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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.553">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="Alice Beittel">
<title>Quarto Code Chunk Practice - Session 2</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
}
pre.numberSource { margin-left: 3em; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
</style>
<script src="example_codechunk_2_files/libs/clipboard/clipboard.min.js"></script>
<script src="example_codechunk_2_files/libs/quarto-html/quarto.js"></script>
<script src="example_codechunk_2_files/libs/quarto-html/popper.min.js"></script>
<script src="example_codechunk_2_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="example_codechunk_2_files/libs/quarto-html/anchor.min.js"></script>
<link href="example_codechunk_2_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="example_codechunk_2_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="example_codechunk_2_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="example_codechunk_2_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="example_codechunk_2_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
</head>
<body class="fullcontent">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Quarto Code Chunk Practice - Session 2</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Alice Beittel </p>
</div>
</div>
</div>
</header>
<section id="quarto" class="level2">
<h2 class="anchored" data-anchor-id="quarto">Quarto</h2>
<p>Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <a href="https://quarto.org" class="uri">https://quarto.org</a>.</p>
</section>
<section id="running-code" class="level2">
<h2 class="anchored" data-anchor-id="running-code">Running Code</h2>
<p>When you click the <strong>Render</strong> button a document will be generated that includes both content and the output of embedded code. You can embed code like this:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="dv">1</span> <span class="sc">+</span> <span class="dv">1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 2</code></pre>
</div>
</div>
<p>You can add options to executable code like this</p>
<div class="cell">
<div class="cell-output cell-output-stdout">
<pre><code>[1] 4</code></pre>
</div>
</div>
<p>The <code>echo: false</code> option disables the printing of code (only output is displayed).</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co">#you can make a vertical line by doing shift and then press the \ key </span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="co"># #| eval: false = this disables printing of code. Only output is displayed. </span></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="co"># #| echo: false = this will remove code from being displayed and only show output </span></span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="dv">1</span><span class="sc">+</span><span class="dv">1</span></span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>a</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 2</code></pre>
</div>
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="st">'this is a string in R'</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>You can use the ` on either side of text/numbers to indicate r code in line.</p>
<p>The sum of 1+1 is 2.</p>
<p>The sum of 1+1 is 2.</p>
<p>You can output a line of text in quarto document like this:</p>
<p>this is a string in R</p>
<div class="cell" data-lable="fig-HR">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: package 'tidyverse' was built under R version 4.4.2</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: package 'dplyr' was built under R version 4.4.1</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.1 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors</code></pre>
</div>
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(BayesFactor)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: package 'BayesFactor' was built under R version 4.4.2</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Loading required package: coda
Loading required package: Matrix
Attaching package: 'Matrix'
The following objects are masked from 'package:tidyr':
expand, pack, unpack
************
Welcome to BayesFactor 0.9.12-4.7. If you have questions, please contact Richard Morey (richarddmorey@gmail.com).
Type BFManual() to open the manual.
************</code></pre>
</div>
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Read data</span></span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a>df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="st">"data/processed/preprocessed-GARP-TSST-data.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Rows: 144 Columns: 211
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (5): Condition, Sex, Snack_UG, Snack_G, Education
dbl (204): VPN, PANAS1_1, PANAS1_2, PANAS1_3, PANAS1_4, PANAS1_5, PANAS1_6,...
dttm (1): Wakeup_Time
date (1): Date
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
</div>
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Convert df to long-format</span></span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a>df_long <span class="ot"><-</span> df <span class="sc">%>%</span></span>
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">pivot_longer</span>(<span class="at">cols =</span> <span class="fu">c</span>(HR_Baseline_Average, HR_TSST_Average),</span>
<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a> <span class="at">names_to =</span> <span class="st">"Measurement"</span>,</span>
<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a> <span class="at">values_to =</span> <span class="st">"HR"</span>)</span>
<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="co">#Drop missing values</span></span>
<span id="cb16-8"><a href="#cb16-8" aria-hidden="true" tabindex="-1"></a>df_long <span class="ot"><-</span> df_long <span class="sc">%>%</span> <span class="fu">drop_na</span>(HR)</span>
<span id="cb16-9"><a href="#cb16-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb16-10"><a href="#cb16-10" aria-hidden="true" tabindex="-1"></a><span class="co">#Make sure columns are coded as factors for analysis</span></span>
<span id="cb16-11"><a href="#cb16-11" aria-hidden="true" tabindex="-1"></a>df_long<span class="sc">$</span>VPN <span class="ot"><-</span> <span class="fu">as.factor</span>(df_long<span class="sc">$</span>VPN)</span>
<span id="cb16-12"><a href="#cb16-12" aria-hidden="true" tabindex="-1"></a>df_long<span class="sc">$</span>Measurement <span class="ot"><-</span> <span class="fu">as.factor</span>(df_long<span class="sc">$</span>Measurement)</span>
<span id="cb16-13"><a href="#cb16-13" aria-hidden="true" tabindex="-1"></a>df_long<span class="sc">$</span>Condition <span class="ot"><-</span> <span class="fu">as.factor</span>(df_long<span class="sc">$</span>Condition)</span>
<span id="cb16-14"><a href="#cb16-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb16-15"><a href="#cb16-15" aria-hidden="true" tabindex="-1"></a><span class="co">#Bayesian Analysis</span></span>
<span id="cb16-16"><a href="#cb16-16" aria-hidden="true" tabindex="-1"></a>BF <span class="ot"><-</span> <span class="fu">anovaBF</span>(<span class="at">formula =</span> HR <span class="sc">~</span> Measurement<span class="sc">*</span>Condition <span class="sc">+</span> VPN,</span>
<span id="cb16-17"><a href="#cb16-17" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> df_long,</span>
<span id="cb16-18"><a href="#cb16-18" aria-hidden="true" tabindex="-1"></a> <span class="at">whichRandom =</span> <span class="st">"VPN"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: data coerced from tibble to data frame</code></pre>
</div>
<div class="sourceCode cell-code" id="cb18"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Evidence for interaction term</span></span>
<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a>BF_interaction <span class="ot"><-</span> BF[<span class="dv">4</span>]<span class="sc">/</span>BF[<span class="dv">3</span>]</span>
<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb18-4"><a href="#cb18-4" aria-hidden="true" tabindex="-1"></a>BF_interaction</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>Bayes factor analysis
--------------
[1] Condition + Measurement + Condition:Measurement + VPN : 348.1916 ±4.21%
Against denominator:
HR ~ Condition + Measurement + VPN
---
Bayes factor type: BFlinearModel, JZS</code></pre>
</div>
<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Summarize to mean / SEM for plot</span></span>
<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a>df_long2 <span class="ot"><-</span> df_long <span class="sc">%>%</span></span>
<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(Measurement, Condition) <span class="sc">%>%</span></span>
<span id="cb20-4"><a href="#cb20-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarize</span>(<span class="at">mean_value =</span> <span class="fu">mean</span>(HR, <span class="at">na.rm =</span> T),</span>
<span id="cb20-5"><a href="#cb20-5" aria-hidden="true" tabindex="-1"></a> <span class="at">sem =</span> <span class="fu">sd</span>(HR, <span class="at">na.rm =</span> T)<span class="sc">/</span><span class="fu">sqrt</span>(<span class="fu">n</span>()))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>`summarise()` has grouped output by 'Measurement'. You can override using the
`.groups` argument.</code></pre>
</div>
<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Create plot</span></span>
<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a>plot <span class="ot"><-</span> <span class="fu">ggplot</span>(df_long2, <span class="fu">aes</span>(Measurement, mean_value, <span class="at">group =</span> Condition, <span class="at">color =</span> Condition)) <span class="sc">+</span></span>
<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_pointrange</span>(<span class="fu">aes</span>(<span class="at">ymin=</span>mean_value<span class="sc">-</span>sem, <span class="at">ymax=</span> mean_value<span class="sc">+</span>sem)) <span class="sc">+</span></span>
<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_line</span>() <span class="sc">+</span></span>
<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_classic</span>() <span class="sc">+</span></span>
<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_x_discrete</span>(<span class="at">labels =</span> <span class="fu">c</span>(<span class="st">"Baseline"</span>,</span>
<span id="cb22-7"><a href="#cb22-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"TSST-G/Control"</span>)) <span class="sc">+</span></span>
<span id="cb22-8"><a href="#cb22-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">ylab</span>(<span class="st">"Mean Heartrate (BPM)"</span>) <span class="sc">+</span></span>
<span id="cb22-9"><a href="#cb22-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_colour_grey</span>(<span class="at">start =</span> <span class="fl">0.5</span>, <span class="at">end =</span> <span class="fl">0.2</span>) <span class="sc">+</span></span>
<span id="cb22-10"><a href="#cb22-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"top"</span>)</span>
<span id="cb22-11"><a href="#cb22-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb22-12"><a href="#cb22-12" aria-hidden="true" tabindex="-1"></a><span class="co">#Print and save plots </span></span>
<span id="cb22-13"><a href="#cb22-13" aria-hidden="true" tabindex="-1"></a>plot</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
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<figure class="figure">
<p><img src="example_codechunk_2_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid figure-img" width="672"></p>
<figcaption>This is an example figure</figcaption>
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<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="co">#ggsave("../output/heartrate.pdf", plot, width = 4, height = 3)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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