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94 KiB
HTML
78 lines
94 KiB
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
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<meta name="generator" content="litedown 0.4">
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<title>R Markdown (v1) Vignettes with knitr</title>
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<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@xiee/utils@1.13.44/css/prism-xcode.min.css">
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<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css">
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<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@xiee/utils@1.13.44/css/default.min.css">
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</head>
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<body>
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<div class="frontmatter">
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<div class="title"><h1>R Markdown (v1) Vignettes with knitr</h1></div>
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<div class="author"><h2>Yihui Xie</h2></div>
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<div class="date"><h3>2024-11-06</h3></div>
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</div>
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<div class="body">
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<!--
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%\VignetteEngine{litedown::vignette}
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%\VignetteIndexEntry{An R Markdown Vignette with knitr}
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-->
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<p>Before R 3.0.0, only Sweave/PDF vignettes were supported in R. Markdown is gaining popularity over the years due to its simplicity, and R 3.0.0 starts to support package vignettes written in R Markdown.</p>
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<blockquote>
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<p>Please note this example is for <a href="https://cran.r-project.org/package=markdown">R Markdown v1</a> only. If you use <a href="https://rmarkdown.rstudio.com">R Markdown v2</a>, you should use the vignette engine <code>knitr::rmarkdown</code> instead of <code>knitr::knitr</code>.</p>
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</blockquote>
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<h2 id="sec:package-vignettes">Package vignettes</h2>
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<p>To enable Markdown vignettes in an R package, you need to</p>
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<ul>
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<li>add <code>*.Rmd</code> files under the <code>vignettes</code> directory</li>
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<li>add <code>VignetteBuilder: knitr</code> to the <code>DESCRIPTION</code> file</li>
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<li>specify the vignette engine <code>\VignetteEngine{knitr::knitr}</code> in the <code>Rmd</code> files (inside HTML comments)</li>
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</ul>
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<h2 id="sec:view-vignettes">View vignettes</h2>
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<p>And R will load the <strong>knitr</strong> package to build these vignettes to HTML files, and you can see them when you open the HTML help:</p>
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<pre><code class="language-r">help(package = 'YourPackage', help_type = 'html')
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# or see a standalone list of vignettes
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browseVignettes('YourPackage')
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</code></pre>
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<h2 id="sec:examples">Examples</h2>
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<p>Below are some code chunks as examples.</p>
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<pre><code class="language-r">if (TRUE) cat('_hello_ **markdown**!', '\n')
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</code></pre>
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<p><em>hello</em> <strong>markdown</strong>!</p>
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<p>Normally you do not need any chunk options.</p>
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<pre><code class="language-r">1+1
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</code></pre>
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<pre><code>#> [1] 2
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</code></pre>
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<pre><code class="language-r">10:1
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</code></pre>
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<pre><code>#> [1] 10 9 8 7 6 5 4 3 2 1
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</code></pre>
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<pre><code class="language-r">rnorm(5)^2
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</code></pre>
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<pre><code>#> [1] 3.98959 0.01359 0.84722 6.17346 0.04204
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</code></pre>
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<pre><code class="language-r">strsplit('hello, markdown vignettes', '')
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</code></pre>
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<pre><code>#> [[1]]
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#> [1] "h" "e" "l" "l" "o" "," " " "m" "a" "r" "k" "d" "o" "w" "n" " " "v" "i" "g"
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#> [20] "n" "e" "t" "t" "e" "s"
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#>
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</code></pre>
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<p>Feel free to draw beautiful plots and write math \(P(X>x)=\alpha/2\).</p>
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<pre><code class="language-r">n=300; set.seed(123)
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par(mar=c(4,4,.1,.1))
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plot(rnorm(n), rnorm(n), pch=21, cex=5*runif(n), col='white', bg='gray')
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</code></pre>
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<p><img src="data:image/png;base64,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</div>
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<script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/components/prism-core.min.js" defer></script>
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<script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/plugins/autoloader/prism-autoloader.min.js" defer></script>
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<script src="https://cdn.jsdelivr.net/combine/npm/katex@0.16.11/dist/katex.min.js,npm/katex@0.16.11/dist/contrib/auto-render.min.js" defer></script>
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</html>
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