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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.1.251">
<title>R4CSR</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<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 -1.6em;
vertical-align: middle;
}
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; 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;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ color: #003b4f; background-color: #f1f3f5; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #003b4f; } /* Normal */
code span.al { color: #ad0000; } /* Alert */
code span.an { color: #5e5e5e; } /* Annotation */
code span.at { color: #657422; } /* Attribute */
code span.bn { color: #ad0000; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #003b4f; } /* ControlFlow */
code span.ch { color: #20794d; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #5e5e5e; } /* Comment */
code span.cv { color: #5e5e5e; font-style: italic; } /* CommentVar */
code span.do { color: #5e5e5e; font-style: italic; } /* Documentation */
code span.dt { color: #ad0000; } /* DataType */
code span.dv { color: #ad0000; } /* DecVal */
code span.er { color: #ad0000; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #ad0000; } /* Float */
code span.fu { color: #4758ab; } /* Function */
code span.im { color: #00769e; } /* Import */
code span.in { color: #5e5e5e; } /* Information */
code span.kw { color: #003b4f; } /* Keyword */
code span.op { color: #5e5e5e; } /* Operator */
code span.ot { color: #003b4f; } /* Other */
code span.pp { color: #ad0000; } /* Preprocessor */
code span.sc { color: #5e5e5e; } /* SpecialChar */
code span.ss { color: #20794d; } /* SpecialString */
code span.st { color: #20794d; } /* String */
code span.va { color: #111111; } /* Variable */
code span.vs { color: #20794d; } /* VerbatimString */
code span.wa { color: #5e5e5e; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css" id="theme">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-captioned.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-captioned) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-captioned.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-captioned .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-captioned .callout-caption p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-captioned.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-captioned.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-caption {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-caption {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-captioned .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-captioned .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-captioned) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-caption {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="center">
<h1 class="title">R4CSR</h1>
</section>
<section>
<section id="book-club" class="title-slide slide level1 center">
<h1>Book club</h1>
<p>This is a slide deck summary of <a href="https://r4csr.org/">R for Clinical Study Reporting and Submission</a></p>
<p>There are three main parts of the book:</p>
<ol type="1">
<li><p>TLFs: a simulation of individual contributions</p></li>
<li><p>Clinical trial projects: a simulation of project leadership</p></li>
<li><p>eCTD submission: a simulation in package submission</p></li>
</ol>
<p>In this summer book club we will get to just the first part, TLFs. <a href="https://datascience.arizona.edu/events/r-clinical-study-reporting">Join us!</a></p>
</section>
<section id="get-r-help-at-uarizona" class="slide level2">
<h2>Get R help at UArizona</h2>
<p><a href="https://datascience.arizona.edu/events/data-viz-drop-0">Data & Visualization Drop-in</a> hours @ Main library</p>
<p><a href="https://datascience.arizona.edu/calendar">Data Science Institute workshops</a></p>
<p><a href="https://datascience.cct.arizona.edu/workshops">CCT Data Science workshops</a></p>
</section>
<section id="preface" class="slide level2">
<h2>Preface</h2>
<ul>
<li><p>R folder structure recommended</p></li>
<li><p><a href="https://github.com/cdisc-org/sdtm-adam-pilot-project/tree/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/analysis/adam/datasets">CDISC pilot</a><a href="https://github.com/elong0527/r4csr/tree/main/data-adam">data</a> is used throughout</p></li>
<li><p>R packages needed</p>
<ul>
<li>not all packages are used in every chapter</li>
</ul></li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">install.packages</span>(<span class="fu">c</span>(</span>
<span id="cb1-2"><a href="#cb1-2"></a> <span class="st">"dplyr"</span> <span class="co"># Manipulate data</span></span>
<span id="cb1-3"><a href="#cb1-3"></a> , <span class="st">"emmeans"</span> <span class="co"># Least-square mean estimation </span></span>
<span id="cb1-4"><a href="#cb1-4"></a> , <span class="st">"haven"</span> <span class="co"># import SAS data </span></span>
<span id="cb1-5"><a href="#cb1-5"></a> , <span class="st">"r2rtf"</span> <span class="co"># Reporting in RTF format</span></span>
<span id="cb1-6"><a href="#cb1-6"></a> , <span class="st">"survival"</span> <span class="co"># kapplan meier curves</span></span>
<span id="cb1-7"><a href="#cb1-7"></a> , <span class="st">"tidyr"</span> <span class="co"># Manipulate data</span></span>
<span id="cb1-8"><a href="#cb1-8"></a> , <span class="st">"table1"</span> <span class="co">#Transfer data</span></span>
<span id="cb1-9"><a href="#cb1-9"></a> ))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="living-list-of-acronyms" class="slide level2 scrollable">
<h2>Living list of acronyms</h2>
<table>
<colgroup>
<col style="width: 26%">
<col style="width: 26%">
<col style="width: 47%">
</colgroup>
<thead>
<tr class="header">
<th>Type</th>
<th>Acronym</th>
<th>Definition/Explanation</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>clinical</td>
<td>CSR</td>
<td>Clinical study report</td>
</tr>
<tr class="even">
<td>clinical</td>
<td>SDTM</td>
<td>standard data tabulation model</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>ADaM</td>
<td>Analysis dataset model</td>
</tr>
<tr class="even">
<td>clinical</td>
<td>TLFs</td>
<td>Tables, listings, and figures</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>A&R</td>
<td>Analysis and reporting</td>
</tr>
<tr class="even">
<td>clinical/computational</td>
<td>eCTD</td>
<td>Electronic common technical document</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>CDISC</td>
<td>Clinical Data Interchange Standards Consortium</td>
</tr>
<tr class="even">
<td>clinical</td>
<td>ICH</td>
<td>International conference on harmonization</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>ICH E3</td>
<td>ICH guidelines on structure and content of clinical study reports</td>
</tr>
<tr class="even">
<td>computational</td>
<td>RTF</td>
<td>Rich text format</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>adae</td>
<td>Analysis dataset for adverse events</td>
</tr>
<tr class="even">
<td>clinical/computational</td>
<td>ADSL</td>
<td>Subject-level analysis dataset</td>
</tr>
<tr class="odd">
<td>clinical/computational</td>
<td>ITT</td>
<td>intention to treat (i.e. none of the patients are excluded and the patients are analyzed according to the randomization scheme)</td>
</tr>
<tr class="even">
<td>statistical</td>
<td>ANCOVA</td>
<td>Analysis of covariance</td>
</tr>
<tr class="odd">
<td>statistical</td>
<td>LOCF</td>
<td>last observation carried forward</td>
</tr>
<tr class="even">
<td>statistical</td>
<td>K-M</td>
<td>Kaplan Meier curve/estimate</td>
</tr>
<tr class="odd">
<td>clinical</td>
<td>AEs</td>
<td>adverse events</td>
</tr>
</tbody>
</table>
</section></section>
<section>
<section id="chapter-1" class="title-slide slide level1 center">
<h1>Chapter 1</h1>
<p>An overview of clinical study reports and the {r2rtf} package.</p>
</section>
<section id="overview" class="slide level2">
<h2>Overview</h2>
<ul>
<li><p>A CSR contains all methods and results of a study in ~16 sections</p>
<ul>
<li>TLFs are found in 10-12, 14, 16, +</li>
</ul></li>
<li><p>often word document format</p>
<ul>
<li>in this book we explore RTF</li>
</ul></li>
<li><p>The {r2rtf} package allows for the creation and export of publication quality tables and figures in rich text format</p>
<ul>
<li>Use the included <code>r2rtf_adae</code> dataset to explore functions in {r2rtf}</li>
</ul></li>
</ul>
</section>
<section id="r2rtf" class="slide level2">
<h2>r2rtf</h2>
<p>After formatting your data as desired by {r2rtf}, a general workflow is as follows:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="fu">head</span>(tbl) <span class="sc">%>%</span></span>
<span id="cb2-2"><a href="#cb2-2"></a> <span class="fu">rtf_body</span>() <span class="sc">%>%</span> <span class="co"># Step 1 Add table attributes</span></span>
<span id="cb2-3"><a href="#cb2-3"></a> <span class="fu">rtf_encode</span>() <span class="sc">%>%</span> <span class="co"># Step 2 Convert attributes to RTF encode</span></span>
<span id="cb2-4"><a href="#cb2-4"></a> <span class="fu">write_rtf</span>(<span class="st">"tlf/intro-ae1.rtf"</span>) <span class="co"># Step 3 Write to a .rtf file</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Each table attribute is added individually, then the attributes are converted to RTF, and finally, you can export an object in RTF.</p>
</section>
<section id="style-with-r2rtf" class="slide level2">
<h2>Style with r2rtf</h2>
<p>Use {r2rtf} to set specific design elements for your ouput:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="fu">head</span>(tbl) <span class="sc">%>%</span></span>
<span id="cb3-2"><a href="#cb3-2"></a> <span class="fu">rtf_colheader</span>(</span>
<span id="cb3-3"><a href="#cb3-3"></a> <span class="at">colheader =</span> <span class="st">" | Treatment"</span>,</span>
<span id="cb3-4"><a href="#cb3-4"></a> <span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="dv">6</span>)</span>
<span id="cb3-5"><a href="#cb3-5"></a> ) <span class="sc">%>%</span></span>
<span id="cb3-6"><a href="#cb3-6"></a> <span class="fu">rtf_colheader</span>(</span>
<span id="cb3-7"><a href="#cb3-7"></a> <span class="at">colheader =</span> <span class="st">"Adverse Events | Placebo | Xanomeline High Dose | Xanomeline Low Dose"</span>,</span>
<span id="cb3-8"><a href="#cb3-8"></a> <span class="at">border_top =</span> <span class="fu">c</span>(<span class="st">""</span>, <span class="st">"single"</span>, <span class="st">"single"</span>, <span class="st">"single"</span>),</span>
<span id="cb3-9"><a href="#cb3-9"></a> <span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="dv">2</span>, <span class="dv">2</span>, <span class="dv">2</span>)</span>
<span id="cb3-10"><a href="#cb3-10"></a> ) <span class="sc">%>%</span></span>
<span id="cb3-11"><a href="#cb3-11"></a> <span class="fu">rtf_body</span>(<span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="dv">2</span>, <span class="dv">2</span>, <span class="dv">2</span>)) <span class="sc">%>%</span></span>
<span id="cb3-12"><a href="#cb3-12"></a> <span class="fu">rtf_encode</span>() <span class="sc">%>%</span></span>
<span id="cb3-13"><a href="#cb3-13"></a> <span class="fu">write_rtf</span>(<span class="st">"tlf/intro-ae7.rtf"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>A single {r2rtf} command may include columns, borders, headers, width designations and many other elements.</p>
</section></section>
<section>
<section id="chapter-2" class="title-slide slide level1 center">
<h1>Chapter 2</h1>
<p>Section 10.1, Disposition of Participants</p>
<blockquote>
<p>The disposition of participants table reports the numbers of participants who were randomized, and who entered and completed each phase of the study, and the reasons for all post-randomization discontinuations, grouped by treatment and by major reason (lost to follow-up, adverse event, poor compliance, etc.) are reported.</p>
</blockquote>
</section>
<section id="disposition" class="slide level2">
<h2>Disposition</h2>
<p><strong>Step 1</strong>: Count participants in the analysis population</p>
<p><strong>Step 2</strong>: Calculate the number and percentage of participants who discontinued the study by treatment arm</p>
<p><strong>Step 3</strong>: Calculate the numbers and percentages of participants who discontinued the study for different reasons, by treatment arm</p>
<p><strong>Step 4</strong>: Calculate the number and percentage of participants who completed the study, by treatment arm</p>
<p><strong>Step 5</strong>: Bind <code>n_rand</code>, <code>n_disc</code>, <code>n_reason</code>, and <code>n_complete</code> by row.</p>
<p><strong>Step 6+</strong>: Write the final table to RTF</p>
</section>
<section id="disposition-of-participants-rtf" class="slide level2">
<h2>Disposition of participants RTF</h2>
<div class="panel-tabset">
<ul id="tabset-1" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-1-1">Code</a></li><li><a href="#tabset-1-2">Comments</a></li></ul>
<div class="tab-content">
<div id="tabset-1-1">
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>tbl_disp <span class="sc">%>%</span></span>
<span id="cb4-2"><a href="#cb4-2"></a> <span class="co"># Table title</span></span>
<span id="cb4-3"><a href="#cb4-3"></a> <span class="fu">rtf_title</span>(<span class="st">"Disposition of Participants"</span>) <span class="sc">%>%</span></span>
<span id="cb4-4"><a href="#cb4-4"></a> <span class="co"># First row of column header</span></span>
<span id="cb4-5"><a href="#cb4-5"></a> <span class="fu">rtf_colheader</span>(<span class="st">" | Placebo | Xanomeline Low Dose| Xanomeline High Dose"</span>,</span>
<span id="cb4-6"><a href="#cb4-6"></a> <span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="fu">rep</span>(<span class="dv">2</span>, <span class="dv">3</span>))</span>
<span id="cb4-7"><a href="#cb4-7"></a> ) <span class="sc">%>%</span></span>
<span id="cb4-8"><a href="#cb4-8"></a> <span class="co"># Second row of column header</span></span>
<span id="cb4-9"><a href="#cb4-9"></a> <span class="fu">rtf_colheader</span>(<span class="st">" | n | (%) | n | (%) | n | (%)"</span>,</span>
<span id="cb4-10"><a href="#cb4-10"></a> <span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="fu">rep</span>(<span class="fu">c</span>(<span class="fl">0.7</span>, <span class="fl">1.3</span>), <span class="dv">3</span>)),</span>
<span id="cb4-11"><a href="#cb4-11"></a> <span class="at">border_top =</span> <span class="fu">c</span>(<span class="st">""</span>, <span class="fu">rep</span>(<span class="st">"single"</span>, <span class="dv">6</span>)),</span>
<span id="cb4-12"><a href="#cb4-12"></a> <span class="at">border_left =</span> <span class="fu">c</span>(<span class="st">"single"</span>, <span class="fu">rep</span>(<span class="fu">c</span>(<span class="st">"single"</span>, <span class="st">""</span>), <span class="dv">3</span>))</span>
<span id="cb4-13"><a href="#cb4-13"></a> ) <span class="sc">%>%</span></span>
<span id="cb4-14"><a href="#cb4-14"></a> <span class="co"># Table body</span></span>
<span id="cb4-15"><a href="#cb4-15"></a> <span class="fu">rtf_body</span>(</span>
<span id="cb4-16"><a href="#cb4-16"></a> <span class="at">col_rel_width =</span> <span class="fu">c</span>(<span class="dv">3</span>, <span class="fu">rep</span>(<span class="fu">c</span>(<span class="fl">0.7</span>, <span class="fl">1.3</span>), <span class="dv">3</span>)),</span>
<span id="cb4-17"><a href="#cb4-17"></a> <span class="at">text_justification =</span> <span class="fu">c</span>(<span class="st">"l"</span>, <span class="fu">rep</span>(<span class="st">"c"</span>, <span class="dv">6</span>)),</span>
<span id="cb4-18"><a href="#cb4-18"></a> <span class="at">border_left =</span> <span class="fu">c</span>(<span class="st">"single"</span>, <span class="fu">rep</span>(<span class="fu">c</span>(<span class="st">"single"</span>, <span class="st">""</span>), <span class="dv">3</span>))</span>
<span id="cb4-19"><a href="#cb4-19"></a> ) <span class="sc">%>%</span></span>
<span id="cb4-20"><a href="#cb4-20"></a> <span class="co"># Encoding RTF syntax</span></span>
<span id="cb4-21"><a href="#cb4-21"></a> <span class="fu">rtf_encode</span>() <span class="sc">%>%</span></span>
<span id="cb4-22"><a href="#cb4-22"></a> <span class="co"># Save to a file</span></span>
<span id="cb4-23"><a href="#cb4-23"></a> <span class="fu">write_rtf</span>(<span class="st">"tlf/tbl_disp.rtf"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<div id="tabset-1-2">
<p>With our bound data we follow our <a href="#/r2rtf">workflow for {r2rtf}</a>: add attributes, convert to RTF, write out</p>
<ul>
<li><code>|</code> separates every item, thus line 5 denotes 4 columns and line 9, 7 cols</li>
<li>line 6 could also read<br>
<code>col_rel_width = c(3, 2, 2, 2)</code></li>
<li>and line 10 could also read<br>
<code>col_rel_width = c(3, 0.7, 1.3, 0.7, 1.3, 0.7, 1.3)</code></li>
</ul>
</div>
</div>
</div>
</section></section>
<section>
<section id="chapter-3" class="title-slide slide level1 center">
<h1>Chapter 3</h1>
<p>Section 11.1, Data Sets Analyzed</p>
<blockquote>
<p>The summary of analysis sets table reports on participants included in each efficacy analysis</p>
</blockquote>
</section>
<section id="writing-functions" class="slide level2">
<h2>Writing functions</h2>
<blockquote>
<p>“You should consider writing a function whenever you’ve copied and pasted a block of code more than twice”</p>
<p>- <a href="https://r4ds.had.co.nz/functions.html#when-should-you-write-a-function">R for Data Science</a></p>
</blockquote>
<p><br>
</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a>fmt_num <span class="ot"><-</span> <span class="cf">function</span>(x, digits, <span class="at">width =</span> digits <span class="sc">+</span> <span class="dv">4</span>) {</span>
<span id="cb5-2"><a href="#cb5-2"></a> <span class="fu">formatC</span>(x,</span>
<span id="cb5-3"><a href="#cb5-3"></a> <span class="at">digits =</span> digits,</span>
<span id="cb5-4"><a href="#cb5-4"></a> <span class="at">format =</span> <span class="st">"f"</span>,</span>
<span id="cb5-5"><a href="#cb5-5"></a> <span class="at">width =</span> width</span>
<span id="cb5-6"><a href="#cb5-6"></a> )</span>
<span id="cb5-7"><a href="#cb5-7"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="summary-of-analysis-sets" class="slide level2">
<h2>Summary of analysis sets</h2>
<p>With helper functions <code>count_by</code> and <code>fmt_num</code> we can more easily prepare the dataset for a summary of analysis sets table with the following steps:<br>
<br>
</p>
<p><strong>Step 1</strong>: Bind the counts/percentages of the ITT population, the efficacy population, and the safety population by row using the <code>count_by()</code> function.<br>
<strong>Step 2+</strong>: Format the output from Step 2 using r2rtf.</p>
</section></section>
<section>
<section id="chapter-4" class="title-slide slide level1 center">
<h1>Chapter 4</h1>
<p>Section 11.2 Demographic and other baseline characteristics</p>
<blockquote>
<p>Creating a simple table to summarize critical demographic and baseline characteristics of the participants</p>
</blockquote>
</section>
<section id="r-package-table1" class="slide level2">
<h2>R package {table1}</h2>
<p>Efficiently summarizes this information and creates a HTML report<br>
<br>
<br>
</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>ana <span class="ot"><-</span> adsl <span class="sc">%>%</span></span>
<span id="cb6-2"><a href="#cb6-2"></a> <span class="fu">mutate</span>(</span>
<span id="cb6-3"><a href="#cb6-3"></a> <span class="at">SEX =</span> <span class="fu">factor</span>(SEX, <span class="fu">c</span>(<span class="st">"F"</span>, <span class="st">"M"</span>), <span class="fu">c</span>(<span class="st">"Female"</span>, <span class="st">"Male"</span>)),</span>
<span id="cb6-4"><a href="#cb6-4"></a> <span class="at">RACE =</span> <span class="fu">toTitleCase</span>(<span class="fu">tolower</span>(RACE))</span>
<span id="cb6-5"><a href="#cb6-5"></a> )</span>
<span id="cb6-6"><a href="#cb6-6"></a></span>
<span id="cb6-7"><a href="#cb6-7"></a>tbl <span class="ot"><-</span> <span class="fu">table1</span>(<span class="sc">~</span> SEX <span class="sc">+</span> AGE <span class="sc">+</span> RACE <span class="sc">|</span> TRT01P, <span class="at">data =</span> ana)</span>
<span id="cb6-8"><a href="#cb6-8"></a>tbl</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="transferring-the-data" class="slide level2">
<h2>Transferring the data</h2>
<p>Transferring the output into a dataframe that contains only ASCII characters, recommended by regulatory agencies<br>
<br>
</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>tbl_base <span class="ot"><-</span> tbl <span class="sc">%>%</span></span>
<span id="cb7-2"><a href="#cb7-2"></a> <span class="fu">as.data.frame</span>() <span class="sc">%>%</span></span>
<span id="cb7-3"><a href="#cb7-3"></a> <span class="fu">as_tibble</span>() <span class="sc">%>%</span></span>
<span id="cb7-4"><a href="#cb7-4"></a> <span class="fu">mutate</span>(<span class="fu">across</span>(</span>
<span id="cb7-5"><a href="#cb7-5"></a> <span class="fu">everything</span>(),</span>
<span id="cb7-6"><a href="#cb7-6"></a> <span class="sc">~</span> <span class="fu">str_replace_all</span>(.x, <span class="fu">intToUtf8</span>(<span class="dv">160</span>), <span class="st">" "</span>)</span>
<span id="cb7-7"><a href="#cb7-7"></a> ))</span>
<span id="cb7-8"><a href="#cb7-8"></a></span>
<span id="cb7-9"><a href="#cb7-9"></a></span>
<span id="cb7-10"><a href="#cb7-10"></a><span class="fu">names</span>(tbl_base) <span class="ot"><-</span> <span class="fu">str_replace_all</span>(<span class="fu">names</span>(tbl_base), <span class="fu">intToUtf8</span>(<span class="dv">160</span>), <span class="st">" "</span>)</span>
<span id="cb7-11"><a href="#cb7-11"></a>tbl_base</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="final-formatting" class="slide level2">
<h2>Final Formatting</h2>
<p>Adjusting columns, headers, and indention.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>colheader1 <span class="ot"><-</span> <span class="fu">paste</span>(<span class="fu">names</span>(tbl_base), <span class="at">collapse =</span> <span class="st">"|"</span>)</span>
<span id="cb8-2"><a href="#cb8-2"></a>colheader2 <span class="ot"><-</span> <span class="fu">paste</span>(tbl_base[<span class="dv">1</span>, ], <span class="at">collapse =</span> <span class="st">"|"</span>)</span>
<span id="cb8-3"><a href="#cb8-3"></a>rel_width <span class="ot"><-</span> <span class="fu">c</span>(<span class="fl">2.5</span>, <span class="fu">rep</span>(<span class="dv">1</span>, <span class="dv">4</span>))</span>
<span id="cb8-4"><a href="#cb8-4"></a></span>
<span id="cb8-5"><a href="#cb8-5"></a>tbl_base[<span class="sc">-</span><span class="dv">1</span>, ] <span class="sc">%>%</span></span>
<span id="cb8-6"><a href="#cb8-6"></a> <span class="fu">rtf_title</span>(</span>
<span id="cb8-7"><a href="#cb8-7"></a> <span class="st">"Baseline Characteristics of Participants"</span>,</span>
<span id="cb8-8"><a href="#cb8-8"></a> <span class="st">"(All Participants Randomized)"</span></span>
<span id="cb8-9"><a href="#cb8-9"></a> ) <span class="sc">%>%</span></span>
<span id="cb8-10"><a href="#cb8-10"></a> <span class="fu">rtf_colheader</span>(colheader1,</span>
<span id="cb8-11"><a href="#cb8-11"></a> <span class="at">col_rel_width =</span> rel_width</span>
<span id="cb8-12"><a href="#cb8-12"></a> ) <span class="sc">%>%</span></span>
<span id="cb8-13"><a href="#cb8-13"></a> <span class="fu">rtf_colheader</span>(colheader2,</span>
<span id="cb8-14"><a href="#cb8-14"></a> <span class="at">border_top =</span> <span class="st">""</span>,</span>
<span id="cb8-15"><a href="#cb8-15"></a> <span class="at">col_rel_width =</span> rel_width</span>
<span id="cb8-16"><a href="#cb8-16"></a> ) <span class="sc">%>%</span></span>
<span id="cb8-17"><a href="#cb8-17"></a> <span class="fu">rtf_body</span>(</span>
<span id="cb8-18"><a href="#cb8-18"></a> <span class="at">col_rel_width =</span> rel_width,</span>
<span id="cb8-19"><a href="#cb8-19"></a> <span class="at">text_justification =</span> <span class="fu">c</span>(<span class="st">"l"</span>, <span class="fu">rep</span>(<span class="st">"c"</span>, <span class="dv">4</span>)),</span>
<span id="cb8-20"><a href="#cb8-20"></a> <span class="at">text_indent_first =</span> <span class="sc">-</span><span class="dv">240</span>,</span>
<span id="cb8-21"><a href="#cb8-21"></a> <span class="at">text_indent_left =</span> <span class="dv">180</span></span>
<span id="cb8-22"><a href="#cb8-22"></a> ) <span class="sc">%>%</span></span>
<span id="cb8-23"><a href="#cb8-23"></a> <span class="fu">rtf_encode</span>() <span class="sc">%>%</span></span>
<span id="cb8-24"><a href="#cb8-24"></a> <span class="fu">write_rtf</span>(<span class="st">"tlf/tlf_base.rtf"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="summary-of-steps" class="slide level2">
<h2>Summary of steps</h2>
<p><strong>Step 1</strong>: Use package {table1}</p>
<p><strong>Step 2</strong>: Transfer the output from Step 1 into an ASCII data frame</p>
<p><strong>Step 3+</strong>: Define the format of the RTF table</p>
</section></section>
<section>
<section id="chapter-5" class="title-slide slide level1 center">
<h1>Chapter 5</h1>
<p>Section 11.4, Efficacy Results and Tabulations of Individual Participant</p>
<blockquote>
<p>Summarizing primary and secondary endpoints</p>
</blockquote>
</section>
<section id="efficacy-table" class="slide level2">
<h2>Efficacy Table</h2>
<p>Combines two informative tables</p>
<ol type="1">
<li><p>Summary of observed data</p>
<ul>
<li>at baseline, week 24, and change from baseline</li>
</ul></li>
<li><p>Pairwise comparisons with placebo</p></li>
</ol>
</section>
<section id="imputation" class="slide level2 center">
<h2>Imputation</h2>
<p>Missing data are inevitable</p>
<p>…why your data are missing can be highly informative</p>
<div style="color: red;">
<p>LOCF imputation is NOT a recommended imputation method</p>
</div>
<p>Read more about the <a href="https://www.ncbi.nlm.nih.gov/books/NBK209904/pdf/Bookshelf_NBK209904.pdf">prevention and treatment of missing data</a></p>
</section>
<section id="ancova" class="slide level2">
<h2>ANCOVA</h2>
<p>Analysis of covariance examines the realationship between an independent and dependent variable while controlling for a covariate</p>
<ul>
<li>Specifically, compare variance around means of different groups</li>
</ul>
<p>Use {emmeans} to calculate within and between group least square means</p>
</section>
<section id="efficacy-tabulation-steps" class="slide level2">
<h2>Efficacy tabulation steps</h2>
<p><strong>Step 1</strong>: Impute the missing values. In this example, we name the <code>ana</code> dataset after imputation as <code>ana_locf</code>.</p>
<p><strong>Step 2</strong>: Calculate the mean and standard derivation of efficacy endpoint (i.e., <code>gluc</code>), and then format it into an RTF table.</p>
<p><strong>Step 3</strong>: Calculate the pairwise comparison by ANCOVA model, and then format it into an RTF table.</p>
<p><strong>Step 4</strong>: Combine the outputs from steps 4 and 5 by rows.</p>
<p><strong>Step 5+</strong>: Format the output from Step 4 using r2rtf.</p>
</section></section>
<section>
<section id="chapter-6" class="title-slide slide level1 center">
<h1>Chapter 6</h1>
<p>Section 11.4, Efficacy Results and Tabulations of Individual Participant</p>
<blockquote>
<p>The primary and secondary efficacy endpoints need to be summarized for each treatment group</p>
</blockquote>
</section>
<section id="survival-analysis" class="slide level2">
<h2>Survival Analysis</h2>
<p><strong>aka time-to-event analysis</strong></p>
<p><br>
</p>
<p>A survival model explores the relationship between an outcome variable and a censored estimate of time to study dropout (for any number of reasons).</p>
<p><br>
</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a>fit <span class="ot"><-</span> <span class="fu">survfit</span>(<span class="fu">Surv</span>(timeToEvent, <span class="dv">1</span> <span class="sc">-</span> censoredTime) <span class="sc">~</span> treatmentGroup</span>
<span id="cb9-2"><a href="#cb9-2"></a> , <span class="at">data =</span> clinicalData)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="efficacy-figure-steps" class="slide level2">
<h2>Efficacy figure steps</h2>
<p><strong>Step 1</strong>: Define the analysis-ready dataset</p>
<p><strong>Step 2</strong>: Save figures into <code>png</code> files</p>
<p><strong>Step 3+</strong>: Create RTF output</p>
</section></section>
<section>
<section id="chapter-7" class="title-slide slide level1 center">
<h1>Chapter 7</h1>
<p>Section 12.2 Adverse event (AEs) summary</p>
<blockquote>
<p>Summarize adverse eventing, the number of patients in each treatment group in whom the event occurred, and the rate of occurrence.</p>
</blockquote>
</section>
<section id="pivot-wider" class="slide level2">
<h2>Pivot wider</h2>
<img data-src="https://www.pipinghotdata.com/posts/2021-08-27-a-tidyverse-pivot-approach-to-data-preparation-in-r/gatherspread_modified.jpg" alt="fuzzy monsters moving colorful rocks to demonstrate items in a dataframe moving between long and wide format" class="r-stretch quarto-figure-center"></section>
<section id="ae-summary-steps" class="slide level2">
<h2>AE summary steps</h2>
<p><strong>Step 1</strong>: Summarize participants in population</p>
<p><strong>Step 2</strong>: Summarize participants in population by AE criteria of interest</p>
<p><strong>Step 3</strong>: Combine summaries</p>
<p><strong>Step 4+</strong>: Format using r2rtf</p>
</section></section>
<section>
<section id="chapter-8" class="title-slide slide level1 center">
<h1>Chapter 8</h1>
<p>Section 12.2 Specific AEs</p>
<blockquote>
<p>Report each adverse event, the number of patients in each treatment group in whom the event occurred, and the rate of occurrence.</p>
</blockquote>
</section>
<section id="page-functions" class="slide level2">
<h2><code>page</code> functions</h2>
<p>The AE table introduces us to two advanced table features:</p>
<ul>
<li><p>group content: AE can be summarized in multiple nested layers. (e.g., by system organ class (SOC, <code>AESOC</code>) and specific AE term (<code>AEDECOD</code>))</p>
<ul>
<li><code>page_by()</code></li>
</ul></li>
<li><p>pagenization: there are many AE terms that can not be covered in one page. Column headers and SOC information need to be repeated on every page.</p>
<ul>
<li><code>pageby_row()</code></li>
</ul></li>
</ul>
</section>
<section id="ae-tabulation-steps" class="slide level2">
<h2>AE tabulation steps</h2>
<p><strong>Step 1</strong>: Count the number of participants by SOC and treatment arm</p>
<p><strong>Step 2</strong>: Count the number of participants in each AE term by SOC, AE term, and treatment arm</p>
<p><strong>Step 3</strong>: Count the number of participants in each arm</p>
<p><strong>Step 4</strong>: Combine counts</p>
<p><strong>Step 5+</strong>: Format the output by using r2rtf</p>
</section></section>
<section>
<section id="chapter-9" class="title-slide slide level1 center">
<h1>Chapter 9</h1>
<p>All TLFs are then assembled by</p>
<ol type="1">
<li><p>Combining RTF source code in individual files into one large RTF file.</p></li>
<li><p>Leveraging the <code>Toggle Fields</code> feature in Microsoft Word to embed RTF files using hyperlinks.</p></li>
</ol>
</section>
<section id="combine-source-code" class="slide level2">
<h2>Combine source code</h2>
<p><br>
</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>tlf_path <span class="ot"><-</span> <span class="fu">c</span>(</span>
<span id="cb10-2"><a href="#cb10-2"></a> <span class="st">"tlf/tbl_disp.rtf"</span>, <span class="co"># Disposition table</span></span>
<span id="cb10-3"><a href="#cb10-3"></a> <span class="st">"tlf/tlf_eff.rtf"</span>, <span class="co"># Efficacy table</span></span>
<span id="cb10-4"><a href="#cb10-4"></a> <span class="st">"tlf/tlf_km.rtf"</span> <span class="co"># K-M plot</span></span>
<span id="cb10-5"><a href="#cb10-5"></a>)</span>
<span id="cb10-6"><a href="#cb10-6"></a></span>
<span id="cb10-7"><a href="#cb10-7"></a>r2rtf<span class="sc">::</span><span class="fu">assemble_rtf</span>(</span>
<span id="cb10-8"><a href="#cb10-8"></a> <span class="at">input =</span> tlf_path,</span>
<span id="cb10-9"><a href="#cb10-9"></a> <span class="at">output =</span> <span class="st">"tlf/rtf-combine.rtf"</span></span>
<span id="cb10-10"><a href="#cb10-10"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="leverage-microsoft-word" class="slide level2">
<h2>Leverage Microsoft Word</h2>
<ul>
<li>Absolute paths</li>
</ul>
<img data-src="https://networkencyclopedia.com/wp-content/uploads/2019/08/absolute-path.jpg" alt="folder icons in a directory tree with numerous examples of absolute (from root) vs relative (to another folder) paths" class="r-stretch"><ul>
<li>Alt + F9 to “Toggle Fields”</li>
</ul>
</section></section>
<section id="thank-you" class="title-slide slide level1 center">
<h1>Thank you!!</h1>
<div class="footer footer-default">
</div>
</section>
</div>
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