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<!DOCTYPE html>
<html >
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title></title>
<meta name="description" content="">
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<div class="book-summary">
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<ul class="summary">
<li><strong><a href="./">MRDA 2018</a></strong></li>
<li class="divider"></li>
<li class="chapter" data-level="0.1" data-path=""><a href="#writing-reports-using-r-markdown"><i class="fa fa-check"></i><b>0.1</b> Writing reports using R-Markdown</a><ul>
<li class="chapter" data-level="0.1.1" data-path=""><a href="#creating-a-new-r-markdown-document"><i class="fa fa-check"></i><b>0.1.1</b> Creating a new R-Markdown document</a></li>
<li class="chapter" data-level="0.1.2" data-path=""><a href="#text-and-equations"><i class="fa fa-check"></i><b>0.1.2</b> Text and Equations</a></li>
<li class="chapter" data-level="0.1.3" data-path=""><a href="#r-code"><i class="fa fa-check"></i><b>0.1.3</b> R-Code</a></li>
<li class="chapter" data-level="0.1.4" data-path=""><a href="#latex-math"><i class="fa fa-check"></i><b>0.1.4</b> LaTeX Math</a></li>
</ul></li>
</ul>
</nav>
</div>
<div class="book-body">
<div class="body-inner">
<div class="book-header" role="navigation">
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./"></a>
</h1>
</div>
<div class="page-wrapper" tabindex="-1" role="main">
<div class="page-inner">
<section class="normal" id="section-">
<!--bookdown:title:end-->
<!--bookdown:title:start-->
<div id="writing-reports-using-r-markdown" class="section level2">
<h2><span class="header-section-number">0.1</span> Writing reports using R-Markdown</h2>
<p>This page will guide you through creating and editing R-Markdown documents. This is a useful tool for reporting your analysis (e.g. for homework assignments). Of course, there is also <a href="https://www.rstudio.org/links/r_markdown_cheat_sheet">a cheat sheet for R-Markdown</a></p>
<div id="creating-a-new-r-markdown-document" class="section level3">
<h3><span class="header-section-number">0.1.1</span> Creating a new R-Markdown document</h3>
<ol start="0" style="list-style-type: decimal">
<li><p>If an R-Markdown file was provided to you, open it with R-Studio and skip to <a href="#step4">step 4</a> after adding your answers.</p></li>
<li><p>Open R-Studio</p></li>
<li><p>Create a new R-Markdown document <img src="rmdExplain/start.PNG" /> <img src="rmdExplain/openDoc.PNG" /> <img src="rmdExplain/enterName.PNG" /> <img src="rmdExplain/template.PNG" /></p></li>
<li><p>Save with appropriate name <img src="rmdExplain/saving.PNG" /></p>
<p>3.1. Add your answers</p>
<p>3.2. Save again</p></li>
</ol>
<p><a name="step4"></a></p>
<ol start="4" style="list-style-type: decimal">
<li><p>“Knit” to HTML <img src="rmdExplain/knit.PNG" /></p></li>
<li><p>Hand in appropriate file (ending in <code>.html</code>) on learn@WU <img src="rmdExplain/handin.PNG" /></p></li>
</ol>
</div>
<div id="text-and-equations" class="section level3">
<h3><span class="header-section-number">0.1.2</span> Text and Equations</h3>
<p>R-Markdown documents are plain text files that include both text and R-code. Using RStudio they can be converted (‘knitted’) to HTML or PDF files that include both the text and the results of the R-code. In fact this website is written using R-Markdown and RStudio. In order for RStudio to be able to interpret the document you have to use certain characters or combinations of characters when formatting text and including R-code to be evaluated. By default the document starts with the options for the text part. You can change the title, date, author and a few more advanced options.</p>
<div class="figure">
<img src="rmdExplain/rmdHead.PNG" alt="First lines of an R-Markdown document" />
<p class="caption">First lines of an R-Markdown document</p>
</div>
<p>The default is text mode, meaning that lines in an Rmd document will be interpreted as text, unless specified otherwise.</p>
<div id="headings" class="section level4">
<h4><span class="header-section-number">0.1.2.1</span> Headings</h4>
<p>Usually you want to include some kind of heading to structure your text. A heading is created using <code>#</code> signs. A single <code>#</code> creates a first level heading, two <code>##</code> a second level and so on.</p>
<div class="figure">
<img src="rmdExplain/headings.PNG" />
</div>
<p>It is important to note here that the <code>#</code> symbol means something different within the code chunks as opposed to outside of them. If you continue to put a <code>#</code> in front of all your regular text, it will all be interpreted as a first level heading, making your text very large.</p>
</div>
<div id="lists" class="section level4">
<h4><span class="header-section-number">0.1.2.2</span> Lists</h4>
<p>Bullet point lists are created using <code>*</code>, <code>+</code> or <code>-</code>. Sub-items are created by indenting the item using 4 spaces or 2 tabs.</p>
<pre><code>* First Item
* Second Item
+ first sub-item
- first sub-sub-item
+ second sub-item</code></pre>
<ul>
<li>First Item</li>
<li>Second Item
<ul>
<li>first sub-item
<ul>
<li>first sub-sub-item</li>
</ul></li>
<li>second sub-item</li>
</ul></li>
</ul>
<p>Ordered lists can be created using numbers and letters. If you need sub-sub-items use <code>A)</code> instead of <code>A.</code> on the third level.</p>
<pre><code>1. First item
a. first sub-item
A) first sub-sub-item
b. second sub-item
2. Second item</code></pre>
<ol style="list-style-type: decimal">
<li>First item
<ol style="list-style-type: lower-alpha">
<li>first sub-item
<ol style="list-style-type: upper-alpha">
<li>first sub-sub-item</li>
</ol></li>
<li>second sub-item</li>
</ol></li>
<li>Second item</li>
</ol>
</div>
<div id="text-formatting" class="section level4">
<h4><span class="header-section-number">0.1.2.3</span> Text formatting</h4>
<p>Text can be formatted in <em>italics</em> (<code>*italics*</code>) or <strong>bold</strong> (<code>**bold**</code>). In addition, you can ad block quotes with <code>></code></p>
<pre><code>> Lorem ipsum dolor amet chillwave lomo ramps, four loko green juice messenger bag raclette forage offal shoreditch chartreuse austin. Slow-carb poutine meggings swag blog, pop-up salvia taxidermy bushwick freegan ugh poke.</code></pre>
<blockquote>
<p>Lorem ipsum dolor amet chillwave lomo ramps, four loko green juice messenger bag raclette forage offal shoreditch chartreuse austin. Slow-carb poutine meggings swag blog, pop-up salvia taxidermy bushwick freegan ugh poke.</p>
</blockquote>
</div>
</div>
<div id="r-code" class="section level3">
<h3><span class="header-section-number">0.1.3</span> R-Code</h3>
<p>R-code is contained in so called “chunks”. These chunks always start with three backticks and <code>r</code> in curly braces (<code>```{r}</code>) and end with three backticks (<code>```</code>). Optionally, parameters can be added after the <code>r</code> to influence how a chunk behaves. Additionally, you can also give each chunk a name. Note that these have to be <strong>unique</strong>, otherwise R will refuse to knit your document.</p>
<div id="global-and-chunk-options" class="section level4">
<h4><span class="header-section-number">0.1.3.1</span> Global and chunk options</h4>
<p>The first chunk always looks as follows</p>
<pre><code>```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```</code></pre>
<p>It is added to the document automatically and sets options for all the following chunks. These options can be overwritten on a per-chunk basis.</p>
<p>Keep <code>knitr::opts_chunk$set(echo = TRUE)</code> to print your code to the document you will hand in. Changing it to <code>knitr::opts_chunk$set(echo = FALSE)</code> will not print your code by default. This can be changed on a per-chunk basis.</p>
<pre><code>```{r cars, echo = FALSE}
summary(cars)
plot(dist~speed, cars)
```</code></pre>
<pre><code>## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00</code></pre>
<p><img src="06-rmdIntro_files/figure-html/cars-1.png" width="672" /></p>
<pre><code>```{r cars2, echo = TRUE}
summary(cars)
plot(dist~speed, cars)
```</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(cars)</code></pre></div>
<pre><code>## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(dist<span class="op">~</span>speed, cars)</code></pre></div>
<p><img src="06-rmdIntro_files/figure-html/cars2-1.png" width="672" /></p>
<p>A good overview of all available global/chunk options can be found <a href="https://yihui.name/knitr/options/#chunk_options">here</a>.</p>
</div>
</div>
<div id="latex-math" class="section level3">
<h3><span class="header-section-number">0.1.4</span> LaTeX Math</h3>
<p>Writing well formatted mathematical formulae is done the same way as in <a href="https://en.wikipedia.org/wiki/LaTeX">LaTeX</a>. Math mode is started and ended using <code>$$</code>.</p>
<pre><code>$$
f_1(\omega) = \frac{\sigma^2}{2 \pi},\ \omega \in[-\pi, \pi]
$$</code></pre>
<p><span class="math display">\[
f_1(\omega) = \frac{\sigma^2}{2 \pi},\ \omega \in[-\pi, \pi]
\]</span></p>
<p>(for those interested this is the spectral density of <a href="https://en.wikipedia.org/wiki/White_noise">white noise</a>)</p>
<p>Including inline mathematical notation is done with a single <code>$</code> symbol.</p>
<pre><code>${2\over3}$ of my code is inline.
</code></pre>
<p><span class="math inline">\({2\over3}\)</span> of my code is inline.</p>
<p><br></p>
<p>Take a look at <a href="https://en.wikibooks.org/wiki/LaTeX/Mathematics#Symbols">this wikibook on Mathematics in LaTeX</a> and <a href="https://www.sharelatex.com/learn/List_of_Greek_letters_and_math_symbols">this list of Greek letters and mathematical symbols</a> if you are not familiar with LaTeX.</p>
<p>In order to write multi-line equations in the same math environment, use <code>\\</code> after every line. In order to insert a space use a single <code>\</code>. To render text inside a math environment use <code>\text{here is the text}</code>. In order to align equations start with <code>\begin{align}</code> and place an <code>&</code> in each line at the point around which it should be aligned. Finally end with <code>\end{align}</code></p>
<pre><code>$$
\begin{align}
\text{First equation: }\ Y &= X \beta + \epsilon_y,\ \forall X \\
\text{Second equation: }\ X &= Z \gamma + \epsilon_x
\end{align}
$$</code></pre>
<p><span class="math display">\[
\begin{align}
\text{First equation: }\ Y &= X \beta + \epsilon_y,\ \forall X \\
\text{Second equation: }\ X &= Z \gamma + \epsilon_x
\end{align}
\]</span></p>
<div id="important-symbols" class="section level4">
<h4><span class="header-section-number">0.1.4.1</span> Important symbols</h4>
<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;">
Symbol
</th>
<th style="text-align:left;">
Code
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a^{2} + b\)</span>
</td>
<td style="text-align:left;">
<code>a^{2} + b</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a^{2+b}\)</span>
</td>
<td style="text-align:left;">
<code>a^{2+b}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a_{1}\)</span>
</td>
<td style="text-align:left;">
<code>a_{1}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \leq b\)</span>
</td>
<td style="text-align:left;">
<code>a \leq b</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \geq b\)</span>
</td>
<td style="text-align:left;">
<code>a \geq b</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \neq b\)</span>
</td>
<td style="text-align:left;">
<code>a \neq b</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \approx b\)</span>
</td>
<td style="text-align:left;">
<code>a \approx b</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \in (0,1)\)</span>
</td>
<td style="text-align:left;">
<code>a \in (0,1)</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a \rightarrow \infty\)</span>
</td>
<td style="text-align:left;">
<code>a \rightarrow \infty</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\frac{a}{b}\)</span>
</td>
<td style="text-align:left;">
<code>\frac{a}{b}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\frac{\partial a}{\partial b}\)</span>
</td>
<td style="text-align:left;">
<code>\frac{\partial a}{\partial b}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\sqrt{a}\)</span>
</td>
<td style="text-align:left;">
<code>\sqrt{a}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\sum_{i = 1}^{b} a_i\)</span>
</td>
<td style="text-align:left;">
<code>\sum_{i = 1}^{b} a_i</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\int_{a}^b f(c) dc\)</span>
</td>
<td style="text-align:left;">
<code>\int_{a}^b f(c) dc</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\prod_{i = 0}^b a_i\)</span>
</td>
<td style="text-align:left;">
<code>\prod_{i = 0}^b a_i</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(c \left( \sum_{i=1}^b a_i \right)\)</span>
</td>
<td style="text-align:left;">
<code>c \left( \sum_{i=1}^b a_i \right)</code>
</td>
</tr>
</tbody>
</table>
<p>The <code>{}</code> after <code>_</code> and <code>^</code> are not strictly necessary if there is only one character in the sub-/superscript. However, in order to place multiple characters in the sub-/superscript they are necessary. e.g.</p>
<table class="table table-striped" style="width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;">
Symbol
</th>
<th style="text-align:left;">
Code
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a^b = a^{b}\)</span>
</td>
<td style="text-align:left;">
<code>a^b = a^{b}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(a^b+c \neq a^{b+c}\)</span>
</td>
<td style="text-align:left;">
<code>a^b+c \neq a^{b+c}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\sum_i a_i = \sum_{i} a_{i}\)</span>
</td>
<td style="text-align:left;">
<code>\sum_i a_i = \sum_{i} a_{i}</code>
</td>
</tr>
<tr>
<td style="text-align:left;">
<span class="math inline">\(\sum_{i=1}^{b+c} a_i \neq \sum_i=1^b+c a_i\)</span>
</td>
<td style="text-align:left;">
<code>\sum_{i=1}^{b+c} a_i \neq \sum_i=1^b+c a_i</code>
</td>
</tr>
</tbody>
</table>
</div>
<div id="greek-letters" class="section level4">
<h4><span class="header-section-number">0.1.4.2</span> Greek letters</h4>
<p><a href="https://en.wikipedia.org/wiki/Greek_alphabet#Letters">Greek letters</a> are preceded by a <code>\</code> followed by their name (<code>$\beta$</code> = <span class="math inline">\(\beta\)</span>). In order to capitalize them simply capitalize the first letter of the name (<code>$\Gamma$</code> = <span class="math inline">\(\Gamma\)</span>).</p>
</div>
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