@@ -4314,7 +4497,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "minus"   "plus"    "unknown"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb91">
+<div class="codewrapper sourceCode" id="cb95">
 <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">
@@ -4327,7 +4510,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   minus    plus unknown 
       9       9      12 </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb93">
+<div class="codewrapper sourceCode" id="cb97">
 <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">
@@ -4341,7 +4524,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
         &lt;dbl&gt;
 1        4.62</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb95">
+<div class="codewrapper sourceCode" id="cb99">
 <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">
@@ -4352,7 +4535,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4.625</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb97">
+<div class="codewrapper sourceCode" id="cb101">
 <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">
@@ -6498,7 +6681,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6597,7 +6780,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6648,7 +6831,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6697,7 +6880,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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diff --git a/images.html b/images.html
index 27c56cb85..e2d5fe3a8 100644
--- a/images.html
+++ b/images.html
@@ -367,9 +367,9 @@ <h3 id="03-basics-factors-dataframes-figure-1">Figure 1</h3>
 <figure><img src="%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure><hr>
 <h3 id="03-basics-factors-dataframes-figure-2">Figure 2</h3>
-<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
-<h3 id="03-basics-factors-dataframes-figure-3">Figure 3</h3>
 <figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="03-basics-factors-dataframes-figure-3">Figure 3</h3>
+<figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
 <h3 id="03-basics-factors-dataframes-figure-4">Figure 4</h3>
 <p aria-hidden="true">Image 1 of 1: ‘RStudio import menu’</p>
 <figure><img src="%22fig/rstudio_import_menu.png%22" alt="RStudio import menu" class="figure mx-auto d-block"><div class="figcaption">RStudio import menu</div>
diff --git a/instructor/00-introduction.html b/instructor/00-introduction.html
index 64dc22269..77f3aec5e 100644
--- a/instructor/00-introduction.html
+++ b/instructor/00-introduction.html
@@ -666,7 +666,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -760,7 +760,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -907,7 +907,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
diff --git a/instructor/01-r-basics.html b/instructor/01-r-basics.html
index 6c221633c..dc0b6da18 100644
--- a/instructor/01-r-basics.html
+++ b/instructor/01-r-basics.html
@@ -172,7 +172,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#creating-objects-in-r">Creating objects in R</a></li>
 <li><a href="#naming-objects-in-r">Naming objects in R</a></li>
 <li><a href="#reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects</a></li>
-<li><a href="#understanding-object-data-types-modes">Understanding object data types (modes)</a></li>
+<li><a href="#understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)</a></li>
 <li><a href="#mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects</a></li>
 <li><a href="#vectors">Vectors</a></li>
 <li><a href="#creating-and-subsetting-vectors">Creating and subsetting vectors</a></li>
@@ -297,7 +297,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics</h1>
-        <p>Last updated on 2024-04-04 |
+        <p>Last updated on 2024-04-10 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -499,7 +499,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <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 id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -605,19 +605,48 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section id="understanding-object-data-types-modes"><h2 class="section-heading">Understanding object data types (modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-modes"></a>
+</section><section id="understanding-object-data-types-classes-and-modes"><h2 class="section-heading">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
-<hr class="half-width"><p>In R, <strong>every object has two properties</strong>:</p>
+<hr class="half-width"><p>In R, <strong>every object has several properties</strong>:</p>
 <ul><li>
 <strong>Length</strong>: How many distinct values are held in that
 object</li>
 <li>
 <strong>Mode</strong>: What is the classification (type) of that
 object.</li>
+<li>
+<strong>Class</strong>: A property assigned to an object that
+determines how a function will operate on it.</li>
 </ul><p>We will get to the “length” property later in the lesson. The
 <strong>“mode” property</strong> <strong>corresponds to the type of data
-an object represents</strong>. The most common modes you will encounter
-in R are:</p>
+an object represents</strong> and the <strong>“class” property
+determines how functions will work with that object.</strong></p>
+<div id="tip-classess-vs.-modes" class="callout">
+<div class="callout-square">
+<i class="callout-icon" data-feather="bell"></i>
+</div>
+<div id="tip-classess-vs.-modes" class="callout-inner">
+<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
+</h3>
+<div class="callout-content">
+<p>The difference between modes and classes is a bit
+<strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
+discussions</a>. Often, these terms are used interchangeably. Do you
+really need to know the difference?</p>
+<p>Well, perhaps. This section is important for you to have a better
+understanding of how R works and how to write usable code. However, you
+might not come across a situation where the difference is crucial while
+you are taking your first steps in learning R. However, the overarching
+concept—<strong>that objects in R have these properties and that you can
+use functions to check or change them</strong>—is very important!</p>
+<p>In this lesson we will mostly stick to <strong>mode</strong> but we
+will throw in a few examples of the <code>class()</code> and
+<code>typeof()</code> so you can see some examples of where it may make
+a difference.</p>
+</div>
+</div>
+</div>
+<p>The most common modes you will encounter in R are:</p>
 <table class="table"><colgroup><col width="7%"><col width="92%"></colgroup><thead><tr class="header"><th>Mode (abbreviation)</th>
 <th>Type of data</th>
 </tr></thead><tbody><tr class="odd"><td>Numeric (num)</td>
@@ -635,9 +664,9 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 natural language where we refer to them as the parts of speech,
 e.g. nouns, verbs, adverbs, etc. Once you know if a word - perhaps an
 unfamiliar one - is a noun, you can probably guess you can count it and
-make it plural if there is more than one (e.g. 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
+make it plural if there is more than one (e.g., 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
 Tuataras). If something is a adjective, you can usually change it into
-an adverb by adding “-ly” (e.g. <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
+an adverb by adding “-ly” (e.g., <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
 jejunely). Depending on the context, you may need to decide if a word is
 in one category or another (e.g “cut” may be a noun when it’s on your
 finger, or a verb when you are preparing vegetables). These concepts
@@ -667,7 +696,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <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 id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <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>
@@ -728,6 +757,88 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
+<h3 class="callout-title">Exercise: Create objects and check their class
+using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
+</h3>
+<div class="callout-content">
+<p>Using the objects created in the previous challenge, use the
+<code>class()</code> function to check their classes.</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution3" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+</button>
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div class="accordion-body">
+<div class="codewrapper sourceCode" id="cb17">
+<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="fu">class</span><span class="op">(</span><span class="va">chromosome_name</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb19">
+<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="fu">class</span><span class="op">(</span><span class="va">od_600_value</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>[1] "numeric"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb21">
+<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="fu">class</span><span class="op">(</span><span class="va">chr_position</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb23">
+<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="fu">class</span><span class="op">(</span><span class="va">spock</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>[1] "logical"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb25">
+<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="fu">class</span><span class="op">(</span><span class="va">pilot</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'pilot' not found</code></pre>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p>Notice that in the two challenges, <code>mode()</code> and
+<code>class()</code> return the same results. This time…</p>
 <p>Notice from the solution that even if a series of numbers is given as
 a value R will consider them to be in the “character” mode if they are
 enclosed as single or double quotes. Also, notice that you cannot take a
@@ -739,7 +850,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 was originally. If we want to create an object called <code>pilot</code>
 that was the <strong>name</strong> “Earhart”, we need to enclose
 <code>Earhart</code> in quotation marks.</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb27">
 <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">
@@ -751,6 +862,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
+<div class="codewrapper sourceCode" id="cb29">
+<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">pilot</span> <span class="op">&lt;-</span> <span class="st">"Earhart"</span></span>
+<span><span class="fu">typeof</span><span class="op">(</span><span class="va">pilot</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>[1] "character"</code></pre>
+</div>
 </section><section id="mathematical-and-functional-operations-on-objects"><h2 class="section-heading">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width"><p>Once an object exists (which by definition also means it has a mode),
@@ -774,7 +897,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tr><tr class="odd"><td>a%%b</td>
 <td>modulus (returns the remainder after division)</td>
 </tr></tbody></table><p>These can be used with literal numbers:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb31">
 <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">
@@ -787,7 +910,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>and importantly, can be used on any object that evaluates to
 (i.e. interpreted by R) a numeric object:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb33">
 <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">
@@ -816,14 +939,14 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb35">
 <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">
@@ -848,7 +971,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 “concatenate” or “combine” function. Inside the function you may enter
 one or more values; for multiple values, separate each value with a
 comma:</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb37">
 <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">
@@ -861,7 +984,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>mode()</code> and <code>length()</code> functions respectively.
 Another useful function that gives both of these pieces of information
 is the <code>str()</code> (structure) function.</p>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -873,7 +996,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -884,7 +1007,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -902,7 +1025,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </section><section id="creating-and-subsetting-vectors"><h2 class="section-heading">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
 </h2>
 <hr class="half-width"><p>Let’s create a few more vectors to play around with:</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -918,7 +1041,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <strong>bracket notation</strong>. We type the name of the vector
 followed by square brackets. In those square brackets we place the index
 (e.g. a number) in that bracket as follows:</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb45">
 <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">
@@ -933,7 +1056,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In R, every item your vector is indexed, starting from the first item
 (1) through to the final number of items in your vector. You can also
 retrieve a range of numbers:</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb47">
 <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">
@@ -949,7 +1072,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>If you want to retrieve several (but not necessarily sequential)
 items from a vector, you pass a <strong>vector of indices</strong>; a
 vector that has the numbered positions you wish to retrieve.</p>
-<div class="codewrapper sourceCode" id="cb37">
+<div class="codewrapper sourceCode" id="cb49">
 <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">
@@ -966,7 +1089,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 subsetting a vector (see <a href="https://thomasleeper.com/Rcourse/Tutorials/vectorindexing.html" class="external-link">these
 examples</a>). Also, several of these subsetting expressions can be
 combined:</p>
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb51">
 <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">
@@ -984,7 +1107,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <hr class="half-width"><p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
-<div class="codewrapper sourceCode" id="cb41">
+<div class="codewrapper sourceCode" id="cb53">
 <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">
@@ -993,7 +1116,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">snp_genes</span> <span class="op">&lt;-</span> <span class="fu">c</span><span class="op">(</span><span class="va">snp_genes</span>, <span class="st">"CYP1A1"</span>, <span class="st">"APOA5"</span><span class="op">)</span></span></code></pre>
 </div>
 <p>We can verify that “snp_genes” contains the new gene entry</p>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb54">
 <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">
@@ -1006,7 +1129,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Using a negative index will return a version of a vector with that
 index’s value removed:</p>
-<div class="codewrapper sourceCode" id="cb44">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1019,7 +1142,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can remove that value from our vector by overwriting it with this
 expression:</p>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1033,7 +1156,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can also explicitly rename or add a value to our index using
 double bracket notation:</p>
-<div class="codewrapper sourceCode" id="cb48">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -1067,12 +1190,12 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li>False - Vectors have both of these properties<br></li>
 <li>True<br></li>
@@ -1094,7 +1217,7 @@ <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 we wanted get all of the SNPs in our vector of SNP positions that were
 greater than 100,000,000. We could index using the ‘&gt;’ (greater than)
 logical operator:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -1140,7 +1263,7 @@ <h3 class="callout-title">The magic of programming<a class="anchor" aria-label="
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
 better understood if you examine what the expression “snp_positions &gt;
 100000000” evaluates to:</p>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -1154,7 +1277,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>The output above is a logical vector, the 4th element of which is
 TRUE. When you pass a logical vector as an index, R will return the true
 values:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -1178,7 +1301,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 positions was the one that was greater than 100,000,000?</p>
 <p>We can use the <code>which()</code> function to return the indices of
 any item that evaluates as TRUE in our comparison:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -1194,7 +1317,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 used when our code is executed. Rather than put in a pre-determined
 value (e.g 100000000) we can use an object that can take on whatever
 value we need. So for example:</p>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -1219,7 +1342,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 for <code>not avaliable</code>). Missing data will get a more detailed
 treatment later, but the <code>is.NA()</code> function will return a
 logical vector, with TRUE for any NA value:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -1237,7 +1360,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 values) is present a vector. You can do this using the comparison
 operator <code>%in%</code>, which will return TRUE for any value in your
 collection that is in the vector you are searching:</p>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -1296,14 +1419,14 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution6" 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="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
-  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
+  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -1314,7 +1437,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -1325,7 +1448,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -1355,14 +1478,14 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution6" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution7" 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="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
-  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
+  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -1374,7 +1497,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971" "rs662799" </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -1386,7 +1509,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "3"  "11" "X"  "6"  "11"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -1422,14 +1545,14 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution7" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution8" 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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
-  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
+  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -1467,14 +1590,14 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 </ul></div>
 </div>
 </div>
-<div id="accordionSolution8" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution9" 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="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
-  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
+  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb90">
 <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">
@@ -1502,14 +1625,14 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution9" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution10" 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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
-  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
+  <h4 class="accordion-header" id="headingSolution10">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb92">
 <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">
@@ -1540,7 +1663,7 @@ <h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#list
 lists using this <a href="https://r4ds.had.co.nz/vectors.html#lists" class="external-link">nice tutorial</a>. In
 this one example, we will create a named list and show you how to
 retrieve items from the list.</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb94">
 <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">
@@ -1569,7 +1692,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get all the values for the <code>position</code> object in the
 list, we use the <code>$</code> notation:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb96">
 <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">
@@ -1584,7 +1707,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get the first value in the <code>position</code> object, use the
 <code>[]</code> notation to index:</p>
-<div class="codewrapper sourceCode" id="cb86">
+<div class="codewrapper sourceCode" id="cb98">
 <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">
@@ -1677,7 +1800,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/01-r-basics.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/01-r-basics.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-04-04",
+  "dateModified": "2024-04-10",
   "datePublished": "2024-04-10"
 }
 
diff --git a/instructor/03-basics-factors-dataframes.html b/instructor/03-basics-factors-dataframes.html
index a87f69e0c..06f4ccd9a 100644
--- a/instructor/03-basics-factors-dataframes.html
+++ b/instructor/03-basics-factors-dataframes.html
@@ -620,13 +620,71 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  $ ALT      : chr  "G" "T" "T" "CTTTTTTTT" ...</code></pre>
 </div>
 <p>Ok, thats a lot up unpack! Some things to notice.</p>
-<ul><li>the object type <code>data.frame</code> is displayed in the first
+<ul><li><p>the object type <code>data.frame</code> is displayed in the first
 row along with its dimensions, in this case 801 observations (rows) and
-4 variables (columns)</li>
-<li>Each variable (column) has a name (e.g. <code>sample_id</code>).
+4 variables (columns)</p></li>
+<li>
+<p>Each variable (column) has a name (e.g. <code>sample_id</code>).
 This is followed by the object mode (e.g. chr, int, etc.). Notice that
 before each variable name there is a <code>$</code> - this will be
-important later.</li>
+important later.</p>
+<div id="challenge2" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
+</h3>
+<div class="callout-content">
+<p>Remeber when we said mode and class are sometimes different? If you
+do, here is a chance to check. What happens when you try the
+following?</p>
+<ol style="list-style-type: decimal"><li><code>mode(variants)</code></li>
+<li><code>class(variants)</code></li>
+</ol></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="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="fu">mode</span><span class="op">(</span><span class="va">variants</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>[1] "list"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb9">
+<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="fu">class</span><span class="op">(</span><span class="va">variants</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>[1] "data.frame"</code></pre>
+</div>
+<p>This result makes sense because <code>mode()</code> (which deals with
+how an object is stored) tells us that <code>variants</code> is treated
+as a <strong>list</strong> in R. A data frame is in some sense a “fancy”
+list. However, data fames do have some specific properties beyond that
+of a basic list, so they have their own class
+(<strong>data.frame</strong>), which is important for functions (and
+programmers) to know.</p>
+</div>
+</div>
+</div>
+</div>
+</li>
 </ul></section><section id="introducing-factors"><h2 class="section-heading">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width"><p>Factors are the final major data structure we will introduce in our R
@@ -640,7 +698,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 alleles. We can use the <code>$</code> operator to access or extract a
 column by its name in data frames (or to extract objects within named
 lists).</p>
-<div class="codewrapper sourceCode" id="cb7">
+<div class="codewrapper sourceCode" id="cb11">
 <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">
@@ -650,7 +708,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>Let’s look at the first few items in our factor using
 <code>head()</code>:</p>
-<div class="codewrapper sourceCode" id="cb8">
+<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">
@@ -664,7 +722,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>There are 801 alleles (one for each row). To simplify, lets look at
 just the single-nucleotide alleles (SNPs). We can use some of the vector
 indexing skills from the last episode.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -678,7 +736,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 but we could treat them as categories of SNP. Doing this will enable
 some nice features. For example, we can try to generate a plot of this
 character vector as it is right now:</p>
-<div class="codewrapper sourceCode" id="cb11">
+<div class="codewrapper sourceCode" id="cb15">
 <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">
@@ -709,14 +767,14 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 to tell R to treat the SNPs as categories (i.e. a factor vector); we
 will create a new object to avoid confusion using the
 <code>factor()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb16">
+<div class="codewrapper sourceCode" id="cb20">
 <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">factor_snps</span> <span class="op">&lt;-</span> <span class="fu">factor</span><span class="op">(</span><span class="va">snps</span><span class="op">)</span></span></code></pre>
 </div>
 <p>Let’s learn a little more about this new type of vector:</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb21">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -741,7 +799,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 1 1 1 1 1 1 1 …“), since”A” is the first level, and the first few items
 in our factor are all “A”s.</p>
 <p>We can see how many items in our vector fall into each category:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb23">
 <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">
@@ -778,13 +836,13 @@ <h3 class="callout-title">Tip: treating objects as categories without
 <hr class="half-width"><p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb25">
 <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="fu">plot</span><span class="op">(</span><span class="va">factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
+<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
 We’ll be learning much more about creating nice, publication-quality
 graphics later in this lesson.</p>
 <p>If you recall, factors are ordered alphabetically. That might make
@@ -792,7 +850,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 an intrinsic order. What if we wanted to order our plot according to the
 numerical value (i.e., in descending order of SNP frequency)? We can
 enforce an order on our factors:</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -815,13 +873,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 the <code>levels=</code> parameter to enforce the ordering of the
 levels.</li>
 </ol><p>Now we see our plot has be reordered:</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb27">
 <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="fu">plot</span><span class="op">(</span><span class="va">ordered_factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
+<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout">
@@ -844,7 +902,7 @@ <h3 class="callout-title">Tip: Packages in R – what are they and why do
 <a href="https://www.tidyverse.org" class="external-link">tidyverse</a> packages such as
 <code>dplyr</code> and <code>ggplot2</code> (which you’ll do in the next
 few lessons), you would use the following command:</p>
-<div class="codewrapper sourceCode" id="cb24">
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 <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">
@@ -860,7 +918,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.5 milliseconds.</code></pre>
+Successfully installed 1 package in 5.4 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -900,15 +958,15 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution3" 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 class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
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 </h3>
 <pre class="downlit sourceCode r">
@@ -920,7 +978,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "SRR2584863"</code></pre>
 </div>
 <ol start="2" style="list-style-type: lower-alpha"><li>
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+</li></ol><div class="codewrapper sourceCode" id="cb32">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -932,7 +990,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] NA</code></pre>
 </div>
 <ol start="3" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb30">
+</li></ol><div class="codewrapper sourceCode" id="cb34">
 <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">
@@ -944,7 +1002,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "T"</code></pre>
 </div>
 <ol start="4" style="list-style-type: lower-alpha"><li>
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+</li></ol><div class="codewrapper sourceCode" id="cb36">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -963,7 +1021,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 2     1             T</code></pre>
 </div>
 <ol start="5" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb34">
+</li></ol><div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -1002,7 +1060,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 7     1             A</code></pre>
 </div>
 <ol start="6" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb36">
+</li></ol><div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -1014,7 +1072,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "SRR2584863" "SRR2584863" "SRR2584863" "SRR2584863"</code></pre>
 </div>
 <ol start="7" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb38">
+</li></ol><div class="codewrapper sourceCode" id="cb42">
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@@ -1047,7 +1105,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 10                                                      ATT</code></pre>
 </div>
 <ol start="8" style="list-style-type: lower-alpha"><li>
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+</li></ol><div class="codewrapper sourceCode" id="cb44">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1060,7 +1118,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [6] "SRR2584863"</code></pre>
 </div>
 <ol style="list-style-type: lower-roman"><li>
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+</li></ol><div class="codewrapper sourceCode" id="cb46">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1099,7 +1157,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 6     1             T</code></pre>
 </div>
 <ol start="10" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb44">
+</li></ol><div class="codewrapper sourceCode" id="cb48">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1138,7 +1196,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 801     1             T</code></pre>
 </div>
 <ol start="11" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb46">
+</li></ol><div class="codewrapper sourceCode" id="cb50">
 <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">
@@ -1151,7 +1209,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [6] "SRR2584863"</code></pre>
 </div>
 <ol start="12" style="list-style-type: lower-alpha"><li>
-</li></ol><div class="codewrapper sourceCode" id="cb48">
+</li></ol><div class="codewrapper sourceCode" id="cb52">
 <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">
@@ -1215,7 +1273,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </ul><p>Finally, in all of the subsetting exercises above, we printed values
 to the screen. You can create a new data frame object by assigning them
 to a new object name:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -1232,7 +1290,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 25 29</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1329,7 +1387,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <p>First, its very important to recognize that coercion happens in R all
 the time. This can be a good thing when R gets it right, or a bad thing
 when the result is not what you expect. Consider:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1345,7 +1403,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 quotes, so we have explicitly told R to consider them as characters.
 However, even if we removed the quotes from the numbers, R would coerce
 everything into a character:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb60">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <pre class="downlit sourceCode r">
@@ -1357,7 +1415,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb62">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1371,7 +1429,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can use the <code>as.</code> functions to explicitly coerce values
 from one form into another. Consider the following vector of characters,
 which all happen to be valid numbers:</p>
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@@ -1383,7 +1441,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb62">
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 <pre class="downlit sourceCode r">
@@ -1396,7 +1454,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Now we can coerce <code>snp_positions_2</code> into a numeric type
 using <code>as.numeric()</code>:</p>
-<div class="codewrapper sourceCode" id="cb64">
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 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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@@ -1408,7 +1466,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "double"</code></pre>
 </div>
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1422,7 +1480,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Sometimes coercion is straight forward, but what would happen if we
 tried using <code>as.numeric()</code> on
 <code>snp_chromosomes_2</code></p>
-<div class="codewrapper sourceCode" id="cb68">
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@@ -1435,7 +1493,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 </div>
 <p>If we check, we will see that an <code>NA</code> value (R’s default
 value for missing data) has been introduced.</p>
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 </h3>
 <pre class="downlit sourceCode r">
@@ -1449,7 +1507,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Trouble can really start when we try to coerce a factor. For example,
 when we try to coerce the <code>factor_snps</code> vector into a numeric
 mode look at the result:</p>
-<div class="codewrapper sourceCode" id="cb72">
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 <pre class="downlit sourceCode r">
@@ -1487,7 +1545,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 notice a problem.</p>
 <p>If you need to coerce an entire column you can overwrite it using an
 expression like this one:</p>
-<div class="codewrapper sourceCode" id="cb74">
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 <pre class="downlit sourceCode r">
@@ -1553,7 +1611,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <code>max()</code> on an individual column. Let’s look at the “DP” or
 filtered depth. This value shows the number of filtered reads that
 support each of the reported variants.</p>
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 <pre class="downlit sourceCode r">
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 </div>
 <p>You can sort a data frame using the <code>order()</code>
 function:</p>
-<div class="codewrapper sourceCode" id="cb78">
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 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
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 <pre class="downlit sourceCode r">
@@ -1617,7 +1675,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 <p>You can rename columns:</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -1643,7 +1701,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <hr class="half-width"><p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -1691,7 +1749,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to adjust. Click the <kbd>Import</kbd> button to import the data.</p>
 <p>Finally, let’s check the first few lines of the
 <code>Ecoli_metadata</code> data frame:</p>
-<div class="codewrapper sourceCode" id="cb85">
+<div class="codewrapper sourceCode" id="cb89">
 <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">
@@ -1743,14 +1801,14 @@ <h3 class="callout-title">Exercise: Putting it all together - data
 </ol></div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb87">
+<div class="codewrapper sourceCode" id="cb91">
 <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">
@@ -1761,7 +1819,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 30  7</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb89">
+<div class="codewrapper sourceCode" id="cb93">
 <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">
@@ -1772,7 +1830,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "minus"   "plus"    "unknown"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb91">
+<div class="codewrapper sourceCode" id="cb95">
 <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">
@@ -1785,7 +1843,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   minus    plus unknown 
       9       9      12 </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb93">
+<div class="codewrapper sourceCode" id="cb97">
 <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">
@@ -1799,7 +1857,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
         &lt;dbl&gt;
 1        4.62</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb95">
+<div class="codewrapper sourceCode" id="cb99">
 <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">
@@ -1810,7 +1868,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4.625</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb97">
+<div class="codewrapper sourceCode" id="cb101">
 <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">
diff --git a/instructor/06-data-visualization.html b/instructor/06-data-visualization.html
index ed6ea09b3..fbd43a7d9 100644
--- a/instructor/06-data-visualization.html
+++ b/instructor/06-data-visualization.html
@@ -899,7 +899,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -996,7 +996,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1045,7 +1045,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1092,7 +1092,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/aio.html b/instructor/aio.html
index 93793a5e3..b6ad0067e 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -720,7 +720,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -817,7 +817,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul>
 <li>
@@ -971,7 +971,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1023,7 +1023,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-01-r-basics"><p>Content from <a href="01-r-basics.html">R Basics</a></p>
 <hr>
-<p>Last updated on 2024-04-04 |
+<p>Last updated on 2024-04-10 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.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> 80 minutes</p>
@@ -1245,7 +1245,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <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 id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1358,10 +1358,10 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section id="understanding-object-data-types-modes"><h2 class="section-heading">Understanding object data types (modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-modes"></a>
+</section><section id="understanding-object-data-types-classes-and-modes"><h2 class="section-heading">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
 <hr class="half-width">
-<p>In R, <strong>every object has two properties</strong>:</p>
+<p>In R, <strong>every object has several properties</strong>:</p>
 <ul>
 <li>
 <strong>Length</strong>: How many distinct values are held in that
@@ -1369,11 +1369,40 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <li>
 <strong>Mode</strong>: What is the classification (type) of that
 object.</li>
+<li>
+<strong>Class</strong>: A property assigned to an object that
+determines how a function will operate on it.</li>
 </ul>
 <p>We will get to the “length” property later in the lesson. The
 <strong>“mode” property</strong> <strong>corresponds to the type of data
-an object represents</strong>. The most common modes you will encounter
-in R are:</p>
+an object represents</strong> and the <strong>“class” property
+determines how functions will work with that object.</strong></p>
+<div id="tip-classess-vs.-modes" class="callout">
+<div class="callout-square">
+<i class="callout-icon" data-feather="bell"></i>
+</div>
+<div id="tip-classess-vs.-modes" class="callout-inner">
+<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
+</h3>
+<div class="callout-content">
+<p>The difference between modes and classes is a bit
+<strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
+discussions</a>. Often, these terms are used interchangeably. Do you
+really need to know the difference?</p>
+<p>Well, perhaps. This section is important for you to have a better
+understanding of how R works and how to write usable code. However, you
+might not come across a situation where the difference is crucial while
+you are taking your first steps in learning R. However, the overarching
+concept—<strong>that objects in R have these properties and that you can
+use functions to check or change them</strong>—is very important!</p>
+<p>In this lesson we will mostly stick to <strong>mode</strong> but we
+will throw in a few examples of the <code>class()</code> and
+<code>typeof()</code> so you can see some examples of where it may make
+a difference.</p>
+</div>
+</div>
+</div>
+<p>The most common modes you will encounter in R are:</p>
 <table class="table">
 <colgroup>
 <col width="7%">
@@ -1407,9 +1436,9 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 natural language where we refer to them as the parts of speech,
 e.g. nouns, verbs, adverbs, etc. Once you know if a word - perhaps an
 unfamiliar one - is a noun, you can probably guess you can count it and
-make it plural if there is more than one (e.g. 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
+make it plural if there is more than one (e.g., 1 <a href="https://en.wikipedia.org/wiki/Tuatara" class="external-link">Tuatara</a>, or 2
 Tuataras). If something is a adjective, you can usually change it into
-an adverb by adding “-ly” (e.g. <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
+an adverb by adding “-ly” (e.g., <a href="https://www.merriam-webster.com/dictionary/jejune" class="external-link">jejune</a> vs.
 jejunely). Depending on the context, you may need to decide if a word is
 in one category or another (e.g “cut” may be a noun when it’s on your
 finger, or a verb when you are preparing vegetables). These concepts
@@ -1441,7 +1470,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <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 id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <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>
@@ -1502,6 +1531,88 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </div>
 </div>
 </div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
+<h3 class="callout-title">Exercise: Create objects and check their class
+using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
+</h3>
+<div class="callout-content">
+<p>Using the objects created in the previous challenge, use the
+<code>class()</code> function to check their classes.</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution3" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+</button>
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div class="accordion-body">
+<div class="codewrapper sourceCode" id="cb17">
+<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="fu">class</span><span class="op">(</span><span class="va">chromosome_name</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb19">
+<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="fu">class</span><span class="op">(</span><span class="va">od_600_value</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>[1] "numeric"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb21">
+<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="fu">class</span><span class="op">(</span><span class="va">chr_position</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>[1] "character"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb23">
+<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="fu">class</span><span class="op">(</span><span class="va">spock</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>[1] "logical"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb25">
+<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="fu">class</span><span class="op">(</span><span class="va">pilot</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'pilot' not found</code></pre>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p>Notice that in the two challenges, <code>mode()</code> and
+<code>class()</code> return the same results. This time…</p>
 <p>Notice from the solution that even if a series of numbers is given as
 a value R will consider them to be in the “character” mode if they are
 enclosed as single or double quotes. Also, notice that you cannot take a
@@ -1513,7 +1624,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 was originally. If we want to create an object called <code>pilot</code>
 that was the <strong>name</strong> “Earhart”, we need to enclose
 <code>Earhart</code> in quotation marks.</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb27">
 <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">
@@ -1525,6 +1636,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
+<div class="codewrapper sourceCode" id="cb29">
+<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">pilot</span> <span class="op">&lt;-</span> <span class="st">"Earhart"</span></span>
+<span><span class="fu">typeof</span><span class="op">(</span><span class="va">pilot</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>[1] "character"</code></pre>
+</div>
 </section><section id="mathematical-and-functional-operations-on-objects"><h2 class="section-heading">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width">
@@ -1573,7 +1696,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tbody>
 </table>
 <p>These can be used with literal numbers:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb31">
 <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">
@@ -1586,7 +1709,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>and importantly, can be used on any object that evaluates to
 (i.e. interpreted by R) a numeric object:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb33">
 <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">
@@ -1615,14 +1738,14 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb35">
 <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">
@@ -1648,7 +1771,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 “concatenate” or “combine” function. Inside the function you may enter
 one or more values; for multiple values, separate each value with a
 comma:</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb37">
 <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">
@@ -1661,7 +1784,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>mode()</code> and <code>length()</code> functions respectively.
 Another useful function that gives both of these pieces of information
 is the <code>str()</code> (structure) function.</p>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb38">
 <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">
@@ -1673,7 +1796,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb40">
 <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">
@@ -1684,7 +1807,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb42">
 <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">
@@ -1703,7 +1826,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h2>
 <hr class="half-width">
 <p>Let’s create a few more vectors to play around with:</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb44">
 <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">
@@ -1719,7 +1842,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <strong>bracket notation</strong>. We type the name of the vector
 followed by square brackets. In those square brackets we place the index
 (e.g. a number) in that bracket as follows:</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb45">
 <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">
@@ -1734,7 +1857,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In R, every item your vector is indexed, starting from the first item
 (1) through to the final number of items in your vector. You can also
 retrieve a range of numbers:</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb47">
 <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">
@@ -1750,7 +1873,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>If you want to retrieve several (but not necessarily sequential)
 items from a vector, you pass a <strong>vector of indices</strong>; a
 vector that has the numbered positions you wish to retrieve.</p>
-<div class="codewrapper sourceCode" id="cb37">
+<div class="codewrapper sourceCode" id="cb49">
 <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">
@@ -1767,7 +1890,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 subsetting a vector (see <a href="https://thomasleeper.com/Rcourse/Tutorials/vectorindexing.html" class="external-link">these
 examples</a>). Also, several of these subsetting expressions can be
 combined:</p>
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb51">
 <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">
@@ -1786,7 +1909,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
-<div class="codewrapper sourceCode" id="cb41">
+<div class="codewrapper sourceCode" id="cb53">
 <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">
@@ -1795,7 +1918,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">snp_genes</span> <span class="op">&lt;-</span> <span class="fu">c</span><span class="op">(</span><span class="va">snp_genes</span>, <span class="st">"CYP1A1"</span>, <span class="st">"APOA5"</span><span class="op">)</span></span></code></pre>
 </div>
 <p>We can verify that “snp_genes” contains the new gene entry</p>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb54">
 <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">
@@ -1808,7 +1931,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Using a negative index will return a version of a vector with that
 index’s value removed:</p>
-<div class="codewrapper sourceCode" id="cb44">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -1821,7 +1944,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can remove that value from our vector by overwriting it with this
 expression:</p>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -1835,7 +1958,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>We can also explicitly rename or add a value to our index using
 double bracket notation:</p>
-<div class="codewrapper sourceCode" id="cb48">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -1869,12 +1992,12 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li>False - Vectors have both of these properties<br>
@@ -1903,7 +2026,7 @@ <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 we wanted get all of the SNPs in our vector of SNP positions that were
 greater than 100,000,000. We could index using the ‘&gt;’ (greater than)
 logical operator:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -1977,7 +2100,7 @@ <h3 class="callout-title">The magic of programming<a class="anchor" aria-label="
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
 better understood if you examine what the expression “snp_positions &gt;
 100000000” evaluates to:</p>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -1991,7 +2114,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>The output above is a logical vector, the 4th element of which is
 TRUE. When you pass a logical vector as an index, R will return the true
 values:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -2015,7 +2138,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 positions was the one that was greater than 100,000,000?</p>
 <p>We can use the <code>which()</code> function to return the indices of
 any item that evaluates as TRUE in our comparison:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -2031,7 +2154,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 used when our code is executed. Rather than put in a pre-determined
 value (e.g 100000000) we can use an object that can take on whatever
 value we need. So for example:</p>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -2057,7 +2180,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 for <code>not avaliable</code>). Missing data will get a more detailed
 treatment later, but the <code>is.NA()</code> function will return a
 logical vector, with TRUE for any NA value:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -2075,7 +2198,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 values) is present a vector. You can do this using the comparison
 operator <code>%in%</code>, which will return TRUE for any value in your
 collection that is in the vector you are searching:</p>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -2134,14 +2257,14 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution6" 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="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
-  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
+  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -2152,7 +2275,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -2163,7 +2286,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -2193,14 +2316,14 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution6" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution7" 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="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
-  <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
+  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -2212,7 +2335,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971" "rs662799" </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -2224,7 +2347,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "3"  "11" "X"  "6"  "11"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -2263,14 +2386,14 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution7" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution8" 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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
-  <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
+  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -2310,14 +2433,14 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution8" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution9" 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="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
-  <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
+  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb90">
 <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">
@@ -2345,14 +2468,14 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 </div>
 </div>
 </div>
-<div id="accordionSolution9" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution10" 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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
-  <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
+  <h4 class="accordion-header" id="headingSolution10">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb92">
 <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">
@@ -2383,7 +2506,7 @@ <h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#list
 lists using this <a href="https://r4ds.had.co.nz/vectors.html#lists" class="external-link">nice tutorial</a>. In
 this one example, we will create a named list and show you how to
 retrieve items from the list.</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb94">
 <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">
@@ -2412,7 +2535,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get all the values for the <code>position</code> object in the
 list, we use the <code>$</code> notation:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb96">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -2427,7 +2550,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>To get the first value in the <code>position</code> object, use the
 <code>[]</code> notation to index:</p>
-<div class="codewrapper sourceCode" id="cb86">
+<div class="codewrapper sourceCode" id="cb98">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -3138,13 +3261,73 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Ok, thats a lot up unpack! Some things to notice.</p>
 <ul>
-<li>the object type <code>data.frame</code> is displayed in the first
+<li><p>the object type <code>data.frame</code> is displayed in the first
 row along with its dimensions, in this case 801 observations (rows) and
-4 variables (columns)</li>
-<li>Each variable (column) has a name (e.g. <code>sample_id</code>).
+4 variables (columns)</p></li>
+<li>
+<p>Each variable (column) has a name (e.g. <code>sample_id</code>).
 This is followed by the object mode (e.g. chr, int, etc.). Notice that
 before each variable name there is a <code>$</code> - this will be
-important later.</li>
+important later.</p>
+<div id="challenge2" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
+</h3>
+<div class="callout-content">
+<p>Remeber when we said mode and class are sometimes different? If you
+do, here is a chance to check. What happens when you try the
+following?</p>
+<ol style="list-style-type: decimal">
+<li><code>mode(variants)</code></li>
+<li><code>class(variants)</code></li>
+</ol>
+</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="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="fu">mode</span><span class="op">(</span><span class="va">variants</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>[1] "list"</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb9">
+<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="fu">class</span><span class="op">(</span><span class="va">variants</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>[1] "data.frame"</code></pre>
+</div>
+<p>This result makes sense because <code>mode()</code> (which deals with
+how an object is stored) tells us that <code>variants</code> is treated
+as a <strong>list</strong> in R. A data frame is in some sense a “fancy”
+list. However, data fames do have some specific properties beyond that
+of a basic list, so they have their own class
+(<strong>data.frame</strong>), which is important for functions (and
+programmers) to know.</p>
+</div>
+</div>
+</div>
+</div>
+</li>
 </ul></section><section id="introducing-factors"><h2 class="section-heading">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width">
@@ -3159,7 +3342,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 alleles. We can use the <code>$</code> operator to access or extract a
 column by its name in data frames (or to extract objects within named
 lists).</p>
-<div class="codewrapper sourceCode" id="cb7">
+<div class="codewrapper sourceCode" id="cb11">
 <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">
@@ -3169,7 +3352,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>Let’s look at the first few items in our factor using
 <code>head()</code>:</p>
-<div class="codewrapper sourceCode" id="cb8">
+<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">
@@ -3183,7 +3366,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>There are 801 alleles (one for each row). To simplify, lets look at
 just the single-nucleotide alleles (SNPs). We can use some of the vector
 indexing skills from the last episode.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -3197,7 +3380,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 but we could treat them as categories of SNP. Doing this will enable
 some nice features. For example, we can try to generate a plot of this
 character vector as it is right now:</p>
-<div class="codewrapper sourceCode" id="cb11">
+<div class="codewrapper sourceCode" id="cb15">
 <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">
@@ -3228,14 +3411,14 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 to tell R to treat the SNPs as categories (i.e. a factor vector); we
 will create a new object to avoid confusion using the
 <code>factor()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb16">
+<div class="codewrapper sourceCode" id="cb20">
 <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">factor_snps</span> <span class="op">&lt;-</span> <span class="fu">factor</span><span class="op">(</span><span class="va">snps</span><span class="op">)</span></span></code></pre>
 </div>
 <p>Let’s learn a little more about this new type of vector:</p>
-<div class="codewrapper sourceCode" id="cb17">
+<div class="codewrapper sourceCode" id="cb21">
 <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">
@@ -3260,7 +3443,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 1 1 1 1 1 1 1 …“), since”A” is the first level, and the first few items
 in our factor are all “A”s.</p>
 <p>We can see how many items in our vector fall into each category:</p>
-<div class="codewrapper sourceCode" id="cb19">
+<div class="codewrapper sourceCode" id="cb23">
 <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">
@@ -3298,13 +3481,13 @@ <h3 class="callout-title">Tip: treating objects as categories without
 <p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
-<div class="codewrapper sourceCode" id="cb21">
+<div class="codewrapper sourceCode" id="cb25">
 <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="fu">plot</span><span class="op">(</span><span class="va">factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
+<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>This isn’t a particularly pretty example of a plot but it works.
 We’ll be learning much more about creating nice, publication-quality
 graphics later in this lesson.</p>
 <p>If you recall, factors are ordered alphabetically. That might make
@@ -3312,7 +3495,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 an intrinsic order. What if we wanted to order our plot according to the
 numerical value (i.e., in descending order of SNP frequency)? We can
 enforce an order on our factors:</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -3337,13 +3520,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 levels.</li>
 </ol>
 <p>Now we see our plot has be reordered:</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb27">
 <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="fu">plot</span><span class="op">(</span><span class="va">ordered_factor_snps</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
+<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout">
@@ -3366,7 +3549,7 @@ <h3 class="callout-title">Tip: Packages in R – what are they and why do
 <a href="https://www.tidyverse.org" class="external-link">tidyverse</a> packages such as
 <code>dplyr</code> and <code>ggplot2</code> (which you’ll do in the next
 few lessons), you would use the following command:</p>
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -3382,7 +3565,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.5 milliseconds.</code></pre>
+Successfully installed 1 package in 5.4 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -3425,16 +3608,16 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 </div>
 </div>
 </div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution3" 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 class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
+  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb30">
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 <pre class="downlit sourceCode r">
@@ -3447,7 +3630,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="2" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb28">
+<div class="codewrapper sourceCode" id="cb32">
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@@ -3460,7 +3643,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="3" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb30">
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@@ -3473,7 +3656,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="4" style="list-style-type: lower-alpha"><li>
 </li></ol>
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@@ -3493,7 +3676,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="5" style="list-style-type: lower-alpha"><li>
 </li></ol>
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@@ -3533,7 +3716,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="6" style="list-style-type: lower-alpha"><li>
 </li></ol>
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@@ -3546,7 +3729,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="7" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb38">
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@@ -3580,7 +3763,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="8" style="list-style-type: lower-alpha"><li>
 </li></ol>
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 <pre class="downlit sourceCode r">
@@ -3594,7 +3777,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol style="list-style-type: lower-roman"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb42">
+<div class="codewrapper sourceCode" id="cb46">
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 <pre class="downlit sourceCode r">
@@ -3634,7 +3817,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="10" style="list-style-type: lower-alpha"><li>
 </li></ol>
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 <pre class="downlit sourceCode r">
@@ -3674,7 +3857,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="11" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb46">
+<div class="codewrapper sourceCode" id="cb50">
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 <pre class="downlit sourceCode r">
@@ -3688,7 +3871,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <ol start="12" style="list-style-type: lower-alpha"><li>
 </li></ol>
-<div class="codewrapper sourceCode" id="cb48">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -3754,7 +3937,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Finally, in all of the subsetting exercises above, we printed values
 to the screen. You can create a new data frame object by assigning them
 to a new object name:</p>
-<div class="codewrapper sourceCode" id="cb50">
+<div class="codewrapper sourceCode" id="cb54">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -3771,7 +3954,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 25 29</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb52">
+<div class="codewrapper sourceCode" id="cb56">
 <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">
@@ -3869,7 +4052,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <p>First, its very important to recognize that coercion happens in R all
 the time. This can be a good thing when R gets it right, or a bad thing
 when the result is not what you expect. Consider:</p>
-<div class="codewrapper sourceCode" id="cb54">
+<div class="codewrapper sourceCode" id="cb58">
 <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">
@@ -3885,7 +4068,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 quotes, so we have explicitly told R to consider them as characters.
 However, even if we removed the quotes from the numbers, R would coerce
 everything into a character:</p>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb60">
 <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">
@@ -3897,7 +4080,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb62">
 <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">
@@ -3911,7 +4094,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can use the <code>as.</code> functions to explicitly coerce values
 from one form into another. Consider the following vector of characters,
 which all happen to be valid numbers:</p>
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb64">
 <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">
@@ -3923,7 +4106,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb62">
+<div class="codewrapper sourceCode" id="cb66">
 <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">
@@ -3936,7 +4119,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>Now we can coerce <code>snp_positions_2</code> into a numeric type
 using <code>as.numeric()</code>:</p>
-<div class="codewrapper sourceCode" id="cb64">
+<div class="codewrapper sourceCode" id="cb68">
 <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">
@@ -3948,7 +4131,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "double"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb66">
+<div class="codewrapper sourceCode" id="cb70">
 <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">
@@ -3962,7 +4145,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Sometimes coercion is straight forward, but what would happen if we
 tried using <code>as.numeric()</code> on
 <code>snp_chromosomes_2</code></p>
-<div class="codewrapper sourceCode" id="cb68">
+<div class="codewrapper sourceCode" id="cb72">
 <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">
@@ -3975,7 +4158,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
 </div>
 <p>If we check, we will see that an <code>NA</code> value (R’s default
 value for missing data) has been introduced.</p>
-<div class="codewrapper sourceCode" id="cb70">
+<div class="codewrapper sourceCode" id="cb74">
 <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">
@@ -3989,7 +4172,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Trouble can really start when we try to coerce a factor. For example,
 when we try to coerce the <code>factor_snps</code> vector into a numeric
 mode look at the result:</p>
-<div class="codewrapper sourceCode" id="cb72">
+<div class="codewrapper sourceCode" id="cb76">
 <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">
@@ -4027,7 +4210,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 notice a problem.</p>
 <p>If you need to coerce an entire column you can overwrite it using an
 expression like this one:</p>
-<div class="codewrapper sourceCode" id="cb74">
+<div class="codewrapper sourceCode" id="cb78">
 <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">
@@ -4097,7 +4280,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data
 <code>max()</code> on an individual column. Let’s look at the “DP” or
 filtered depth. This value shows the number of filtered reads that
 support each of the reported variants.</p>
-<div class="codewrapper sourceCode" id="cb76">
+<div class="codewrapper sourceCode" id="cb80">
 <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">
@@ -4110,7 +4293,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>You can sort a data frame using the <code>order()</code>
 function:</p>
-<div class="codewrapper sourceCode" id="cb78">
+<div class="codewrapper sourceCode" id="cb82">
 <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">
@@ -4137,14 +4320,14 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 </div>
 </div>
 </div>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution4" 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="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
-  <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
+  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb80">
+<div class="codewrapper sourceCode" id="cb84">
 <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">
@@ -4161,7 +4344,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 <p>You can rename columns:</p>
-<div class="codewrapper sourceCode" id="cb82">
+<div class="codewrapper sourceCode" id="cb86">
 <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">
@@ -4188,7 +4371,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
-<div class="codewrapper sourceCode" id="cb84">
+<div class="codewrapper sourceCode" id="cb88">
 <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">
@@ -4237,7 +4420,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to adjust. Click the <kbd>Import</kbd> button to import the data.</p>
 <p>Finally, let’s check the first few lines of the
 <code>Ecoli_metadata</code> data frame:</p>
-<div class="codewrapper sourceCode" id="cb85">
+<div class="codewrapper sourceCode" id="cb89">
 <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">
@@ -4291,14 +4474,14 @@ <h3 class="callout-title">Exercise: Putting it all together - data
 </div>
 </div>
 </div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
+<div id="accordionSolution5" 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="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
-  <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
+  <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb87">
+<div class="codewrapper sourceCode" id="cb91">
 <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">
@@ -4309,7 +4492,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 30  7</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb89">
+<div class="codewrapper sourceCode" id="cb93">
 <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">
@@ -4320,7 +4503,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "minus"   "plus"    "unknown"</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb91">
+<div class="codewrapper sourceCode" id="cb95">
 <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">
@@ -4333,7 +4516,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   minus    plus unknown 
       9       9      12 </code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb93">
+<div class="codewrapper sourceCode" id="cb97">
 <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">
@@ -4347,7 +4530,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
         &lt;dbl&gt;
 1        4.62</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb95">
+<div class="codewrapper sourceCode" id="cb99">
 <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">
@@ -4358,7 +4541,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 4.625</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb97">
+<div class="codewrapper sourceCode" id="cb101">
 <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">
@@ -6507,7 +6690,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6606,7 +6789,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6657,7 +6840,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6706,7 +6889,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/images.html b/instructor/images.html
index f0869d7fc..f561076e8 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -369,9 +369,9 @@ <h3 id="03-basics-factors-dataframes-figure-1">Figure 1</h3>
 <figure><img src="../%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure><hr>
 <h3 id="03-basics-factors-dataframes-figure-2">Figure 2</h3>
-<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-14-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
-<h3 id="03-basics-factors-dataframes-figure-3">Figure 3</h3>
 <figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="03-basics-factors-dataframes-figure-3">Figure 3</h3>
+<figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-18-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
 <h3 id="03-basics-factors-dataframes-figure-4">Figure 4</h3>
 <p aria-hidden="true">Image 1 of 1: ‘RStudio import menu’</p>
 <figure><img src="../%22fig/rstudio_import_menu.png%22" alt="RStudio import menu" class="figure mx-auto d-block"><div class="figcaption">RStudio import menu</div>
diff --git a/md5sum.txt b/md5sum.txt
index 01939743b..08b2b8e41 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,9 +4,9 @@
 "config.yaml" "b91cd97fa3b408bd1ac0a00e67ab3219" "site/built/config.yaml" "2024-04-04"
 "index.md" "7f9c30e6487338a0c3f8ecc4018873ab" "site/built/index.md" "2024-04-04"
 "episodes/00-introduction.Rmd" "e1354ed92fb458179c8c00b00ee1cf55" "site/built/00-introduction.md" "2024-04-04"
-"episodes/01-r-basics.Rmd" "2f4b7fd244990f97e0c2fe88bae2618b" "site/built/01-r-basics.md" "2024-04-04"
+"episodes/01-r-basics.Rmd" "ba3faa27a6f2eb8087acf99679a7ac03" "site/built/01-r-basics.md" "2024-04-10"
 "episodes/02-data-prelude.Rmd" "ab2b1fd3cdaae919f9e409f713a0a8ad" "site/built/02-data-prelude.md" "2024-04-04"
-"episodes/03-basics-factors-dataframes.Rmd" "78de77380f2b4bfd76622a8fc1e10f99" "site/built/03-basics-factors-dataframes.md" "2024-04-10"
+"episodes/03-basics-factors-dataframes.Rmd" "109ed19fade231fe8e1da43903b06539" "site/built/03-basics-factors-dataframes.md" "2024-04-10"
 "episodes/04-bioconductor-vcfr.Rmd" "10eb69b4697d7ecb9695d36c0d974208" "site/built/04-bioconductor-vcfr.md" "2024-04-04"
 "episodes/05-dplyr.Rmd" "f74055bd8677338a213e0a0c6c430119" "site/built/05-dplyr.md" "2024-04-04"
 "episodes/06-data-visualization.Rmd" "0b45534421bad05f040b24c40b6da71b" "site/built/06-data-visualization.md" "2024-04-04"
diff --git a/pkgdown.yml b/pkgdown.yml
index 5b3c4746c..48dcb6d57 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.8
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-04-10T15:58Z
+last_built: 2024-04-10T16:53Z