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 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
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diff --git a/dev/about-the-authors.html b/dev/about-the-authors.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
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diff --git a/dev/acknowledgments.html b/dev/acknowledgments.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
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diff --git a/dev/classification1.html b/dev/classification1.html
diff --git a/dev/classification2.html b/dev/classification2.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -668,7 +668,8 @@ <h2><span class="header-section-number">6.3</span> Evaluating performance<a href
 disastrous error, since it may lead to a patient who requires treatment not receiving it.
 Since we are particularly interested in identifying malignant cases, this
 classifier would likely be unacceptable even with an accuracy of 89%.</p>
-<p>Focusing more on one label than the other is
+<p>Focusing more on one label than the other
+is
 common in classification problems. In such cases, we typically refer to the label we are more
 interested in identifying as the <em>positive</em> label, and the other as the
 <em>negative</em> label. In the tumor example, we would refer to malignant
@@ -1568,7 +1569,8 @@ <h3><span class="header-section-number">6.6.4</span> Evaluating on the test set<
 ## Best k: 36</code></pre>
 <p>Then to make predictions and assess the estimated accuracy of the best model on the test data, we use the
 <code>predict</code> and <code>metrics</code> functions as we did earlier in the chapter. We can then pass those predictions to
-the <code>precision</code>, <code>recall</code>, and <code>conf_mat</code> functions to assess the estimated precision and recall, and print a confusion matrix.</p>
+the <code>precision</code>, <code>recall</code>, and <code>conf_mat</code> functions to assess the estimated precision and recall, and print a confusion matrix.
+</p>
 <div class="sourceCode" id="cb372"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb372-1"><a href="classification2.html#cb372-1" tabindex="-1"></a>cancer_test_predictions <span class="ot">&lt;-</span> <span class="fu">predict</span>(knn_fit, cancer_test) <span class="sc">|&gt;</span></span>
 <span id="cb372-2"><a href="classification2.html#cb372-2" tabindex="-1"></a>  <span class="fu">bind_cols</span>(cancer_test)</span>
 <span id="cb372-3"><a href="classification2.html#cb372-3" tabindex="-1"></a></span>

diff --git a/dev/clustering.html b/dev/clustering.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -1065,42 +1065,6 @@ <h2><span class="header-section-number">9.6</span> K-means in R<a href="clusteri
 ## 16           46.7               195 Cluster_3    
 ## 17           52.2               197 Cluster_3    
 ## 18           46.8               189 Cluster_3</code></pre>
-<!--
-If for some reason we need access to just the cluster assignments,
-we can extract those from the fit as a data frame using
-the `extract_cluster_assignment` function. Note that in this case,
-the cluster assignments variable is named `.cluster`, while the `augment`
-function earlier creates a variable named `.pred_cluster`.
-
-
-```r
-extract_cluster_assignment(kmeans_fit)
-```
-
-```
-## # A tibble: 18 × 1
-##    .cluster 
-##    <fct>    
-##  1 Cluster_1
-##  2 Cluster_1
-##  3 Cluster_1
-##  4 Cluster_1
-##  5 Cluster_1
-##  6 Cluster_1
-##  7 Cluster_1
-##  8 Cluster_1
-##  9 Cluster_2
-## 10 Cluster_2
-## 11 Cluster_2
-## 12 Cluster_2
-## 13 Cluster_2
-## 14 Cluster_2
-## 15 Cluster_3
-## 16 Cluster_3
-## 17 Cluster_3
-## 18 Cluster_3
-```
--->
 <p>Now that we have the cluster assignments included in the <code>clustered_data</code> tidy data frame, we can
 visualize them as shown in Figure <a href="clustering.html#fig:10-plot-clusters-2">9.13</a>.
 Note that we are plotting the <em>un-standardized</em> data here; if we for some reason wanted to

diff --git a/dev/foreword.html b/dev/foreword.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
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diff --git a/dev/index.html b/dev/index.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
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@@ -550,7 +550,7 @@ <h1 class="title"><p><img src="img/frontmatter/ds-a-first-intro-graphic.jpg" />
 Data Science</p></h1>
 <h2 class="subtitle"><em>A First Introduction</em></h2>
 <p class="author"><em>Tiffany Timbers, Trevor Campbell, and Melissa Lee</em></p>
-<p class="date"><em>2023-11-16</em></p>
+<p class="date"><em>2023-11-17</em></p>
 </div>
 <div id="welcome" class="section level1 unnumbered hasAnchor">
 <h1>Welcome!<a href="index.html#welcome" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/dev/inference.html b/dev/inference.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
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diff --git a/dev/intro.html b/dev/intro.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
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diff --git a/dev/jupyter.html b/dev/jupyter.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
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diff --git a/dev/preface.html b/dev/preface.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
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diff --git a/dev/reading.html b/dev/reading.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
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@@ -648,7 +648,8 @@ <h2><span class="header-section-number">2.3</span> Absolute and relative file pa
 <p>Note that there is no forward slash at the beginning of a relative path; if we accidentally typed <code>"/data/happiness_report.csv"</code>,
 R would look for a folder named <code>data</code> in the root folder of the computer—but that doesn’t exist!</p>
 <p>Aside from specifying places to go in a path using folder names (like <code>data</code> and <code>worksheet_02</code>), we can also specify two additional
-special places: the <em>current directory</em> and the <em>previous directory</em>. We indicate the current working directory with a single dot <code>.</code>, and
+special places: the <em>current directory</em> and the <em>previous directory</em>.
+We indicate the current working directory with a single dot <code>.</code>, and
 the previous directory with two dots <code>..</code>. So for instance, if we wanted to reach the <code>bike_share.csv</code> file from the <code>worksheet_02</code> folder, we could
 use the relative path <code>../tutorial_01/bike_share.csv</code>. We can even combine these two; for example, we could reach the <code>bike_share.csv</code> file using
 the (very silly) path <code>../tutorial_01/../tutorial_01/./bike_share.csv</code> with quite a few redundant directions: it says to go back a folder, then open <code>tutorial_01</code>,
@@ -1720,12 +1721,12 @@ <h3><span class="header-section-number">2.8.2</span> Using an API<a href="readin
 idea that you can learn how to use another API if needed. In particular, in this book we will show you the basics
 of how to use the <code>httr2</code> package in R to access data from the NASA “Astronomy Picture
 of the Day” API (a great source of desktop backgrounds, by the way—take a look at the stunning
-picture of the Rho-Ophiuchi cloud complex in Figure <a href="reading.html#fig:NASA-API-Rho-Ophiuchi">2.8</a> from July 13, 2023!).</p>
+picture of the Rho-Ophiuchi cloud complex <span class="citation">(<a href="#ref-rhoophiuchi">NASA et al. 2023</a>)</span> in Figure <a href="reading.html#fig:NASA-API-Rho-Ophiuchi">2.8</a> from July 13, 2023!).</p>
 
 <div class="figure" style="text-align: center"><span style="display:block;" id="fig:NASA-API-Rho-Ophiuchi"></span>
-<img src="img/reading/NASA-API-Rho-Ophiuchi.png" alt="The James Webb Space Telescope’s NIRCam image of the Rho Ophiuchi molecular cloud complex (NASA et al. 2023)." width="60%" />
+<img src="img/reading/NASA-API-Rho-Ophiuchi.png" alt="The James Webb Space Telescope’s NIRCam image of the Rho Ophiuchi molecular cloud complex." width="60%" />
 <p class="caption">
-Figure 2.8: The James Webb Space Telescope’s NIRCam image of the Rho Ophiuchi molecular cloud complex <span class="citation">(<a href="#ref-rhoophiuchi">NASA et al. 2023</a>)</span>.
+Figure 2.8: The James Webb Space Telescope’s NIRCam image of the Rho Ophiuchi molecular cloud complex.
 </p>
 </div>
 <p>First, you will need to visit the <a href="https://api.nasa.gov/">NASA APIs page</a> and generate an API key (i.e., a password used to identify you when accessing the API).
@@ -1804,7 +1805,8 @@ <h4>Accessing the NASA API<a href="reading.html#accessing-the-nasa-api" class="a
 <span id="cb102-15"><a href="reading.html#cb102-15" tabindex="-1"></a><span class="st">Rho Ophiuchi&quot;</span><span class="fu">,</span><span class="dt">&quot;url&quot;</span><span class="fu">:</span><span class="st">&quot;https://apod.nasa.gov/apod/image/2307/STScI-01_RhoOph1024.png&quot;</span><span class="fu">}</span></span></code></pre></div>
 <p>Neat! There is definitely some data there, but it’s a bit hard to
 see what it all is. As it turns out, this is a common format for data called
-<em>JSON</em> (JavaScript Object Notation). We won’t encounter this kind of data much in this book,
+<em>JSON</em> (JavaScript Object Notation).
+We won’t encounter this kind of data much in this book,
 but for now you can interpret this data as <code>key : value</code> pairs separated by
 commas. For example, if you look closely, you’ll see that the first entry is
 <code>"date":"2023-07-13"</code>, which indicates that we indeed successfully received
@@ -1813,7 +1815,8 @@ <h4>Accessing the NASA API<a href="reading.html#accessing-the-nasa-api" class="a
 the <code>httr2</code> package, and construct the query using the <code>request</code> function, which takes a single URL argument;
 you will recognize the same query URL that we pasted into the browser earlier.
 We will then send the query using the <code>req_perform</code> function, and finally
-obtain a JSON representation of the response using the <code>resp_body_json</code> function.</p>
+obtain a JSON representation of the response using the <code>resp_body_json</code> function.
+</p>
 <!-- we have disabled the below code for reproducibility, with hidden setting
 of the nasa_data object. But you can reproduce this using the DEMO_KEY key -->
 <div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb103-1"><a href="reading.html#cb103-1" tabindex="-1"></a><span class="fu">library</span>(httr2)</span>

diff --git a/dev/references.html b/dev/references.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/dev/regression1.html b/dev/regression1.html
diff --git a/dev/regression2.html b/dev/regression2.html
diff --git a/dev/search_index.json b/dev/search_index.json
diff --git a/dev/setup.html b/dev/setup.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -613,7 +613,8 @@ <h3><span class="header-section-number">13.4.1</span> Windows<a href="setup.html
 <p><strong>Installation</strong> To install Docker on Windows,
 visit <a href="https://docs.docker.com/desktop/install/windows-install/">the online Docker documentation</a>,
 and download the <code>Docker Desktop Installer.exe</code> file. Double-click the file to open the installer
-and follow the instructions on the installation wizard, choosing <strong>WSL-2</strong> instead of <strong>Hyper-V</strong> when prompted.</p>
+and follow the instructions on the installation wizard, choosing <strong>WSL-2</strong> instead of <strong>Hyper-V</strong> when prompted.
+</p>
 <blockquote>
 <p><strong>Note:</strong> Occasionally, when you first run Docker on Windows, you will encounter an error message. Some common errors you may see:</p>
 <ul>
@@ -711,7 +712,8 @@ <h3><span class="header-section-number">13.4.3</span> Ubuntu<a href="setup.html#
 curl -fsSL https://get.docker.com -o get-docker.sh
 sudo chmod u+x get-docker.sh
 sudo sh get-docker.sh</code></pre>
-<p><strong>Running JupyterLab</strong> First, open the <a href="https://raw.githubusercontent.com/UBC-DSCI/data-science-a-first-intro-worksheets/main/Dockerfile"><code>Dockerfile</code> in the worksheets repository</a>,
+<p><strong>Running JupyterLab</strong> First, open
+the <a href="https://raw.githubusercontent.com/UBC-DSCI/data-science-a-first-intro-worksheets/main/Dockerfile"><code>Dockerfile</code> in the worksheets repository</a>,
 and look for the line <code>FROM ubcdsci/r-dsci-100:</code> followed by a tag consisting of a sequence of numbers and letters.
 Then in the terminal, navigate to the directory where you want to run JupyterLab, and run
 the following command, replacing <code>TAG</code> with the <em>tag</em> you found earlier.</p>

diff --git a/dev/version-control.html b/dev/version-control.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -670,7 +670,8 @@ <h2><span class="header-section-number">12.4</span> Version control repositories
 a workspace on a server (e.g., JupyterHub).
 The other copy is typically stored in a repository hosting service (e.g., GitHub), where
 we can easily share it with our collaborators.
-This copy is commonly referred to as the <strong>remote repository</strong>.</p>
+This copy is commonly referred to as the <strong>remote repository</strong>.
+</p>
 <div class="figure" style="text-align: center"><span style="display:block;" id="fig:vc1-no-changes"></span>
 <img src="_main_files/figure-html/vc1-no-changes-1.png" alt="Schematic of local and remote version control repositories." width="100%" />
 <p class="caption">
@@ -731,7 +732,7 @@ <h3><span class="header-section-number">12.5.1</span> Committing changes to a lo
 </p>
 </div>
 <p>Once you reach a point that you want Git to keep a record
-of the current version of your work, you need to commit
+of the current version of your work, you need to <strong>commit</strong>
 (i.e., snapshot) your changes. A prerequisite to this is telling Git which
 files should be included in that snapshot. We call this step <strong>adding</strong> the
 files to the <strong>staging area</strong>.
@@ -1047,8 +1048,6 @@ <h3><span class="header-section-number">12.7.1</span> Generating a GitHub person
 </div>
 <div id="cloning-a-repository-using-jupyter" class="section level3 hasAnchor" number="12.7.2">
 <h3><span class="header-section-number">12.7.2</span> Cloning a repository using Jupyter<a href="version-control.html#cloning-a-repository-using-jupyter" class="anchor-section" aria-label="Anchor link to header"></a></h3>
-<!--Now that we have everything we need for authentication,
-the next step is -->
 <p><em>Cloning</em> a remote repository from GitHub
 to create a local repository results in a
 copy that knows where it was obtained from so that it knows where to send/receive

diff --git a/dev/viz.html b/dev/viz.html
@@ -23,7 +23,7 @@
 <meta name="author" content="Tiffany Timbers, Trevor Campbell, and Melissa Lee" />
 
 
-<meta name="date" content="2023-11-16" />
+<meta name="date" content="2023-11-17" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />