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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="slides_files/libs/clipboard/clipboard.min.js"></script>
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<link href="slides_files/libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
<link href="slides_files/libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.3.11">
<title>slides</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="slides_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="slides_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;
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pre.numberSource code > span > a:first-child::before
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position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
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color: #aaaaaa;
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pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ color: #003b4f; background-color: #f1f3f5; }
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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code span { color: #003b4f; } /* Normal */
code span.al { color: #ad0000; } /* Alert */
code span.an { color: #5e5e5e; } /* Annotation */
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code span.cv { color: #5e5e5e; font-style: italic; } /* CommentVar */
code span.do { color: #5e5e5e; font-style: italic; } /* Documentation */
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<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
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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;
}
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border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
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flex-grow: 1;
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font-weight: 400;
}
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margin-bottom: -0.2em;
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margin-bottom: 0.5em;
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margin-top: 0;
}
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margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
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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 {
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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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<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="dry-package-development-in-r" class="slide level2" style="text-align: center;">
<h2>DRY Package Development in R</h2>
<div style="text-align: center;">
<p>Indrajeet Patil</p>
</div>
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<!-- - [Link to slides](https://indrajeetpatil.github.io/dry-r-package-development/) -->
<!-- - [Github repo](https://github.com/IndrajeetPatil/dry-r-package-development/) -->
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</section>
<section id="section" class="title-slide slide level1 center">
<h1></h1>
<p><em>“Copy and paste is a design error.”</em> - David Parnas</p>
</section>
<section>
<section id="why-so-dry" class="title-slide slide level1 center">
<h1>Why So DRY</h1>
<p>Why should you not repeat yourself?</p>
</section>
<section id="dont-repeat-yourself-dry-principle" class="slide level2 smaller">
<h2>Don’t Repeat Yourself (DRY) Principle</h2>
<div class="columns">
<div class="column" style="width:60%;">
<p>The DRY Principles states that:</p>
<p><em>Every piece of <strong>knowledge</strong> must have a <strong>single</strong> representation in the codebase.</em></p>
<p>That is, you should not express the same thing in multiple places in multiple ways.</p>
</div><div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="media/dry.gif"></p>
</div>
</div>
</div>
</div>
<div class="fragment">
<div class="callout callout-note callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>It’s about <em>knowledge</em> and not just <em>code</em></strong></p>
</div>
<div class="callout-content">
<p>The DRY principle is about duplication of knowledge. Thus, it applies to all programming entities that encode knowledge:</p>
<ul>
<li>You should not duplicate code.</li>
<li>You should not duplicate intent across code and comments.</li>
<li>You should not duplicate knowledge in data structures.</li>
<li>…</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="benefits-of-dry-codebase" class="slide level2 smaller">
<h2>Benefits of DRY codebase</h2>
<ul>
<li><p>When code is duplicated, if you make change in one place, you need to make parallel changes in other places. When code is DRY, parallel modifications become unnecessary.</p></li>
<li><p>Easy to maintain since there is only a single representation of knowledge that needs to be updated if the underlying knowledge changes.</p></li>
<li><p>As a side effect, routines developed to remove duplicated code can become part of general-purpose utilities.</p></li>
</ul>
<p><br></p>
<div class="fragment">
<div class="callout callout-tip callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Further Reading</strong></p>
</div>
<div class="callout-content">
<ul>
<li><p>Thomas, D., & Hunt, A. (2019). <em>The Pragmatic Programmer</em>. Addison-Wesley Professional. (<strong>pp. 30-38</strong>)</p></li>
<li><p>Understand distinction between DRY and <a href="https://stackoverflow.com/questions/6453235/what-does-damp-not-dry-mean-when-talking-about-unit-tests" target="_blank">DAMP (Descriptive And Meaningful Phrases)</a></p></li>
</ul>
</div>
</div>
</div>
</div>
</section></section>
<section id="plan" class="title-slide slide level1 center">
<h1>Plan</h1>
<p>Let’s see how to apply DRY principle to remove duplication in following aspects of package development:</p>
<ul>
<li>Documentation</li>
<li>Unit testing</li>
<li>Vignette setup</li>
<li>Importing external functions</li>
<li>Conditions</li>
</ul>
</section>
<section>
<section id="documentation" class="title-slide slide level1 center">
<h1>Documentation</h1>
<p>How not to repeat yourself while writing documentation.</p>
</section>
<section id="what-do-users-read" class="slide level2 smaller">
<h2>What do users read?</h2>
<p>What users consult to find needed information maybe context-dependent.</p>
<p><br></p>
<div class="fragment">
<p><i class="fa-brands fa-readme fa-2xl" aria-label="readme"></i> <strong>README</strong>: While exploring the package repository.</p>
<p><br></p>
<p><i class="fa-solid fa-file-pdf fa-2xl" aria-label="file-pdf"></i> <strong>Manual</strong>: While reading PDF manual or help pages in the IDE.</p>
<p><br></p>
<p><i class="fa-solid fa-file fa-2xl" aria-label="file"></i> <strong>Vignettes</strong>: While reading documentation on CRAN.</p>
<p><br></p>
</div>
<div class="fragment">
<p>Thus, including crucial information <strong>only in one place</strong> makes it likely that the users might miss out on it in certain contexts.</p>
</div>
</section>
<section id="go-forth-and-multiply-without-repetition" class="slide level2 smaller">
<h2>Go forth and multiply (without repetition)</h2>
<div class="columns">
<div class="column" style="width:40%;">
<p>Some documentation is important enough to be included in multiple places (e.g. in the function documentation and in a vignette).</p>
<p><br></p>
<blockquote>
<p>How can you document something just <em>once</em> but include it in <em>multiple</em> locations?</p>
</blockquote>
</div><div class="column" style="width:60%;">
<div class="cell">
<div class="cell-output-display">
<p><img data-src="media/spiderman.jpeg" style="width:100.0%"></p>
</div>
</div>
</div>
</div>
</section>
<section id="child-documents" class="slide level2">
<h2>Child documents</h2>
<p>You can stitch an R Markdown document from smaller <a href="https://bookdown.org/yihui/rmarkdown-cookbook/child-document.html" target="_blank">child documents</a>.</p>
<p> <i class="fa-regular fa-file fa-5x" aria-label="file"></i> <i class="fa-regular fa-plus fa-5x" aria-label="plus"></i> <i class="fa-regular fa-file-lines fa-5x" aria-label="file-lines"></i> <i class="fa-soliud fa-equals fa-5x" aria-label="equals"></i> <i class="fa-solid fa-file-lines fa-5x" aria-label="file-lines"></i></p>
<p>(parent Rmd) (child Rmd) (result Rmd)</p>
<div class="fragment">
<p>Thus, the information to repeat can be stored <em>once</em> in child documents and reused <em>multiple</em> times across parents.</p>
</div>
</section>
<section id="storing-child-documents-in-package" class="slide level2 smaller">
<h2>Storing child documents in package</h2>
<p>Stratagem: You can store child documents in the manual directory and reuse them.</p>
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>Child documents</strong></p>
<pre><code>├── DESCRIPTION
├── man
│ └── rmd-children
│ └── doc1.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:70%;">
<p><code>man/rmd-children/doc1.Rmd</code> example.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb2-1"><a href="#cb2-1"></a>This is some crucial information to be repeated across documentation.</span>
<span id="cb2-2"><a href="#cb2-2"></a></span>
<span id="cb2-3"><a href="#cb2-3"></a>```{r}</span>
<span id="cb2-4"><a href="#cb2-4"></a>1 + 1</span>
<span id="cb2-5"><a href="#cb2-5"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
<div class="callout callout-tip callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Tips</strong></p>
</div>
<div class="callout-content">
<ul>
<li>You can include as many child documents as you want.</li>
<li>The child document is just like any <code>.Rmd</code> file and can include everything that any other <code>.Rmd</code> file can include.</li>
<li>You can choose a different name for the folder containing child documents (e.g. <code>rmd-fragments</code>).</li>
<li>Make sure to include <code>Roxygen: list(markdown = TRUE)</code> field in the <code>DESCRIPTION</code> file.</li>
<li>The child documents will not pose a problem either for <code>R CMD check</code> or for <code>{pkgdown}</code> website.</li>
</ul>
</div>
</div>
</div>
</section>
<section id="using-child-documents-in-package" class="slide level2 smaller">
<h2>Using child documents in package</h2>
<p>You can now insert contents of these child documents in the package documentation anywhere and as many as times as you want.</p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>Vignette</strong></p>
<pre><code>├── DESCRIPTION
├── vignettes
│ └── vignette1.Rmd
│ └── ...
│ └── web_only
│ └── vignette2.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:70%;">
<p><strong>Example</strong> (<code>vignettes/vignette1.Rmd</code>)</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb4-1"><a href="#cb4-1"></a>---</span>
<span id="cb4-2"><a href="#cb4-2"></a>output: html_vignette</span>
<span id="cb4-3"><a href="#cb4-3"></a>---</span>
<span id="cb4-4"><a href="#cb4-4"></a></span>
<span id="cb4-5"><a href="#cb4-5"></a>Some content.</span>
<span id="cb4-6"><a href="#cb4-6"></a></span>
<span id="cb4-7"><a href="#cb4-7"></a>```{r, child = "../man/rmd-children/doc1.Rmd"}</span>
<span id="cb4-8"><a href="#cb4-8"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
<div class="fragment">
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>README</strong></p>
<pre><code>├── DESCRIPTION
├── README.Rmd</code></pre>
</div><div class="column" style="width:70%;">
<p><strong>Example</strong> (<code>README.Rmd</code>)</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb6-1"><a href="#cb6-1"></a>---</span>
<span id="cb6-2"><a href="#cb6-2"></a>output: github_document</span>
<span id="cb6-3"><a href="#cb6-3"></a>---</span>
<span id="cb6-4"><a href="#cb6-4"></a></span>
<span id="cb6-5"><a href="#cb6-5"></a>Some content.</span>
<span id="cb6-6"><a href="#cb6-6"></a></span>
<span id="cb6-7"><a href="#cb6-7"></a>```{r, child = "man/rmd-children/doc1.Rmd"}</span>
<span id="cb6-8"><a href="#cb6-8"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
<div class="fragment">
<p><strong>etc.</strong></p>
</div>
</section>
<section id="self-study" class="slide level2">
<h2>Self-study</h2>
<p>Example packages that use child documents to repeat documentation.</p>
<ul>
<li><p><a href="https://github.com/r-lib/pkgdown/tree/main/man/rmd-fragments" target="_blank"><code>{pkgdown}</code></a></p></li>
<li><p><a href="https://github.com/IndrajeetPatil/statsExpressions/tree/main/man/rmd-fragments" target="_blank"><code>{statsExpressions}</code></a></p></li>
</ul>
</section></section>
<section>
<section id="vignette-setup" class="title-slide slide level1 center">
<h1>Vignette Setup</h1>
<p>How not to repeat yourself while setting up vignettes.</p>
</section>
<section id="setup-chunks-in-vignettes" class="slide level2 smaller">
<h2>Setup chunks in vignettes</h2>
<p>Another duplication that occurs is in setup chunks for vignettes.</p>
<p>For example, some parts of the setup can be same across vignettes.</p>
<p><br></p>
<div class="columns">
<div class="column" style="width:25%;">
<pre><code>├── DESCRIPTION
├── vignettes
│ └── vignette1.Rmd
│ └── vignette2.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:37%;">
<div class="sourceCode" id="cb8"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb8-1"><a href="#cb8-1"></a>---</span>
<span id="cb8-2"><a href="#cb8-2"></a>title: "Vignette-1"</span>
<span id="cb8-3"><a href="#cb8-3"></a>output: html_vignette</span>
<span id="cb8-4"><a href="#cb8-4"></a>---</span>
<span id="cb8-5"><a href="#cb8-5"></a></span>
<span id="cb8-6"><a href="#cb8-6"></a>```{r}</span>
<span id="cb8-7"><a href="#cb8-7"></a>knitr::opts_chunk$set(</span>
<span id="cb8-8"><a href="#cb8-8"></a> message = FALSE,</span>
<span id="cb8-9"><a href="#cb8-9"></a> collapse = TRUE,</span>
<span id="cb8-10"><a href="#cb8-10"></a> comment = "#>"</span>
<span id="cb8-11"><a href="#cb8-11"></a>)</span>
<span id="cb8-12"><a href="#cb8-12"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:37%;">
<div class="sourceCode" id="cb9"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb9-1"><a href="#cb9-1"></a>---</span>
<span id="cb9-2"><a href="#cb9-2"></a>title: "Vignette-2"</span>
<span id="cb9-3"><a href="#cb9-3"></a>output: html_vignette</span>
<span id="cb9-4"><a href="#cb9-4"></a>---</span>
<span id="cb9-5"><a href="#cb9-5"></a></span>
<span id="cb9-6"><a href="#cb9-6"></a>```{r}</span>
<span id="cb9-7"><a href="#cb9-7"></a>knitr::opts_chunk$set(</span>
<span id="cb9-8"><a href="#cb9-8"></a> message = FALSE,</span>
<span id="cb9-9"><a href="#cb9-9"></a> collapse = TRUE,</span>
<span id="cb9-10"><a href="#cb9-10"></a> comment = "#>"</span>
<span id="cb9-11"><a href="#cb9-11"></a>)</span>
<span id="cb9-12"><a href="#cb9-12"></a></span>
<span id="cb9-13"><a href="#cb9-13"></a>options(crayon.enabled = TRUE)</span>
<span id="cb9-14"><a href="#cb9-14"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
<p>How can this repetition be avoided?</p>
</section>
<section id="sourcing-setup-chunks-in-vignettes" class="slide level2 smaller">
<h2>Sourcing setup chunks in vignettes</h2>
<div class="columns">
<div class="column" style="width:80%;">
<p>To avoid repeating the same setup across vignettes, you can extract the <strong>common</strong> setup out into a script (<code>vignettes/setup/setup.R</code>), and source it from vignettes.</p>
</div><div class="column" style="width:20%;">
<pre><code>
├── DESCRIPTION
├── vignettes
│ └── setup
│ └── setup.R</code></pre>
</div>
</div>
<p><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:26%;">
<p><code>setup.R</code> contents</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a>knitr<span class="sc">::</span>opts_chunk<span class="sc">$</span><span class="fu">set</span>(</span>
<span id="cb11-2"><a href="#cb11-2"></a> <span class="at">message =</span> <span class="cn">FALSE</span>,</span>
<span id="cb11-3"><a href="#cb11-3"></a> <span class="at">collapse =</span> <span class="cn">TRUE</span>,</span>
<span id="cb11-4"><a href="#cb11-4"></a> <span class="at">comment =</span> <span class="st">"#>"</span></span>
<span id="cb11-5"><a href="#cb11-5"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:37%;">
<p>Sourcing common setup</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb12-1"><a href="#cb12-1"></a>---</span>
<span id="cb12-2"><a href="#cb12-2"></a>title: "Vignette-1"</span>
<span id="cb12-3"><a href="#cb12-3"></a>output: html_vignette</span>
<span id="cb12-4"><a href="#cb12-4"></a>---</span>
<span id="cb12-5"><a href="#cb12-5"></a></span>
<span id="cb12-6"><a href="#cb12-6"></a>```{r setup, include = FALSE}</span>
<span id="cb12-7"><a href="#cb12-7"></a>source("setup/setup.R")</span>
<span id="cb12-8"><a href="#cb12-8"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:37%;">
<p>Sourcing common setup</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb13-1"><a href="#cb13-1"></a>---</span>
<span id="cb13-2"><a href="#cb13-2"></a>title: "Vignette-2"</span>
<span id="cb13-3"><a href="#cb13-3"></a>output: html_vignette</span>
<span id="cb13-4"><a href="#cb13-4"></a>---</span>
<span id="cb13-5"><a href="#cb13-5"></a></span>
<span id="cb13-6"><a href="#cb13-6"></a>```{r setup, include = FALSE}</span>
<span id="cb13-7"><a href="#cb13-7"></a>source("setup/setup.R")</span>
<span id="cb13-8"><a href="#cb13-8"></a>options(crayon.enabled = TRUE)</span>
<span id="cb13-9"><a href="#cb13-9"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
<div class="fragment">
<div class="callout callout-tip callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>No parallel modification</strong></p>
</div>
<div class="callout-content">
<p>Now common setup can be modified with a change in only <em>one</em> place!</p>
</div>
</div>
</div>
</div>
</section>
<section id="self-study-1" class="slide level2">
<h2>Self-study</h2>
<p>Packages in the wild that use this trick.</p>
<ul>
<li><a href="https://github.com/cynkra/dm/blob/main/vignettes/setup/setup.R" target="_blank"><code>{dm}</code></a></li>
</ul>
</section></section>
<section>
<section id="data" class="title-slide slide level1 center">
<h1>Data</h1>
<p>How not to repeat yourself while creating and re-using example datasets.</p>
</section>
<section id="illustrative-example-datasets" class="slide level2 smaller">
<h2>Illustrative example datasets</h2>
<p>If none of the existing datasets are useful to illustrate your functions, you can create new datasets.</p>
<div class="fragment">
<p>Let’s say your example dataset is called <code>exdat</code> and function is called <code>foo()</code>. Using it in examples, vignettes, README, etc. requires that it be define <em>multiple</em> times.</p>
<div class="columns">
<div class="column" style="width:33%;">
<p><strong>In examples</strong></p>
<div class="sourceCode" id="cb14"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1"></a><span class="co">#' @examples</span></span>
<span id="cb14-2"><a href="#cb14-2"></a><span class="co">#' exdat <- matrix(c(71, 50))</span></span>
<span id="cb14-3"><a href="#cb14-3"></a><span class="co">#' foo(exdat)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:33%;">
<p><strong>In vignettes</strong></p>
<div class="sourceCode" id="cb15"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb15-1"><a href="#cb15-1"></a>---</span>
<span id="cb15-2"><a href="#cb15-2"></a>title: "My Vignette"</span>
<span id="cb15-3"><a href="#cb15-3"></a>output: html_vignette</span>
<span id="cb15-4"><a href="#cb15-4"></a>---</span>
<span id="cb15-5"><a href="#cb15-5"></a></span>
<span id="cb15-6"><a href="#cb15-6"></a>```{r}</span>
<span id="cb15-7"><a href="#cb15-7"></a>exdat <- matrix(c(71, 50))</span>
<span id="cb15-8"><a href="#cb15-8"></a>foo(exdat)</span>
<span id="cb15-9"><a href="#cb15-9"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:33%;">
<p><strong>In README</strong></p>
<div class="sourceCode" id="cb16"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb16-1"><a href="#cb16-1"></a>---</span>
<span id="cb16-2"><a href="#cb16-2"></a>output: github_document</span>
<span id="cb16-3"><a href="#cb16-3"></a>---</span>
<span id="cb16-4"><a href="#cb16-4"></a></span>
<span id="cb16-5"><a href="#cb16-5"></a>```{r}</span>
<span id="cb16-6"><a href="#cb16-6"></a>exdat <- matrix(c(71, 50))</span>
<span id="cb16-7"><a href="#cb16-7"></a>foo(exdat)</span>
<span id="cb16-8"><a href="#cb16-8"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
</div>
<div class="fragment">
<p>How can this repetition be avoided?</p>
</div>
</section>
<section id="shipping-data-in-a-package" class="slide level2 smaller">
<h2>Shipping data in a package</h2>
<p>You can avoid this repetition by defining the data just <em>once</em>, saving and shipping it with the package.</p>
<p>The datasets are stored in <code>data/</code>, and documented in <code>R/data.R</code>.</p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:70%;">
<p><strong>Saving data</strong></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a><span class="co"># In `exdat.R`</span></span>
<span id="cb17-2"><a href="#cb17-2"></a>exdat <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="fu">c</span>(<span class="dv">71</span>, <span class="dv">50</span>))</span>
<span id="cb17-3"><a href="#cb17-3"></a><span class="fu">save</span>(exdat, <span class="at">file =</span> <span class="st">"data/exdat.rdata"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div><div class="column" style="width:30%;">
<p><strong>Directory structure</strong></p>
<pre><code>├── DESCRIPTION
├── R
├── data-raw
│ └── exdat.R
├── data
│ └── exdat.rdata
├── R
│ └── data.R</code></pre>
</div>
</div>
</div>
<div class="fragment">
<div class="callout callout-caution callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Don’t forget!</strong></p>
</div>
<div class="callout-content">
<ul>
<li>For future reference, save script (in <code>data-raw/</code> folder) to (re)create or update the dataset.</li>
<li>If you include datasets, set <code>LazyData: true</code> in the <code>DESCRIPTION</code> file.</li>
</ul>
</div>
</div>
</div>
</div>
</section>
<section id="reusable-dataset" class="slide level2 smaller">
<h2>Reusable dataset</h2>
<p><code>exdat</code> can now be used in examples, tests, vignettes, etc.; there is no need to define it every time it is used.</p>
<div class="columns">
<div class="column" style="width:33%;">
<p><strong>In examples</strong></p>
<div class="sourceCode" id="cb19"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a><span class="co">#' @examples</span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="co">#' foo(exdat)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:33%;">
<p><strong>In vignettes</strong></p>
<div class="sourceCode" id="cb20"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb20-1"><a href="#cb20-1"></a>---</span>
<span id="cb20-2"><a href="#cb20-2"></a>title: "My Vignette"</span>
<span id="cb20-3"><a href="#cb20-3"></a>output: html_vignette</span>
<span id="cb20-4"><a href="#cb20-4"></a>---</span>
<span id="cb20-5"><a href="#cb20-5"></a></span>
<span id="cb20-6"><a href="#cb20-6"></a>```{r}</span>
<span id="cb20-7"><a href="#cb20-7"></a>foo(exdat)</span>
<span id="cb20-8"><a href="#cb20-8"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:33%;">
<p><strong>In README</strong></p>
<div class="sourceCode" id="cb21"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb21-1"><a href="#cb21-1"></a>---</span>
<span id="cb21-2"><a href="#cb21-2"></a>output: github_document</span>
<span id="cb21-3"><a href="#cb21-3"></a>---</span>
<span id="cb21-4"><a href="#cb21-4"></a></span>
<span id="cb21-5"><a href="#cb21-5"></a>```{r}</span>
<span id="cb21-6"><a href="#cb21-6"></a>foo(exdat)</span>
<span id="cb21-7"><a href="#cb21-7"></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
<div class="callout callout-tip callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>No parallel modification</strong></p>
</div>
<div class="callout-content">
<p>Note that if you now wish to update the dataset, you need to change its definition only in <em>one</em> place!</p>
</div>
</div>
</div>
</section>
<section id="self-study-2" class="slide level2">
<h2>Self-study</h2>
<p>Examples of R packages that define datasets and use them repeatedly.</p>
<ul>
<li><p><a href="https://github.com/IndrajeetPatil/ggstatsplot" target="_blank"><code>{ggstatsplot}</code></a></p></li>
<li><p><a href="https://github.com/easystats/effectsize" target="_blank"><code>{effectsize}</code></a></p></li>
</ul>
</section></section>
<section>
<section id="unit-testing" class="title-slide slide level1 center">
<h1>Unit testing</h1>
<p>How not to repeat yourself while writing unit tests.</p>
</section>
<section id="repeated-test-patterns" class="slide level2 smaller">
<h2>Repeated test patterns</h2>
<p>A <strong>unit test</strong> records the code to describe expected output.</p>
<p><br></p>
<p>(actual) <i class="fa-regular fa-file-code fa-2xl" aria-label="file-code"></i> <i class="fa-solid fa-arrows-left-right fa-2xl" aria-label="arrows-left-right"></i> <i class="fa-solid fa-file-code fa-2xl" aria-label="file-code"></i> (expected)</p>
<p><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:40%;">
<p>Unit testing involves checking function output with a <strong>range of inputs</strong>, and this can involve recycling a test pattern.</p>
<div class="callout callout-caution callout-captioned callout-style-default">
<div class="callout-body">
<div class="callout-caption">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Not DRY</strong></p>
</div>
<div class="callout-content">
<p>But such recycling violates the DRY principle. How can you avoid this?</p>
</div>
</div>
</div>
</div><div class="column" style="width:60%;">
<div class="sourceCode" id="cb22"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1"></a><span class="co"># Function to test</span></span>
<span id="cb22-2"><a href="#cb22-2"></a>multiplier <span class="ot"><-</span> <span class="cf">function</span>(x, y) {</span>
<span id="cb22-3"><a href="#cb22-3"></a> x <span class="sc">*</span> y</span>
<span id="cb22-4"><a href="#cb22-4"></a>}</span>
<span id="cb22-5"><a href="#cb22-5"></a></span>
<span id="cb22-6"><a href="#cb22-6"></a><span class="co"># Tests</span></span>
<span id="cb22-7"><a href="#cb22-7"></a><span class="fu">test_that</span>(</span>
<span id="cb22-8"><a href="#cb22-8"></a> <span class="at">desc =</span> <span class="st">"multiplier works as expected"</span>,</span>
<span id="cb22-9"><a href="#cb22-9"></a> <span class="at">code =</span> {</span>
<span id="cb22-10"><a href="#cb22-10"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="sc">-</span><span class="dv">1</span>, <span class="dv">3</span>), <span class="sc">-</span><span class="dv">3</span>)</span>
<span id="cb22-11"><a href="#cb22-11"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="dv">0</span>, <span class="fl">3.4</span>), <span class="dv">0</span>)</span>
<span id="cb22-12"><a href="#cb22-12"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="cn">NA</span>, <span class="dv">4</span>), <span class="cn">NA_real_</span>)</span>
<span id="cb22-13"><a href="#cb22-13"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="sc">-</span><span class="dv">2</span>, <span class="sc">-</span><span class="dv">2</span>), <span class="dv">4</span>)</span>
<span id="cb22-14"><a href="#cb22-14"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="dv">3</span>, <span class="dv">3</span>), <span class="dv">9</span>)</span>
<span id="cb22-15"><a href="#cb22-15"></a> }</span>
<span id="cb22-16"><a href="#cb22-16"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<section id="parametrized-unit-testing" class="slide level2 smaller">
<h2>Parametrized unit testing</h2>
<p>To avoid such repetition, you can write parameterized unit tests using <a href="https://github.com/google/patrick" target="_blank"><code>{patrick}</code></a>.</p>
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<p><strong>Repeated test pattern</strong></p>
<p><code>expect_identical()</code> used repeatedly.</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a><span class="fu">test_that</span>(</span>
<span id="cb23-2"><a href="#cb23-2"></a> <span class="at">desc =</span> <span class="st">"multiplier works as expected"</span>,</span>
<span id="cb23-3"><a href="#cb23-3"></a> <span class="at">code =</span> {</span>
<span id="cb23-4"><a href="#cb23-4"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="sc">-</span><span class="dv">1</span>, <span class="dv">3</span>), <span class="sc">-</span><span class="dv">3</span>)</span>
<span id="cb23-5"><a href="#cb23-5"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="dv">0</span>, <span class="fl">3.4</span>), <span class="dv">0</span>)</span>
<span id="cb23-6"><a href="#cb23-6"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="cn">NA</span>, <span class="dv">4</span>), <span class="cn">NA_real_</span>)</span>
<span id="cb23-7"><a href="#cb23-7"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="sc">-</span><span class="dv">2</span>, <span class="sc">-</span><span class="dv">2</span>), <span class="dv">4</span>)</span>
<span id="cb23-8"><a href="#cb23-8"></a> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(<span class="dv">3</span>, <span class="dv">3</span>), <span class="dv">9</span>)</span>
<span id="cb23-9"><a href="#cb23-9"></a> }</span>
<span id="cb23-10"><a href="#cb23-10"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p><strong>Parametrized test pattern</strong></p>
<p><code>expect_identical()</code> used once.</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>patrick<span class="sc">::</span><span class="fu">with_parameters_test_that</span>(</span>
<span id="cb24-2"><a href="#cb24-2"></a> <span class="at">desc_stub =</span> <span class="st">"multiplier works as expected"</span>,</span>
<span id="cb24-3"><a href="#cb24-3"></a> <span class="at">code =</span> <span class="fu">expect_identical</span>(<span class="fu">multiplier</span>(x, y), res),</span>
<span id="cb24-4"><a href="#cb24-4"></a> <span class="at">.cases =</span> tibble<span class="sc">::</span><span class="fu">tribble</span>(</span>
<span id="cb24-5"><a href="#cb24-5"></a> <span class="sc">~</span>x, <span class="sc">~</span>y, <span class="sc">~</span>res,</span>
<span id="cb24-6"><a href="#cb24-6"></a> <span class="sc">-</span><span class="dv">1</span>, <span class="dv">3</span>, <span class="sc">-</span><span class="dv">3</span>,</span>
<span id="cb24-7"><a href="#cb24-7"></a> <span class="dv">0</span>, <span class="fl">3.4</span>, <span class="dv">0</span>,</span>
<span id="cb24-8"><a href="#cb24-8"></a> <span class="cn">NA</span>, <span class="dv">4</span>, <span class="cn">NA_real_</span>,</span>
<span id="cb24-9"><a href="#cb24-9"></a> <span class="sc">-</span><span class="dv">2</span>, <span class="sc">-</span><span class="dv">2</span>, <span class="dv">4</span>,</span>
<span id="cb24-10"><a href="#cb24-10"></a> <span class="dv">3</span>, <span class="dv">3</span>, <span class="dv">9</span></span>
<span id="cb24-11"><a href="#cb24-11"></a> )</span>
<span id="cb24-12"><a href="#cb24-12"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p><strong>Combinatorial explosion</strong></p>
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<p>Although the parametrized version may not seem impressive for this simple example, it becomes exceedingly useful when there is a combinatorial explosion of possibilities that need to be tested. Doing so manually will be cumbersome and error-prone.</p>
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<section id="repeated-usage-of-testing-datasets" class="slide level2 smaller">
<h2>Repeated usage of testing datasets</h2>