EVOLUTION-MANAGER

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<p>This is an example of Markdown vignettes in R. 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>

<blockquote>
<p>Please note this example is for <a href="http://rmarkdown.rstudio.com/authoring_migrating_from_v1.html">R Markdown v1</a> only. If you use <a href="http://rmarkdown.rstudio.com/">R Markdown v2</a>, you should use the vignette engine <code>knitr::rmarkdown</code> instead of <code>knitr::knitr</code>.</p>
</blockquote>

<h2>Package vignettes</h2>

<p>To enable Markdown vignettes in an R package, you need to</p>

<ul>
<li>add <code>*.Rmd</code> files under the <code>vignettes</code> directory</li>
<li>add <code>VignetteBuilder: knitr</code> to the <code>DESCRIPTION</code> file</li>
<li>specify the vignette engine <code>\VignetteEngine{knitr::knitr}</code> in the <code>Rmd</code> files (inside HTML comments)</li>
</ul>

<h2>View vignettes</h2>

<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>

<pre><code class="r">help(package = &#39;YourPackage&#39;, help_type = &#39;html&#39;)
# or see a standalone list of vignettes
browseVignettes(&#39;YourPackage&#39;)
</code></pre>

<h2>Examples</h2>

<p>Below are some code chunks as examples.</p>

<pre><code class="r">if (TRUE) cat(&#39;_hello_ **markdown**!&#39;, &#39;\n&#39;)
</code></pre>

<p><em>hello</em> <strong>markdown</strong>! </p>

<p>Normally you do not need any chunk options.</p>

<pre><code class="r">1+1
## [1] 2
10:1
##  [1] 10  9  8  7  6  5  4  3  2  1
rnorm(5)^2
## [1] 0.008458 2.221310 3.826440 0.909318 0.285807
strsplit(&#39;hello, markdown vignettes&#39;, &#39;&#39;)
## [[1]]
##  [1] &quot;h&quot; &quot;e&quot; &quot;l&quot; &quot;l&quot; &quot;o&quot; &quot;,&quot; &quot; &quot; &quot;m&quot; &quot;a&quot; &quot;r&quot; &quot;k&quot; &quot;d&quot; &quot;o&quot; &quot;w&quot; &quot;n&quot; &quot; &quot; &quot;v&quot; &quot;i&quot; &quot;g&quot;
## [20] &quot;n&quot; &quot;e&quot; &quot;t&quot; &quot;t&quot; &quot;e&quot; &quot;s&quot;
</code></pre>

<p>Feel free to draw beautiful plots and write math $P(X>x)=\alpha/2$.</p>

<pre><code class="r">n=300; set.seed(123)
par(mar=c(4,4,.1,.1))
plot(rnorm(n), rnorm(n), pch=21, cex=5*runif(n), col=&#39;white&#39;, bg=&#39;gray&#39;)
</code></pre>

<p>You can use your own CSS file instead of the built-in style in the <strong>markdown</strong> package &ndash; just set the option <code>markdown.HTML.stylesheet</code>, e.g.</p>

<pre><code class="r">options(markdown.HTML.stylesheet = &#39;path/to/a/custom/style.css&#39;)
</code></pre>

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