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<!DOCTYPE html>
<html lang="en"><head>
<script src="slides_files/libs/clipboard/clipboard.min.js"></script>
<script src="slides_files/libs/quarto-html/tabby.min.js"></script>
<script src="slides_files/libs/quarto-html/popper.min.js"></script>
<script src="slides_files/libs/quarto-html/tippy.umd.min.js"></script>
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<link href="slides_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<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-1.5.39">
<meta name="keywords" content="software-engineering, r-packages, best-practices, DRY">
<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;}
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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;
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/* CSS for syntax highlighting */
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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; }
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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code span { color: #003b4f; } /* Normal */
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background-size: 1rem 1rem;
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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>
<!-- Don't render this file manually. Run `renderer.R` script instead. -->
<div style="text-align: center;">
<p>Indrajeet Patil</p>
</div>
<p><img data-src="media/simpsons.png" class="absolute" style="top: 155px; left: 70px; width: 900px; height: 500px; "></p>
<!-- Need to install extension from https://github.com/quarto-ext/fontawesome -->
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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 Principle states that:</p>
<div style="color: red;">
<p><em>Every piece of <strong>knowledge</strong> must have a <strong>single</strong> representation in the codebase.</em></p>
</div>
<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">
<div>
<figure>
<p><img data-src="media/dry.gif"></p>
</figure>
</div>
</div>
</div>
</div>
</div>
<div class="fragment">
<div class="callout callout-note callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<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-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<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>Apply the DRY principle to remove duplication in following aspects of R package development:</p>
<ul>
<li>Documentation</li>
<li>Vignette setup</li>
<li>Unit testing</li>
<li>Dependency management</li>
<li>Exceptions</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 may be 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 fa-2xl" aria-label="file"></i> <strong>Vignettes</strong>: When first learning how to use a package.</p>
<p><br></p>
<p><i class="fa-solid fa-file-invoice fa-2xl" aria-label="file-invoice"></i> <strong>Manual</strong>: When checking details about a specific function.</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">
<div>
<figure>
<p><img data-src="media/spiderman.jpeg" style="width:100.0%"></p>
</figure>
</div>
</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
│ └── info1.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:70%;">
<p><code>info1.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=""></a>This is some crucial information to be repeated across documentation.</span>
<span id="cb2-2"><a href=""></a></span>
<span id="cb2-3"><a href=""></a>```{r}</span>
<span id="cb2-4"><a href=""></a>1 + 1</span>
<span id="cb2-5"><a href=""></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-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<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-part-1" class="slide level2 smaller">
<h2>Using child documents in package: Part-1</h2>
<p>Include contents of child documents in the documentation in multiple locations.</p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>Vignette</strong></p>
<pre><code>├── DESCRIPTION
├── vignettes
│ └── vignette1.Rmd
│ └── ...
│ └── web_only
│ └── vignette2.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:50%;">
<p><strong>README</strong></p>
<pre><code>├── DESCRIPTION
├── README.Rmd</code></pre>
</div>
</div>
</div>
<div class="fragment">
<div class="columns">
<div class="column" style="width:50%;">
<p>In <code>vignette1.Rmd</code></p>
<div class="sourceCode" id="cb5"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb5-1"><a href=""></a>---</span>
<span id="cb5-2"><a href=""></a>output: html_vignette</span>
<span id="cb5-3"><a href=""></a>---</span>
<span id="cb5-4"><a href=""></a></span>
<span id="cb5-5"><a href=""></a>Vignette content.</span>
<span id="cb5-6"><a href=""></a></span>
<span id="cb5-7"><a href=""></a>```{r, child="../man/rmd-children/info1.Rmd"}</span>
<span id="cb5-8"><a href=""></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:50%;">
<p>In <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=""></a>---</span>
<span id="cb6-2"><a href=""></a>output: github_document</span>
<span id="cb6-3"><a href=""></a>---</span>
<span id="cb6-4"><a href=""></a></span>
<span id="cb6-5"><a href=""></a>README content.</span>
<span id="cb6-6"><a href=""></a></span>
<span id="cb6-7"><a href=""></a>```{r, child="man/rmd-children/info1.Rmd"}</span>
<span id="cb6-8"><a href=""></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</section>
<section id="using-child-documents-in-package-part-2" class="slide level2 smaller">
<h2>Using child documents in package: Part-2</h2>
<p>Include contents of child documents in the documentation in multiple locations.</p>
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>Manual</strong></p>
<pre><code>├── DESCRIPTION
├── R
│ └── foo1.R
│ └── foo2.R
├── man
│ └── foo1.Rd
│ └── foo2.Rd
│ └── ...</code></pre>
</div><div class="column" style="width:50%;">
<p>In <code>foo1.R</code></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=""></a><span class="co">#' @title Foo1</span></span>
<span id="cb8-2"><a href=""></a><span class="co">#' @section Information:</span></span>
<span id="cb8-3"><a href=""></a><span class="co">#' </span></span>
<span id="cb8-4"><a href=""></a><span class="co">#' ```{r, child="man/rmd-children/info1.Rmd"}</span></span>
<span id="cb8-5"><a href=""></a><span class="co">#' ```</span></span>
<span id="cb8-6"><a href=""></a>foo1 <span class="ot"><-</span> <span class="cf">function</span>() { ... }</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
<p><br></p>
<div class="callout callout-important callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Important</strong></p>
</div>
<div class="callout-content">
<p>The underlying assumption here is that you are using <a href="https://roxygen2.r-lib.org/"><code>{roxygen2}</code></a> to generate package documentation.</p>
</div>
</div>
</div>
</section>
<section id="what-about-non-child-documents" class="slide level2 smaller">
<h2>What about non-child documents?</h2>
<p>You can include contents from <strong>any</strong> file in <code>.Rmd</code>, not just a child document!</p>
<p><br></p>
<p> <i class="fa-regular fa-file fa-5x" aria-label="file"></i> <i class="fa-regular fa-plus fa-3x" aria-label="plus"></i> <i class="fa-regular fa-file-lines fa-5x" aria-label="file-lines"></i> <i class="fa-regular fa-plus fa-3x" aria-label="plus"></i> <i class="fa-regular fa-file-code fa-5x" aria-label="file-code"></i> <i class="fa-regular fa-plus fa-3x" aria-label="plus"></i> <i class="fa-regular fa-file-image fa-5x" aria-label="file-image"></i> <i class="fa-regular fa-plus fa-3x" aria-label="plus"></i> <i class="fa-solid fa-ellipsis fa-2x" aria-label="ellipsis"></i></p>
<p>(parent Rmd) (child Rmd) (<code>.R</code> + <code>R</code> engine) (<code>.md</code> + <code>asis</code> engine) </p>
<p><br></p>
<p> <i class="fa-regular fa-equals fa-3x" aria-label="equals"></i> <i class="fa-solid fa-file-lines fa-5x" aria-label="file-lines"></i></p>
<p> (result Rmd)</p>
</section>
<section id="storing-other-documentation-files-in-package" class="slide level2 smaller">
<h2>Storing other documentation files in package</h2>
<p>Like child documents, other types of documents are also stored in <code>man/</code> folder.</p>
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>Reusable content</strong></p>
<pre><code>├── DESCRIPTION
├── man
│ └── rmd-children
│ └── info1.Rmd
│ └── ...
│ └── md-fragments
│ └── fragment1.md
│ └── ...
│ └── r-chunks
│ └── chunk1.R
│ └── ...</code></pre>
</div><div class="column" style="width:35%;">
<p><code>fragment1.md</code> example:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb10-1"><a href=""></a>This `.md` file contains </span>
<span id="cb10-2"><a href=""></a>content to be included *as is*</span>
<span id="cb10-3"><a href=""></a>across multiple locations</span>
<span id="cb10-4"><a href=""></a>in the documentation.</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:35%;">
<p><code>chunk1.R</code> example:</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb11-1"><a href=""></a># some comment and code</span>
<span id="cb11-2"><a href=""></a>1 + 1</span>
<span id="cb11-3"><a href=""></a></span>
<span id="cb11-4"><a href=""></a># more comments and code</span>
<span id="cb11-5"><a href=""></a>2 + 3</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-note callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Folder names</strong></p>
</div>
<div class="callout-content">
<p>You can name these folders however you wish, but it is advisable that the names provide information about file contents (e.g., <code>r-examples</code>, <code>yaml-snippets</code>, <code>md-fragments</code>, etc.).</p>
</div>
</div>
</div>
</section>
<section id="using-non-child-documents-in-package-part-1" class="slide level2 smaller">
<h2>Using non-child documents in package: Part-1</h2>
<p>Include contents of various files in the documentation in multiple locations.</p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>Vignette</strong></p>
<pre><code>├── DESCRIPTION
├── vignettes
│ └── vignette1.Rmd
│ └── ...
│ └── web_only
│ └── vignette2.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:50%;">
<p><strong>README</strong></p>
<pre><code>├── DESCRIPTION
├── README.Rmd</code></pre>
</div>
</div>
</div>
<div class="fragment">
<div class="columns">
<div class="column" style="width:50%;">
<p>In <code>vignette1.Rmd</code></p>
<div class="sourceCode" id="cb14"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb14-1"><a href=""></a>---</span>
<span id="cb14-2"><a href=""></a>output: html_vignette</span>
<span id="cb14-3"><a href=""></a>---</span>
<span id="cb14-4"><a href=""></a></span>
<span id="cb14-5"><a href=""></a>Vignette content.</span>
<span id="cb14-6"><a href=""></a></span>
<span id="cb14-7"><a href=""></a>```{asis, file="../man/md-fragments/fragment1.md"}</span>
<span id="cb14-8"><a href=""></a>```</span>
<span id="cb14-9"><a href=""></a></span>
<span id="cb14-10"><a href=""></a>```{r, file="../man/r-chunks/chunk1.R"}</span>
<span id="cb14-11"><a href=""></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:50%;">
<p>In <code>README.Rmd</code></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=""></a>---</span>
<span id="cb15-2"><a href=""></a>output: github_document</span>
<span id="cb15-3"><a href=""></a>---</span>
<span id="cb15-4"><a href=""></a></span>
<span id="cb15-5"><a href=""></a>README content.</span>
<span id="cb15-6"><a href=""></a></span>
<span id="cb15-7"><a href=""></a>```{asis, file="man/md-fragments/fragment1.md"}</span>
<span id="cb15-8"><a href=""></a>```</span>
<span id="cb15-9"><a href=""></a></span>
<span id="cb15-10"><a href=""></a>```{r, file="man/r-chunks/chunk1.R"}</span>
<span id="cb15-11"><a href=""></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</section>
<section id="using-non-child-documents-in-package-part-2" class="slide level2 smaller">
<h2>Using non-child documents in package: Part-2</h2>
<p>Include contents of child documents in the documentation in multiple locations.</p>
<div class="columns">
<div class="column" style="width:30%;">
<p><strong>Manual</strong></p>
<pre><code>├── DESCRIPTION
├── R
│ └── foo1.R
│ └── ...
├── man
│ └── foo1.Rd
│ └── ...</code></pre>
</div><div class="column" style="width:50%;">
<p>In <code>foo1.R</code></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=""></a><span class="co">#' @title Foo1</span></span>
<span id="cb17-2"><a href=""></a><span class="co">#' @section Information:</span></span>
<span id="cb17-3"><a href=""></a><span class="co">#' </span></span>
<span id="cb17-4"><a href=""></a><span class="co">#' ```{r, file="man/md-fragments/fragment1.Rmd"}</span></span>
<span id="cb17-5"><a href=""></a><span class="co">#' ```</span></span>
<span id="cb17-6"><a href=""></a><span class="co">#' </span></span>
<span id="cb17-7"><a href=""></a><span class="co">#' @example man/r-chunks/chunk1.R</span></span>
<span id="cb17-8"><a href=""></a>foo1 <span class="ot"><-</span> <span class="cf">function</span>() { ... }</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
<p><br></p>
<div class="callout callout-important callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Important</strong></p>
</div>
<div class="callout-content">
<p>The underlying assumption here is that you are using <a href="https://roxygen2.r-lib.org/"><code>{roxygen2}</code></a> to generate package documentation.</p>
</div>
</div>
</div>
</section>
<section id="section-1" class="slide level2">
<h2></h2>
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Summary on how to repeat documentation</strong></p>
</div>
<div class="callout-content">
<p>If you are overwhelmed by this section, note that you actually need to remember only the following rules:</p>
<ul>
<li><p>Store reusable document files in the <code>/man</code> folder.</p></li>
<li><p>When you wish to include their contents, provide paths to these files <strong>relative</strong> to the document you are linking from.</p></li>
<li><p>If it’s a child <code>.Rmd</code> document, use the <code>child</code> option to include its contents.</p></li>
<li><p>If it’s not an <code>.Rmd</code> document, use the <code>file</code> option to include its contents and use appropriate <code>{knitr}</code> engine. To see available engines, run <code>names(knitr::knit_engines$get())</code>.</p></li>
</ul>
</div>
</div>
</div>
</section>
<section id="self-study" class="slide level2">
<h2>Self-study</h2>
<p>Example packages that use reusable component documents to repeat documentation.</p>
<ul>
<li><p><a href="https://github.com/r-lib/pkgdown/tree/main/man/rmd-fragments" target="_blank"><code>{pkgdown}</code></a></p></li>
<li><p><a href="https://github.com/IndrajeetPatil/ggstatsplot/tree/main/man" target="_blank"><code>{ggstatsplot}</code></a></p></li>
<li><p><a href="https://github.com/IndrajeetPatil/statsExpressions/tree/main/man" target="_blank"><code>{statsExpressions}</code></a></p></li>
</ul>
</section></section>
<section>
<section id="vignette-setup" class="title-slide slide level1 center">
<h1>Vignette Setup</h1>
<p>How not to repeat yourself while setting up vignettes.</p>
</section>
<section id="setup-chunks-in-vignettes" class="slide level2 smaller">
<h2>Setup chunks in vignettes</h2>
<p>Another duplication that occurs is in setup chunks for vignettes.</p>
<p>For example, some parts of the setup can be same across vignettes.</p>
<p><br></p>
<div class="columns">
<div class="column" style="width:25%;">
<pre><code>├── DESCRIPTION
├── vignettes
│ └── vignette1.Rmd
│ └── vignette2.Rmd
│ └── ...</code></pre>
</div><div class="column" style="width:37%;">
<div class="sourceCode" id="cb19"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb19-1"><a href=""></a>---</span>
<span id="cb19-2"><a href=""></a>title: "Vignette-1"</span>
<span id="cb19-3"><a href=""></a>output: html_vignette</span>
<span id="cb19-4"><a href=""></a>---</span>
<span id="cb19-5"><a href=""></a></span>
<span id="cb19-6"><a href=""></a>```{r}</span>
<span id="cb19-7"><a href=""></a>knitr::opts_chunk$set(</span>
<span id="cb19-8"><a href=""></a> message = FALSE,</span>
<span id="cb19-9"><a href=""></a> collapse = TRUE,</span>
<span id="cb19-10"><a href=""></a> comment = "#>"</span>
<span id="cb19-11"><a href=""></a>)</span>
<span id="cb19-12"><a href=""></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="cb20"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb20-1"><a href=""></a>---</span>
<span id="cb20-2"><a href=""></a>title: "Vignette-2"</span>
<span id="cb20-3"><a href=""></a>output: html_vignette</span>
<span id="cb20-4"><a href=""></a>---</span>
<span id="cb20-5"><a href=""></a></span>
<span id="cb20-6"><a href=""></a>```{r}</span>
<span id="cb20-7"><a href=""></a>knitr::opts_chunk$set(</span>
<span id="cb20-8"><a href=""></a> message = FALSE,</span>
<span id="cb20-9"><a href=""></a> collapse = TRUE,</span>
<span id="cb20-10"><a href=""></a> comment = "#>"</span>
<span id="cb20-11"><a href=""></a>)</span>
<span id="cb20-12"><a href=""></a></span>
<span id="cb20-13"><a href=""></a>options(crayon.enabled = TRUE)</span>
<span id="cb20-14"><a href=""></a>```</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
<p><br></p>
<p>How can this repetition be avoided?</p>
</section>
<section id="sourcing-setup-chunks-in-vignettes" class="slide level2 smaller">
<h2>Sourcing setup chunks in vignettes</h2>
<div class="columns">
<div class="column" style="width:60%;">
<p>This repetition can be avoided by moving the <strong>common</strong> setup to a script, and sourcing it from vignettes. Storing this script in a folder (<code>/setup</code>) is advisable if there are many reusable artifacts.</p>
</div><div class="column" style="width:20%;">
<p><strong>Option 1</strong></p>
<pre><code>├── DESCRIPTION
├── vignettes
│ └── setup.R</code></pre>
</div><div class="column" style="width:20%;">
<p><strong>Option 2</strong></p>
<pre><code>├── DESCRIPTION
├── vignettes
│ └── setup
│ └── setup.R</code></pre>
</div>
</div>
<div class="fragment">
<div class="columns">
<div class="column" style="width:26%;">
<p><code>setup.R</code> contents</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href=""></a>knitr<span class="sc">::</span>opts_chunk<span class="sc">$</span><span class="fu">set</span>(</span>
<span id="cb23-2"><a href=""></a> <span class="at">message =</span> <span class="cn">FALSE</span>,</span>
<span id="cb23-3"><a href=""></a> <span class="at">collapse =</span> <span class="cn">TRUE</span>,</span>
<span id="cb23-4"><a href=""></a> <span class="at">comment =</span> <span class="st">"#>"</span></span>
<span id="cb23-5"><a href=""></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="cb24"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb24-1"><a href=""></a>---</span>
<span id="cb24-2"><a href=""></a>title: "Vignette-1"</span>
<span id="cb24-3"><a href=""></a>output: html_vignette</span>
<span id="cb24-4"><a href=""></a>---</span>
<span id="cb24-5"><a href=""></a></span>
<span id="cb24-6"><a href=""></a>```{r setup, include = FALSE}</span>
<span id="cb24-7"><a href=""></a>source("setup/setup.R")</span>
<span id="cb24-8"><a href=""></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="cb25"><pre class="sourceCode numberSource default number-lines code-with-copy"><code class="sourceCode default"><span id="cb25-1"><a href=""></a>---</span>
<span id="cb25-2"><a href=""></a>title: "Vignette-2"</span>
<span id="cb25-3"><a href=""></a>output: html_vignette</span>
<span id="cb25-4"><a href=""></a>---</span>
<span id="cb25-5"><a href=""></a></span>
<span id="cb25-6"><a href=""></a>```{r setup, include = FALSE}</span>
<span id="cb25-7"><a href=""></a>source("setup/setup.R")</span>
<span id="cb25-8"><a href=""></a>options(crayon.enabled = TRUE)</span>
<span id="cb25-9"><a href=""></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-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<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><p><a href="https://github.com/cynkra/dm/blob/main/vignettes/setup/setup.R" target="_blank"><code>{dm}</code></a></p></li>
<li><p><a href="https://github.com/IndrajeetPatil/statsExpressions/blob/main/vignettes/setup.R" target="_blank"><code>{statsExpressions}</code></a></p></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>
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<h2>Illustrative example datasets</h2>
<p>If none of the existing datasets are useful to illustrate your functions, you can create new datasets.</p>
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<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>
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<p><strong>In examples</strong></p>