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<li class="chapter" data-level="2.2.3" data-path="command-line.html"><a href="command-line.html#paths"><i class="fa fa-check"></i><b>2.2.3</b> Paths</a></li>
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<li class="chapter" data-level="4.1" data-path="git-basics.html"><a href="git-basics.html#what-is-this-git-thing-anyway"><i class="fa fa-check"></i><b>4.1</b> What is this <em>git</em> thing anyway?</a><ul>
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<li class="chapter" data-level="4.2" data-path="git-basics.html"><a href="git-basics.html#installation-setup"><i class="fa fa-check"></i><b>4.2</b> Installation & Setup</a><ul>
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<li class="chapter" data-level="4.3.1" data-path="git-basics.html"><a href="git-basics.html#adding-files"><i class="fa fa-check"></i><b>4.3.1</b> Adding Files</a></li>
<li class="chapter" data-level="4.3.2" data-path="git-basics.html"><a href="git-basics.html#committing"><i class="fa fa-check"></i><b>4.3.2</b> Committing</a></li>
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<li class="chapter" data-level="4.3.4" data-path="git-basics.html"><a href="git-basics.html#reviewing-the-process"><i class="fa fa-check"></i><b>4.3.4</b> Reviewing the Process</a></li>
<li class="chapter" data-level="4.3.5" data-path="git-basics.html"><a href="git-basics.html#gitignore"><i class="fa fa-check"></i><b>4.3.5</b> The <code>.gitignore</code> File</a></li>
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<li class="chapter" data-level="4.4.2" data-path="git-basics.html"><a href="git-basics.html#pushing-and-pulling"><i class="fa fa-check"></i><b>4.4.2</b> Pushing and Pulling</a></li>
<li class="chapter" data-level="4.4.3" data-path="git-basics.html"><a href="git-basics.html#reviewing-the-process-1"><i class="fa fa-check"></i><b>4.4.3</b> Reviewing The Process</a></li>
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<li class="chapter" data-level="4.5" data-path="git-basics.html"><a href="git-basics.html#course-assignments-on-github"><i class="fa fa-check"></i><b>4.5</b> Course Assignments on GitHub</a></li>
<li class="chapter" data-level="4.6" data-path="git-basics.html"><a href="git-basics.html#command-summary"><i class="fa fa-check"></i><b>4.6</b> Command Summary</a></li>
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<li class="chapter" data-level="5" data-path="r-intro.html"><a href="r-intro.html"><i class="fa fa-check"></i><b>5</b> Introduction to R</a><ul>
<li class="chapter" data-level="5.1" data-path="r-intro.html"><a href="r-intro.html#programming-with-r"><i class="fa fa-check"></i><b>5.1</b> Programming with R</a></li>
<li class="chapter" data-level="5.2" data-path="r-intro.html"><a href="r-intro.html#running-r-scripts"><i class="fa fa-check"></i><b>5.2</b> Running R Scripts</a><ul>
<li class="chapter" data-level="5.2.1" data-path="r-intro.html"><a href="r-intro.html#running-r-cmd"><i class="fa fa-check"></i><b>5.2.1</b> Command-Line</a></li>
<li class="chapter" data-level="5.2.2" data-path="r-intro.html"><a href="r-intro.html#running-r-rstudio"><i class="fa fa-check"></i><b>5.2.2</b> RStudio</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="r-intro.html"><a href="r-intro.html#comments"><i class="fa fa-check"></i><b>5.3</b> Comments</a></li>
<li class="chapter" data-level="5.4" data-path="r-intro.html"><a href="r-intro.html#variables"><i class="fa fa-check"></i><b>5.4</b> Variables</a><ul>
<li class="chapter" data-level="5.4.1" data-path="r-intro.html"><a href="r-intro.html#basic-data-types"><i class="fa fa-check"></i><b>5.4.1</b> Basic Data Types</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="r-intro.html"><a href="r-intro.html#gettinghelp"><i class="fa fa-check"></i><b>5.5</b> Getting Help</a></li>
<li class="chapter" data-level="" data-path="r-intro.html"><a href="r-intro.html#resources-4"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="functions.html"><a href="functions.html"><i class="fa fa-check"></i><b>6</b> Functions</a><ul>
<li class="chapter" data-level="6.1" data-path="functions.html"><a href="functions.html#what-are-functions"><i class="fa fa-check"></i><b>6.1</b> What are Functions?</a></li>
<li class="chapter" data-level="6.2" data-path="functions.html"><a href="functions.html#how-to-use-functions"><i class="fa fa-check"></i><b>6.2</b> How to Use Functions</a></li>
<li class="chapter" data-level="6.3" data-path="functions.html"><a href="functions.html#built-in-r-functions"><i class="fa fa-check"></i><b>6.3</b> Built-in R Functions</a></li>
<li class="chapter" data-level="6.4" data-path="functions.html"><a href="functions.html#loading-functions"><i class="fa fa-check"></i><b>6.4</b> Loading Functions</a></li>
<li class="chapter" data-level="6.5" data-path="functions.html"><a href="functions.html#writing-functions"><i class="fa fa-check"></i><b>6.5</b> Writing Functions</a></li>
<li class="chapter" data-level="6.6" data-path="functions.html"><a href="functions.html#conditional-statements"><i class="fa fa-check"></i><b>6.6</b> Conditional Statements</a></li>
<li class="chapter" data-level="" data-path="functions.html"><a href="functions.html#resources-5"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="vectors.html"><a href="vectors.html"><i class="fa fa-check"></i><b>7</b> Vectors</a><ul>
<li class="chapter" data-level="7.1" data-path="vectors.html"><a href="vectors.html#what-is-a-vector"><i class="fa fa-check"></i><b>7.1</b> What is a Vector?</a></li>
<li class="chapter" data-level="7.2" data-path="vectors.html"><a href="vectors.html#creating-vectors"><i class="fa fa-check"></i><b>7.2</b> Creating Vectors</a></li>
<li class="chapter" data-level="7.3" data-path="vectors.html"><a href="vectors.html#vector-indices"><i class="fa fa-check"></i><b>7.3</b> Vector Indices</a><ul>
<li class="chapter" data-level="7.3.1" data-path="vectors.html"><a href="vectors.html#simple-numeric-indices"><i class="fa fa-check"></i><b>7.3.1</b> Simple Numeric Indices</a></li>
<li class="chapter" data-level="7.3.2" data-path="vectors.html"><a href="vectors.html#multiple-indices"><i class="fa fa-check"></i><b>7.3.2</b> Multiple Indices</a></li>
<li class="chapter" data-level="7.3.3" data-path="vectors.html"><a href="vectors.html#logical-indexing"><i class="fa fa-check"></i><b>7.3.3</b> Logical Indexing</a></li>
<li class="chapter" data-level="7.3.4" data-path="vectors.html"><a href="vectors.html#named-vectors-and-character-indexing"><i class="fa fa-check"></i><b>7.3.4</b> Named Vectors and Character Indexing</a></li>
</ul></li>
<li class="chapter" data-level="7.4" data-path="vectors.html"><a href="vectors.html#modifying-vectors"><i class="fa fa-check"></i><b>7.4</b> Modifying Vectors</a></li>
<li class="chapter" data-level="7.5" data-path="vectors.html"><a href="vectors.html#vectorized-operations"><i class="fa fa-check"></i><b>7.5</b> Vectorized Operations</a><ul>
<li class="chapter" data-level="7.5.1" data-path="vectors.html"><a href="vectors.html#vectorized-operators"><i class="fa fa-check"></i><b>7.5.1</b> Vectorized Operators</a></li>
<li class="chapter" data-level="7.5.2" data-path="vectors.html"><a href="vectors.html#vectorized-functions"><i class="fa fa-check"></i><b>7.5.2</b> Vectorized Functions</a></li>
<li class="chapter" data-level="7.5.3" data-path="vectors.html"><a href="vectors.html#recycling"><i class="fa fa-check"></i><b>7.5.3</b> Recycling</a></li>
<li class="chapter" data-level="7.5.4" data-path="vectors.html"><a href="vectors.html#r-is-a-vectorized-world"><i class="fa fa-check"></i><b>7.5.4</b> R Is a Vectorized World</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="vectors.html"><a href="vectors.html#resources-6"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="lists.html"><a href="lists.html"><i class="fa fa-check"></i><b>8</b> Lists</a><ul>
<li class="chapter" data-level="8.1" data-path="lists.html"><a href="lists.html#what-is-a-list"><i class="fa fa-check"></i><b>8.1</b> What is a List?</a></li>
<li class="chapter" data-level="8.2" data-path="lists.html"><a href="lists.html#creating-lists"><i class="fa fa-check"></i><b>8.2</b> Creating Lists</a></li>
<li class="chapter" data-level="8.3" data-path="lists.html"><a href="lists.html#accessing-list-elements"><i class="fa fa-check"></i><b>8.3</b> Accessing List Elements</a><ul>
<li class="chapter" data-level="8.3.1" data-path="lists.html"><a href="lists.html#lists-indexing-by-position"><i class="fa fa-check"></i><b>8.3.1</b> Indexing by position</a></li>
<li class="chapter" data-level="8.3.2" data-path="lists.html"><a href="lists.html#indexing-by-name"><i class="fa fa-check"></i><b>8.3.2</b> Indexing by Name</a></li>
<li class="chapter" data-level="8.3.3" data-path="lists.html"><a href="lists.html#indexing-by-logical-vector"><i class="fa fa-check"></i><b>8.3.3</b> Indexing by Logical Vector</a></li>
<li class="chapter" data-level="8.3.4" data-path="lists.html"><a href="lists.html#lists-dollar-shortcut"><i class="fa fa-check"></i><b>8.3.4</b> Extracting named elements with <code>$</code></a></li>
<li class="chapter" data-level="8.3.5" data-path="lists.html"><a href="lists.html#single-vs.double-brackets-vs.dollar"><i class="fa fa-check"></i><b>8.3.5</b> Single vs. Double Brackets vs. Dollar</a></li>
</ul></li>
<li class="chapter" data-level="8.4" data-path="lists.html"><a href="lists.html#modifying-lists"><i class="fa fa-check"></i><b>8.4</b> Modifying Lists</a></li>
<li class="chapter" data-level="8.5" data-path="lists.html"><a href="lists.html#the-lapply-function"><i class="fa fa-check"></i><b>8.5</b> The <code>lapply()</code> Function</a></li>
<li class="chapter" data-level="" data-path="lists.html"><a href="lists.html#resources-7"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="data-frames.html"><a href="data-frames.html"><i class="fa fa-check"></i><b>9</b> Data Frames</a><ul>
<li class="chapter" data-level="9.1" data-path="data-frames.html"><a href="data-frames.html#what-is-a-data-frame"><i class="fa fa-check"></i><b>9.1</b> What is a Data Frame?</a><ul>
<li class="chapter" data-level="9.1.1" data-path="data-frames.html"><a href="data-frames.html#creating-data-frames"><i class="fa fa-check"></i><b>9.1.1</b> Creating Data Frames</a></li>
<li class="chapter" data-level="9.1.2" data-path="data-frames.html"><a href="data-frames.html#describing-structure-of-data-frames"><i class="fa fa-check"></i><b>9.1.2</b> Describing Structure of Data Frames</a></li>
<li class="chapter" data-level="9.1.3" data-path="data-frames.html"><a href="data-frames.html#accessing-data-in-data-frames"><i class="fa fa-check"></i><b>9.1.3</b> Accessing Data in Data Frames</a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="data-frames.html"><a href="data-frames.html#csv-files"><i class="fa fa-check"></i><b>9.2</b> Working with CSV Data</a><ul>
<li class="chapter" data-level="9.2.1" data-path="data-frames.html"><a href="data-frames.html#working-directory"><i class="fa fa-check"></i><b>9.2.1</b> Working Directory</a></li>
</ul></li>
<li class="chapter" data-level="9.3" data-path="data-frames.html"><a href="data-frames.html#factors"><i class="fa fa-check"></i><b>9.3</b> Factor Variables</a></li>
<li class="chapter" data-level="" data-path="data-frames.html"><a href="data-frames.html#resources-8"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="dplyr.html"><a href="dplyr.html"><i class="fa fa-check"></i><b>10</b> The <code>dplyr</code> Library</a><ul>
<li class="chapter" data-level="10.1" data-path="dplyr.html"><a href="dplyr.html#a-grammar-of-data-manipulation"><i class="fa fa-check"></i><b>10.1</b> A Grammar of Data Manipulation</a></li>
<li class="chapter" data-level="10.2" data-path="dplyr.html"><a href="dplyr.html#using-dplyr-functions"><i class="fa fa-check"></i><b>10.2</b> Using <code>dplyr</code> Functions</a><ul>
<li class="chapter" data-level="10.2.1" data-path="dplyr.html"><a href="dplyr.html#select"><i class="fa fa-check"></i><b>10.2.1</b> Select</a></li>
<li class="chapter" data-level="10.2.2" data-path="dplyr.html"><a href="dplyr.html#filter"><i class="fa fa-check"></i><b>10.2.2</b> Filter</a></li>
<li class="chapter" data-level="10.2.3" data-path="dplyr.html"><a href="dplyr.html#mutate"><i class="fa fa-check"></i><b>10.2.3</b> Mutate</a></li>
<li class="chapter" data-level="10.2.4" data-path="dplyr.html"><a href="dplyr.html#arrange"><i class="fa fa-check"></i><b>10.2.4</b> Arrange</a></li>
<li class="chapter" data-level="10.2.5" data-path="dplyr.html"><a href="dplyr.html#summarize"><i class="fa fa-check"></i><b>10.2.5</b> Summarize</a></li>
<li class="chapter" data-level="10.2.6" data-path="dplyr.html"><a href="dplyr.html#distinct"><i class="fa fa-check"></i><b>10.2.6</b> Distinct</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="dplyr.html"><a href="dplyr.html#multiple-operations"><i class="fa fa-check"></i><b>10.3</b> Multiple Operations</a><ul>
<li class="chapter" data-level="10.3.1" data-path="dplyr.html"><a href="dplyr.html#the-pipe-operator"><i class="fa fa-check"></i><b>10.3.1</b> The Pipe Operator</a></li>
</ul></li>
<li class="chapter" data-level="10.4" data-path="dplyr.html"><a href="dplyr.html#grouped-operations"><i class="fa fa-check"></i><b>10.4</b> Grouped Operations</a></li>
<li class="chapter" data-level="10.5" data-path="dplyr.html"><a href="dplyr.html#joins"><i class="fa fa-check"></i><b>10.5</b> Joins</a></li>
<li class="chapter" data-level="10.6" data-path="dplyr.html"><a href="dplyr.html#non-standard-evaluation-vs.standard-evaluation"><i class="fa fa-check"></i><b>10.6</b> Non-Standard Evaluation vs. Standard Evaluation</a><ul>
<li class="chapter" data-level="10.6.1" data-path="dplyr.html"><a href="dplyr.html#explicit-standard-evaluation"><i class="fa fa-check"></i><b>10.6.1</b> Explicit Standard Evaluation</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="dplyr.html"><a href="dplyr.html#resources-9"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="apis.html"><a href="apis.html"><i class="fa fa-check"></i><b>11</b> Accessing Web APIs</a><ul>
<li class="chapter" data-level="11.1" data-path="apis.html"><a href="apis.html#what-is-a-web-api"><i class="fa fa-check"></i><b>11.1</b> What is a Web API?</a></li>
<li class="chapter" data-level="11.2" data-path="apis.html"><a href="apis.html#restful-requests"><i class="fa fa-check"></i><b>11.2</b> RESTful Requests</a><ul>
<li class="chapter" data-level="11.2.1" data-path="apis.html"><a href="apis.html#uris"><i class="fa fa-check"></i><b>11.2.1</b> URIs</a></li>
<li class="chapter" data-level="11.2.2" data-path="apis.html"><a href="apis.html#http-verbs"><i class="fa fa-check"></i><b>11.2.2</b> HTTP Verbs</a></li>
</ul></li>
<li class="chapter" data-level="11.3" data-path="apis.html"><a href="apis.html#accessing-web-apis"><i class="fa fa-check"></i><b>11.3</b> Accessing Web APIs</a></li>
<li class="chapter" data-level="11.4" data-path="apis.html"><a href="apis.html#json"><i class="fa fa-check"></i><b>11.4</b> JSON Data</a><ul>
<li class="chapter" data-level="11.4.1" data-path="apis.html"><a href="apis.html#parsing-json"><i class="fa fa-check"></i><b>11.4.1</b> Parsing JSON</a></li>
<li class="chapter" data-level="11.4.2" data-path="apis.html"><a href="apis.html#flattening-data"><i class="fa fa-check"></i><b>11.4.2</b> Flattening Data</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="apis.html"><a href="apis.html#resources-10"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="r-markdown.html"><a href="r-markdown.html"><i class="fa fa-check"></i><b>12</b> R Markdown</a><ul>
<li class="chapter" data-level="12.1" data-path="r-markdown.html"><a href="r-markdown.html#r-markdown-and-rstudio"><i class="fa fa-check"></i><b>12.1</b> R Markdown and RStudio</a><ul>
<li class="chapter" data-level="12.1.1" data-path="r-markdown.html"><a href="r-markdown.html#creating-.rmd-files"><i class="fa fa-check"></i><b>12.1.1</b> Creating <code>.Rmd</code> Files</a></li>
<li class="chapter" data-level="12.1.2" data-path="r-markdown.html"><a href="r-markdown.html#rmd-content"><i class="fa fa-check"></i><b>12.1.2</b> <code>.Rmd</code> Content</a></li>
<li class="chapter" data-level="12.1.3" data-path="r-markdown.html"><a href="r-markdown.html#knitting-documents"><i class="fa fa-check"></i><b>12.1.3</b> Knitting Documents</a></li>
<li class="chapter" data-level="12.1.4" data-path="r-markdown.html"><a href="r-markdown.html#html"><i class="fa fa-check"></i><b>12.1.4</b> HTML</a></li>
</ul></li>
<li class="chapter" data-level="12.2" data-path="r-markdown.html"><a href="r-markdown.html#r-markdown-syntax"><i class="fa fa-check"></i><b>12.2</b> R Markdown Syntax</a><ul>
<li class="chapter" data-level="12.2.1" data-path="r-markdown.html"><a href="r-markdown.html#r-code-chunks"><i class="fa fa-check"></i><b>12.2.1</b> R Code Chunks</a></li>
<li class="chapter" data-level="12.2.2" data-path="r-markdown.html"><a href="r-markdown.html#inline-code"><i class="fa fa-check"></i><b>12.2.2</b> Inline Code</a></li>
</ul></li>
<li class="chapter" data-level="12.3" data-path="r-markdown.html"><a href="r-markdown.html#rendering-data"><i class="fa fa-check"></i><b>12.3</b> Rendering Data</a><ul>
<li class="chapter" data-level="12.3.1" data-path="r-markdown.html"><a href="r-markdown.html#rendering-strings"><i class="fa fa-check"></i><b>12.3.1</b> Rendering Strings</a></li>
<li class="chapter" data-level="12.3.2" data-path="r-markdown.html"><a href="r-markdown.html#rendering-lists"><i class="fa fa-check"></i><b>12.3.2</b> Rendering Lists</a></li>
<li class="chapter" data-level="12.3.3" data-path="r-markdown.html"><a href="r-markdown.html#rendering-tables"><i class="fa fa-check"></i><b>12.3.3</b> Rendering Tables</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="r-markdown.html"><a href="r-markdown.html#resources-11"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="ggplot2.html"><a href="ggplot2.html"><i class="fa fa-check"></i><b>13</b> The <code>gglot2</code> Library</a><ul>
<li class="chapter" data-level="13.1" data-path="ggplot2.html"><a href="ggplot2.html#a-grammar-of-graphics"><i class="fa fa-check"></i><b>13.1</b> A Grammar of Graphics</a></li>
<li class="chapter" data-level="13.2" data-path="ggplot2.html"><a href="ggplot2.html#basic-plotting-with-ggplot2"><i class="fa fa-check"></i><b>13.2</b> Basic Plotting with <code>ggplot2</code></a><ul>
<li class="chapter" data-level="13.2.1" data-path="ggplot2.html"><a href="ggplot2.html#ggplot2-library"><i class="fa fa-check"></i><b>13.2.1</b> <em>ggplot2</em> library</a></li>
<li class="chapter" data-level="13.2.2" data-path="ggplot2.html"><a href="ggplot2.html#mpg-data"><i class="fa fa-check"></i><b>13.2.2</b> <em>mpg</em> data</a></li>
<li class="chapter" data-level="13.2.3" data-path="ggplot2.html"><a href="ggplot2.html#our-first-ggplot"><i class="fa fa-check"></i><b>13.2.3</b> Our first ggplot</a></li>
<li class="chapter" data-level="13.2.4" data-path="ggplot2.html"><a href="ggplot2.html#aesthetic-mappings"><i class="fa fa-check"></i><b>13.2.4</b> Aesthetic Mappings</a></li>
</ul></li>
<li class="chapter" data-level="13.3" data-path="ggplot2.html"><a href="ggplot2.html#complex-plots"><i class="fa fa-check"></i><b>13.3</b> Complex Plots</a><ul>
<li class="chapter" data-level="13.3.1" data-path="ggplot2.html"><a href="ggplot2.html#specifying-geometry"><i class="fa fa-check"></i><b>13.3.1</b> Specifying Geometry</a></li>
<li class="chapter" data-level="13.3.2" data-path="ggplot2.html"><a href="ggplot2.html#styling-with-scales"><i class="fa fa-check"></i><b>13.3.2</b> Styling with Scales</a></li>
<li class="chapter" data-level="13.3.3" data-path="ggplot2.html"><a href="ggplot2.html#coordinate-systems"><i class="fa fa-check"></i><b>13.3.3</b> Coordinate Systems</a></li>
<li class="chapter" data-level="13.3.4" data-path="ggplot2.html"><a href="ggplot2.html#facets"><i class="fa fa-check"></i><b>13.3.4</b> Facets</a></li>
<li class="chapter" data-level="13.3.5" data-path="ggplot2.html"><a href="ggplot2.html#labels-annotations"><i class="fa fa-check"></i><b>13.3.5</b> Labels & Annotations</a></li>
</ul></li>
<li class="chapter" data-level="13.4" data-path="ggplot2.html"><a href="ggplot2.html#plotting-in-scripts"><i class="fa fa-check"></i><b>13.4</b> Plotting in Scripts</a></li>
<li class="chapter" data-level="13.5" data-path="ggplot2.html"><a href="ggplot2.html#other-visualization-libraries"><i class="fa fa-check"></i><b>13.5</b> Other Visualization Libraries</a></li>
<li class="chapter" data-level="" data-path="ggplot2.html"><a href="ggplot2.html#resources-12"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="git-branches.html"><a href="git-branches.html"><i class="fa fa-check"></i><b>14</b> Git Branches</a><ul>
<li class="chapter" data-level="14.1" data-path="git-branches.html"><a href="git-branches.html#git-branches-1"><i class="fa fa-check"></i><b>14.1</b> Git Branches</a></li>
<li class="chapter" data-level="14.2" data-path="git-branches.html"><a href="git-branches.html#merging"><i class="fa fa-check"></i><b>14.2</b> Merging</a><ul>
<li class="chapter" data-level="14.2.1" data-path="git-branches.html"><a href="git-branches.html#merge-conflicts"><i class="fa fa-check"></i><b>14.2.1</b> Merge Conflicts</a></li>
</ul></li>
<li class="chapter" data-level="14.3" data-path="git-branches.html"><a href="git-branches.html#undoing-changes"><i class="fa fa-check"></i><b>14.3</b> Undoing Changes</a></li>
<li class="chapter" data-level="14.4" data-path="git-branches.html"><a href="git-branches.html#github-and-branches"><i class="fa fa-check"></i><b>14.4</b> GitHub and Branches</a><ul>
<li class="chapter" data-level="14.4.1" data-path="git-branches.html"><a href="git-branches.html#github-pages"><i class="fa fa-check"></i><b>14.4.1</b> GitHub Pages</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="git-branches.html"><a href="git-branches.html#resources-13"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="git-collaboration.html"><a href="git-collaboration.html"><i class="fa fa-check"></i><b>15</b> Git Collaboration</a><ul>
<li class="chapter" data-level="15.1" data-path="git-collaboration.html"><a href="git-collaboration.html#centralized-workflow"><i class="fa fa-check"></i><b>15.1</b> Centralized Workflow</a></li>
<li class="chapter" data-level="15.2" data-path="git-collaboration.html"><a href="git-collaboration.html#feature-branch-workflow"><i class="fa fa-check"></i><b>15.2</b> Feature Branch Workflow</a></li>
<li class="chapter" data-level="15.3" data-path="git-collaboration.html"><a href="git-collaboration.html#forking-workflow"><i class="fa fa-check"></i><b>15.3</b> Forking Workflow</a><ul>
<li class="chapter" data-level="15.3.1" data-path="git-collaboration.html"><a href="git-collaboration.html#pull-requests"><i class="fa fa-check"></i><b>15.3.1</b> Pull Requests</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="git-collaboration.html"><a href="git-collaboration.html#resources-14"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="16" data-path="shiny.html"><a href="shiny.html"><i class="fa fa-check"></i><b>16</b> The <code>shiny</code> Framework</a><ul>
<li class="chapter" data-level="16.1" data-path="shiny.html"><a href="shiny.html#creating-shiny-apps"><i class="fa fa-check"></i><b>16.1</b> Creating Shiny Apps</a><ul>
<li class="chapter" data-level="16.1.1" data-path="shiny.html"><a href="shiny.html#application-structure"><i class="fa fa-check"></i><b>16.1.1</b> Application Structure</a></li>
<li class="chapter" data-level="16.1.2" data-path="shiny.html"><a href="shiny.html#the-ui"><i class="fa fa-check"></i><b>16.1.2</b> The UI</a></li>
<li class="chapter" data-level="16.1.3" data-path="shiny.html"><a href="shiny.html#the-server"><i class="fa fa-check"></i><b>16.1.3</b> The Server</a></li>
</ul></li>
<li class="chapter" data-level="16.2" data-path="shiny.html"><a href="shiny.html#publishing-shiny-apps"><i class="fa fa-check"></i><b>16.2</b> Publishing Shiny Apps</a></li>
<li class="chapter" data-level="" data-path="shiny.html"><a href="shiny.html#resources-15"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="appendix"><span><b>Special Topics</b></span></li>
<li class="chapter" data-level="A" data-path="plotly.html"><a href="plotly.html"><i class="fa fa-check"></i><b>A</b> Plotly</a><ul>
<li class="chapter" data-level="A.1" data-path="plotly.html"><a href="plotly.html#getting-started"><i class="fa fa-check"></i><b>A.1</b> Getting Started</a></li>
<li class="chapter" data-level="A.2" data-path="plotly.html"><a href="plotly.html#basic-charts"><i class="fa fa-check"></i><b>A.2</b> Basic Charts</a></li>
<li class="chapter" data-level="A.3" data-path="plotly.html"><a href="plotly.html#layout"><i class="fa fa-check"></i><b>A.3</b> Layout</a></li>
<li class="chapter" data-level="A.4" data-path="plotly.html"><a href="plotly.html#hovers"><i class="fa fa-check"></i><b>A.4</b> Hovers</a></li>
<li class="chapter" data-level="" data-path="plotly.html"><a href="plotly.html#resources-16"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<li class="chapter" data-level="B" data-path="control-structures.html"><a href="control-structures.html"><i class="fa fa-check"></i><b>B</b> R Language Control Structures</a><ul>
<li class="chapter" data-level="B.1" data-path="control-structures.html"><a href="control-structures.html#loops"><i class="fa fa-check"></i><b>B.1</b> Loops</a><ul>
<li class="chapter" data-level="B.1.1" data-path="control-structures.html"><a href="control-structures.html#for-loop"><i class="fa fa-check"></i><b>B.1.1</b> For Loop</a></li>
<li class="chapter" data-level="B.1.2" data-path="control-structures.html"><a href="control-structures.html#while-loop"><i class="fa fa-check"></i><b>B.1.2</b> While-loop</a></li>
<li class="chapter" data-level="B.1.3" data-path="control-structures.html"><a href="control-structures.html#repeat-loop"><i class="fa fa-check"></i><b>B.1.3</b> repeat-loop</a></li>
<li class="chapter" data-level="B.1.4" data-path="control-structures.html"><a href="control-structures.html#leaving-early-break-and-next"><i class="fa fa-check"></i><b>B.1.4</b> Leaving Early: <code>break</code> and <code>next</code></a></li>
<li class="chapter" data-level="B.1.5" data-path="control-structures.html"><a href="control-structures.html#when-not-to-use-loops-in-r"><i class="fa fa-check"></i><b>B.1.5</b> When (Not) To Use Loops In R?</a></li>
</ul></li>
<li class="chapter" data-level="B.2" data-path="control-structures.html"><a href="control-structures.html#more-about-if-and-else"><i class="fa fa-check"></i><b>B.2</b> More about <code>if</code> and <code>else</code></a><ul>
<li class="chapter" data-level="B.2.1" data-path="control-structures.html"><a href="control-structures.html#where-to-put-else"><i class="fa fa-check"></i><b>B.2.1</b> Where To Put Else</a></li>
<li class="chapter" data-level="B.2.2" data-path="control-structures.html"><a href="control-structures.html#return-value"><i class="fa fa-check"></i><b>B.2.2</b> Return Value</a></li>
</ul></li>
<li class="chapter" data-level="B.3" data-path="control-structures.html"><a href="control-structures.html#switch-choosing-between-multiple-conditions"><i class="fa fa-check"></i><b>B.3</b> <code>switch</code>: Choosing Between Multiple Conditions</a></li>
</ul></li>
<li class="chapter" data-level="C" data-path="data-tables.html"><a href="data-tables.html"><i class="fa fa-check"></i><b>C</b> Thinking Big: Data Tables</a><ul>
<li class="chapter" data-level="C.1" data-path="data-tables.html"><a href="data-tables.html#background-passing-by-value-and-passing-by-reference"><i class="fa fa-check"></i><b>C.1</b> Background: Passing By Value And Passing By Reference</a></li>
<li class="chapter" data-level="C.2" data-path="data-tables.html"><a href="data-tables.html#data-tables-introduction"><i class="fa fa-check"></i><b>C.2</b> Data Tables: Introduction</a><ul>
<li class="chapter" data-level="C.2.1" data-path="data-tables.html"><a href="data-tables.html#replacement-for-data-frames-sort-of"><i class="fa fa-check"></i><b>C.2.1</b> Replacement for Data Frames (Sort of)</a></li>
<li class="chapter" data-level="C.2.2" data-path="data-tables.html"><a href="data-tables.html#fast-reading-and-writing"><i class="fa fa-check"></i><b>C.2.2</b> Fast Reading and Writing</a></li>
</ul></li>
<li class="chapter" data-level="C.3" data-path="data-tables.html"><a href="data-tables.html#indexing-the-major-powerhorse-of-data-tables"><i class="fa fa-check"></i><b>C.3</b> Indexing: The Major Powerhorse of Data Tables</a><ul>
<li class="chapter" data-level="C.3.1" data-path="data-tables.html"><a href="data-tables.html#i-select-observations"><i class="fa fa-check"></i><b>C.3.1</b> i: Select Observations</a></li>
<li class="chapter" data-level="C.3.2" data-path="data-tables.html"><a href="data-tables.html#j-work-with-columns"><i class="fa fa-check"></i><b>C.3.2</b> j: Work with Columns</a></li>
<li class="chapter" data-level="C.3.3" data-path="data-tables.html"><a href="data-tables.html#group-in-by"><i class="fa fa-check"></i><b>C.3.3</b> Group in <code>by</code></a></li>
</ul></li>
<li class="chapter" data-level="C.4" data-path="data-tables.html"><a href="data-tables.html#create-variables-by-reference"><i class="fa fa-check"></i><b>C.4</b> <code>:=</code>–Create variables by reference</a></li>
<li class="chapter" data-level="C.5" data-path="data-tables.html"><a href="data-tables.html#keys"><i class="fa fa-check"></i><b>C.5</b> keys</a></li>
<li class="chapter" data-level="C.6" data-path="data-tables.html"><a href="data-tables.html#resources-17"><i class="fa fa-check"></i><b>C.6</b> Resources</a></li>
</ul></li>
<li class="chapter" data-level="D" data-path="remote-server.html"><a href="remote-server.html"><i class="fa fa-check"></i><b>D</b> Using Remote Server</a><ul>
<li class="chapter" data-level="D.1" data-path="remote-server.html"><a href="remote-server.html#server-setup"><i class="fa fa-check"></i><b>D.1</b> Server Setup</a></li>
<li class="chapter" data-level="D.2" data-path="remote-server.html"><a href="remote-server.html#connecting-to-the-remote-server"><i class="fa fa-check"></i><b>D.2</b> Connecting to the Remote Server</a></li>
<li class="chapter" data-level="D.3" data-path="remote-server.html"><a href="remote-server.html#copying-files"><i class="fa fa-check"></i><b>D.3</b> Copying Files</a><ul>
<li class="chapter" data-level="D.3.1" data-path="remote-server.html"><a href="remote-server.html#scp"><i class="fa fa-check"></i><b>D.3.1</b> scp</a></li>
<li class="chapter" data-level="D.3.2" data-path="remote-server.html"><a href="remote-server.html#rsync"><i class="fa fa-check"></i><b>D.3.2</b> rsync</a></li>
<li class="chapter" data-level="D.3.3" data-path="remote-server.html"><a href="remote-server.html#graphical-frontends"><i class="fa fa-check"></i><b>D.3.3</b> Graphical Frontends</a></li>
<li class="chapter" data-level="D.3.4" data-path="remote-server.html"><a href="remote-server.html#remote-editing"><i class="fa fa-check"></i><b>D.3.4</b> Remote Editing</a></li>
</ul></li>
<li class="chapter" data-level="D.4" data-path="remote-server.html"><a href="remote-server.html#r-and-rscript"><i class="fa fa-check"></i><b>D.4</b> R and Rscript</a><ul>
<li class="chapter" data-level="D.4.1" data-path="remote-server.html"><a href="remote-server.html#graphics-output-with-no-gui"><i class="fa fa-check"></i><b>D.4.1</b> Graphics Output with No GUI</a></li>
</ul></li>
<li class="chapter" data-level="D.5" data-path="remote-server.html"><a href="remote-server.html#life-on-server"><i class="fa fa-check"></i><b>D.5</b> Life on Server</a><ul>
<li class="chapter" data-level="D.5.1" data-path="remote-server.html"><a href="remote-server.html#be-social"><i class="fa fa-check"></i><b>D.5.1</b> Be Social!</a></li>
<li class="chapter" data-level="D.5.2" data-path="remote-server.html"><a href="remote-server.html#useful-things-to-do"><i class="fa fa-check"></i><b>D.5.2</b> Useful Things to Do</a></li>
<li class="chapter" data-level="D.5.3" data-path="remote-server.html"><a href="remote-server.html#permissions-and-ownership"><i class="fa fa-check"></i><b>D.5.3</b> Permissions and ownership</a></li>
<li class="chapter" data-level="D.5.4" data-path="remote-server.html"><a href="remote-server.html#more-than-one-connection"><i class="fa fa-check"></i><b>D.5.4</b> More than One Connection</a></li>
</ul></li>
<li class="chapter" data-level="D.6" data-path="remote-server.html"><a href="remote-server.html#advanced-usage"><i class="fa fa-check"></i><b>D.6</b> Advanced Usage</a><ul>
<li class="chapter" data-level="D.6.1" data-path="remote-server.html"><a href="remote-server.html#ssh-keys-.sshconfig"><i class="fa fa-check"></i><b>D.6.1</b> ssh keys, .ssh/config</a></li>
<li class="chapter" data-level="D.6.2" data-path="remote-server.html"><a href="remote-server.html#more-about-command-line-pipes-and-shell-patterns"><i class="fa fa-check"></i><b>D.6.2</b> More about command line: pipes and shell patterns</a></li>
<li class="chapter" data-level="D.6.3" data-path="remote-server.html"><a href="remote-server.html#running-rscript-in-ssh-session"><i class="fa fa-check"></i><b>D.6.3</b> Running RScript in ssh Session</a></li>
</ul></li>
</ul></li>
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<div id="r-markdown" class="section level1">
<h1><span class="header-section-number">Chapter 12</span> R Markdown</h1>
<p>R Markdown is a package that supports using <code>R</code> to dynamically create <em>documents</em>, such as websites (<code>.html</code> files), reports (<code>.pdf</code> files), slideshows (using <code>ioslides</code> or <code>slidy</code>), and even interactive web apps (using <code>shiny</code>).</p>
<p>As you may have guessed, R Markdown does this by providing the ability to blend Markdown syntax and <code>R</code> code so that, when executed, scripts will automatically inject your code results into a formatted document. The ability to automatically generate reports and documents from a computer script eliminates the need to manually update the <em>results</em> of a data analysis project, enabling you to more effectively share the <em>information</em> that you’ve produced from your data. In this chapter, you’ll learn the fundamentals of the RMarkdown library to create well-formatted documents that combine analysis and reporting.</p>
<div id="r-markdown-and-rstudio" class="section level2">
<h2><span class="header-section-number">12.1</span> R Markdown and RStudio</h2>
<p>R Markdown documents are created from a combination of two libraries: <code>rmarkdown</code> (which process the markdown and generates the output) and <code>knitr</code> (which runs R code and produces Markdown-like output). These packages are already included in RStudio, which provides built-in support for creating and viewing R Markdown documents.</p>
<div id="creating-.rmd-files" class="section level3">
<h3><span class="header-section-number">12.1.1</span> Creating <code>.Rmd</code> Files</h3>
<p>The easiest way to begin a new R-Markdown document in RStudio is to use the <strong>File > New File > R Markdown</strong> menu option:</p>
<div class="figure">
<img src="img/r-markdown/new-file.png" title="new R-Markdown document menu" alt="Create a new R Markdown document in RStudio." />
<p class="caption">Create a new R Markdown document in RStudio.</p>
</div>
<p>RStudio will then prompt you to provide some additional details abour what kind of R Markdown document you want. In particular, you will need to choose a default <em>document type</em> and <em>output format</em>. You can also provide a title and author information which will be included in the document. This chapter will focus on creating HTML documents (websites; the default format)—other formats require the installation of additional software.</p>
<div class="figure">
<img src="img/r-markdown/document-type.png" title="specify document type prompt" alt="Specify document type." />
<p class="caption">Specify document type.</p>
</div>
<p>Once you’ve chosen <em>R Markdown</em> as your desired file type, you’ll be prompted to choose a default <em>document type</em> and <em>output format</em> that you would like to create. In this module, we’ll discuss creating HTML documents (websites).</p>
<p>Once you’ve chosen your desired document type and output format, RStudio will open up a new script file for you. The file contains some example code for you.</p>
</div>
<div id="rmd-content" class="section level3">
<h3><span class="header-section-number">12.1.2</span> <code>.Rmd</code> Content</h3>
<p>At the top of the file is some text that has the format:</p>
<div class="sourceCode" id="cb160"><pre class="sourceCode yaml"><code class="sourceCode yaml"><a class="sourceLine" id="cb160-1" data-line-number="1"><span class="ot">---</span></a>
<a class="sourceLine" id="cb160-2" data-line-number="2"><span class="fu">title:</span><span class="at"> </span><span class="st">"Example"</span></a>
<a class="sourceLine" id="cb160-3" data-line-number="3"><span class="fu">author:</span><span class="at"> </span><span class="st">"YOUR NAME HERE"</span></a>
<a class="sourceLine" id="cb160-4" data-line-number="4"><span class="fu">date:</span><span class="at"> </span><span class="st">"1/30/2017"</span></a>
<a class="sourceLine" id="cb160-5" data-line-number="5"><span class="fu">output:</span><span class="at"> html_document</span></a>
<a class="sourceLine" id="cb160-6" data-line-number="6"><span class="ot">---</span></a></code></pre></div>
<p>This is the document “header” information, which tells R Markdown details about the file and how the file should be processed. For example, the <code>title</code>, <code>author</code>, and <code>date</code> will automatically be added to the top of your document. You can include additional information as well, such as <a href="http://rmarkdown.rstudio.com/html_document_format.html">whether there should be a table of contents</a> or even <a href="http://rmarkdown.rstudio.com/developer_parameterized_reports.html">variable defaults</a>.</p>
<ul>
<li>The header is written in <a href="https://en.wikipedia.org/wiki/YAML">YAML</a> format, which is yet another way of formatting structured data similar to <code>.csv</code> or JSON (in fact, YAML is a superset of JSON and can represent the same data structure, just using indentation and dashes instead of braces and commas).</li>
</ul>
<p>Below the header, you will find two types of content:</p>
<ul>
<li><strong>Markdown</strong>: normal Markdown text like you learned in <a href="markdown.html#markdown">Chapter 3</a>. For example, you can use two pound symbols (<code>##</code>) for a second-level heading.</li>
<li><strong>Code Chunks</strong>: These are segments (chunks) of R code that look like normal code block elements (using <code>```</code>), but with an extra <code>{r}</code> immediately after the opening backticks.</li>
</ul>
<p>R Markdown will be able to execute the R code you include in code chunks, and render that output <em>in your Markdown</em>. More on this <a href="r-markdown.html#r-markdown-syntax">below</a>.</p>
<p class="alert alert-warning">
<strong>Important</strong> This file should be saved with the extension <strong><code>.Rmd</code></strong> (for “R Markdown”), which tells the computer and RStudio that the document contains Markdown content with embedded <code>R</code> code.
</p>
</div>
<div id="knitting-documents" class="section level3">
<h3><span class="header-section-number">12.1.3</span> Knitting Documents</h3>
<p>RStudio provides an easy interface to compile your <code>.Rmd</code> source code into an actual document (a process called <strong>“knitting”</strong>). Simply click the <strong>Knit</strong> button at the top of the script panel:</p>
<div class="figure">
<img src="img/r-markdown/knit-button.png" title="knit button location" alt="RStudio’s Knit button" />
<p class="caption">RStudio’s Knit button</p>
</div>
<p>This will generate the document (in the same directory as your <code>.Rmd</code> file), as well as open up a preview window in RStudio.</p>
<p>While it is easy to generate such documents, the knitting process can make it hard to debug errors in your <code>R</code> code (whether syntax or logical), in part because the output may or may not show up in the document! We suggest that you write complex <code>R</code> code in another script and then <code>source()</code> that script into your <code>.Rmd</code> file for use the the output. This makes it possible to test your data processing work outside of the knit application, as well as <em>separates the concerns</em> of the data and its representation—which is good programming practice.</p>
<p>Nevertheless, you should still be sure and knit your document frequently, paying close attention to any errors that appear in the console.</p>
<p class="alert alert-info">
<em>Pro-tip</em>: If you’re having trouble finding your error, a good strategy is to systematically remove segments of your code and attempt to re-knit the document. This will help you identify the problematic syntax.
</p>
</div>
<div id="html" class="section level3">
<h3><span class="header-section-number">12.1.4</span> HTML</h3>
<p>Assuming that you’ve chosen HTML as your desired output type, RStudio will knit your <code>.Rmd</code> into a <code>.html</code> file. HTML stands for <em><strong>H</strong>yper<strong>T</strong>ext <strong>M</strong>arkup <strong>L</strong>anguage</em> and, like Markdown, is a syntax for describing the structure and formatting of content (though HTML is <strong>far</strong> more extensive and detailed). In particular, HTML is a markup language that can be automatically rendered by web browsers, and thus is the language used to create web pages. As such, the <code>.html</code> files you create can be put online as web pages for others to view—you will learn how to do this in a future chapter. For now, you can open a <code>.html</code> file in any browser (such as by double-clicking on the file) to see the content outside of RStudio!</p>
<ul>
<li>As it turns out, it’s quite simple to use GitHub to host publicly available webpages (like the <code>.html</code> files you create with RMarkdown). But, this will require learning a bit more about <code>git</code> and GitHub. For instructions on publishing your <code>.html</code> files as web-pages, see <a href="git-branches.html#git-branches">chapter 14</a>.</li>
</ul>
</div>
</div>
<div id="r-markdown-syntax" class="section level2">
<h2><span class="header-section-number">12.2</span> R Markdown Syntax</h2>
<p>What makes R Markdown distinct from simple Markdown code is the ability to actually <em>execute your <code>R</code> code and include the output directly in the document</em>. <code>R</code> code can be executed and included in the document in blocks of code, or even inline in the document!</p>
<div id="r-code-chunks" class="section level3">
<h3><span class="header-section-number">12.2.1</span> R Code Chunks</h3>
<p>Code that is to be executed (rather than simply displayed as formatted text) is called a <strong>code chunk</strong>. To specify a code chunk, you need to include <strong><code>{r}</code></strong> immediately after the backticks that start the code block (the <code>```</code>). For example:</p>
<pre class="rmd"><code>Write normal **markdown** out here, then create a code block:
```{r}
# Execute R code in here
x <- 201
```
Back to writing _markdown_ out here.</code></pre>
<p>Note that by default, the code chunk will <em>render</em> any raw expressions (e.g., <code>x</code>)—just like you would see in the console if you selected all the code in the chunk and used <code>ctrl-enter</code> to execute it.</p>
<p>It is also possible to specify additional configuration <strong>options</strong> by including a comma-separate list of named arguments (like you’ve done with lists and functions) inside the curly braces following the <code>r</code>:</p>
<pre class="rmd"><code>```{r options_example, echo=FALSE, message=TRUE}
# a code chunk named "options_example", with parameter `echo` assigned FALSE
# and parameter `message` assigned TRUE
# Would execute R code in here
```</code></pre>
<ul>
<li>The first “argument” (<code>options_example</code>) is a “name” for the chunk, and the following are named arguments for the options. Chunks should be named as a variable or function, based on what code is being executed and/or rendered by the chunk. It’s always a good idea to name individual code chunks as a form of documentation.</li>
</ul>
<p>There are <a href="https://yihui.name/knitr/options/">many options</a> for creating code chunks (see also the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">reference</a>). However some of the most useful ones have to do with how the code is outputted in the the document. These include:</p>
<ul>
<li><strong><code>echo</code></strong> indicates whether you want the <em>R code itself</em> to be displayed in the document (e.g., if you want readers to be able to see your work and reproduce your calculations and analysis). Value is either <code>TRUE</code> (do display; the default) or <code>FALSE</code> (do not display).</li>
<li><strong><code>message</code></strong> indicates whether you want any messages generated by the code to be displayed. This includes print statements! Value is either <code>TRUE</code> (do display; the default) or <code>FALSE</code> (do not display).</li>
</ul>
<p>If you only want to <em>show</em> your <code>R</code> code (and not <em>evaluate</em> it), you can alternatively use a standard Markdown codeblock that indicates the <code>r</code> language (<code>```r</code>, <em>not</em> <code>```{r}</code>), or set the <code>eval</code> option to <code>FALSE</code>.</p>
</div>
<div id="inline-code" class="section level3">
<h3><span class="header-section-number">12.2.2</span> Inline Code</h3>
<p>In addition to creating distinct code blocks, you may want to execute R code <em>inline</em> with the rest of your text. This empowers you to <strong>reference a variable</strong> from your code-chunk in a section of Markdown—injected that variable into the text you have written. This allows you to easily include a specific result inside a paragraph of text. So if the computation changes, re-knitting your document will update the values inside the text without any further work needed.</p>
<p>As with code blocks, you’ll follow the Markdown convention of using single backticks (<strong><code>`</code></strong>), but put the letter <strong><code>r</code></strong> immediately after the first backtick. For example:</p>
<!-- RMarkdown doesn't provide built-in escaping. See https://stackoverflow.com/q/20409172 for
details on the workaround. -->
<div class="sourceCode" id="cb163"><pre class="sourceCode markdown"><code class="sourceCode markdown"><a class="sourceLine" id="cb163-1" data-line-number="1">To calculate 3 + 4 inside some text, we can use <span class="bn">`r 3 + 4`</span> right in the _middle_.</a></code></pre></div>
<p>When you knit the text above, the <code>`r 3 + 4`</code> would be replaced with the number <code>7</code>.</p>
<p class="alert alert-info">
Note you can also reference values computed in the code blocks preceding your inline code; it is <strong>best practice</strong> to do your calculations in a code block (with <code>echo=FALSE</code>), save the result in a variable, and then simply inline that variable with e.g., <code>`r my.variable`</code>.
</p>
</div>
</div>
<div id="rendering-data" class="section level2">
<h2><span class="header-section-number">12.3</span> Rendering Data</h2>
<p>R Markdown’s code chunks let you perform data analysis directly in your document, but often you will want to include more complex data output. This section discusses a few tips for specifying dynamic, complex output to render using R Markdown.</p>
<div id="rendering-strings" class="section level3">
<h3><span class="header-section-number">12.3.1</span> Rendering Strings</h3>
<p>If you experiment with knitting R Markdown, you will quickly notice that using <code>print()</code> will generate a code block with content that looks like a printed vector:</p>
<pre class="rmd"><code>```{r echo=FALSE}
print("Hello world")
```</code></pre>
<pre><code>## [1] "Hello world"</code></pre>
<p>For this reason, you usually want to have the code block generate a string that you save in a variable, which you can then display with an inline expression (e.g., on its own line):</p>
<pre class="rmd"><code>```{r echo=FALSE}
msg <- "Hello world"
```
Below is the message to see:
`r msg`</code></pre>
<p>Note that any Markdown syntax included in the variable (e.g., if you had <code>msg <- "**Hello** world"</code>) will be rendered as well—the <code>`r msg `</code>is replaced by the value of the expression just as if you had typed that Markdown in directly. This allows you to even include dynamic styling if you construct a “Markdown string” out of your data.</p>
<p>Alternatively, you can use as <a href="https://yihui.name/knitr/options/#text-results"><code>results</code></a> option of <code>'asis'</code>, which will cause the “output” to be rendered directly into the markdown. When combined with the <a href="https://www.rdocumentation.org/packages/base/versions/3.4.3/topics/cat"><code>cat()</code></a> function (which con<strong>cat</strong>enates content without specifying additional information like vector position), you can make a code chunk effectively render a specific string:</p>
<pre class="rmd"><code>```{r results='asis', echo=FALSE}
cat("Hello world")
```</code></pre>
</div>
<div id="rendering-lists" class="section level3">
<h3><span class="header-section-number">12.3.2</span> Rendering Lists</h3>
<p>Because outputted strings render any Markdown they contain, it’s possible to specify complex Markdown such as <em>lists</em> by constructing these strings to contain the <code>-</code> symbols utilized (note that each item will need to be separated by a line break or a <code>\n</code> character):</p>
<pre class="rmd"><code>```{r echo=FALSE}
markdown.list <- "
- Lions
- Tigers
- Bears
"
```
`r markdown.list`</code></pre>
<p>Would output a list that looks like:</p>
<div class="list-condensed">
<ul>
<li>Lions</li>
<li>Tigers</li>
<li>Bears</li>
</ul>
</div>
<p>Combined with the vectorized <code>paste()</code> function, it’s to easily convert vectors into Markdown lists that can be rendered</p>
<pre class="rmd"><code>```{r echo=FALSE}
animals <- c("Lions", "Tigers", "Bears")
# paste a `-` in front of each, then cat the items with newlines between
markdown.list <- paste(paste('-',animals), collapse='\n')
```
`r markdown.list`</code></pre>
<p>And of course, the contents of the vector (e.g., the text <code>"Lions"</code>) could easily have additional Markdown syntax syntax to include bold, italic, or hyperlinked text.</p>
<ul>
<li>Creating a “helper function” to do this conversion is perfectly reasonable; or see libraries such as <a href="http://rapporter.github.io/pander/"><code>pander</code></a> which defines a number of such functions.</li>
</ul>
</div>
<div id="rendering-tables" class="section level3">
<h3><span class="header-section-number">12.3.3</span> Rendering Tables</h3>
<p>Because data frames are so central to programming with R, R Markdown includes capabilities to easily render data frames as Markdown <em>tables</em> via the <a href="https://www.rdocumentation.org/packages/knitr/versions/1.19/topics/kable"><strong><code>knitr::kable()</code></strong></a> function. This function takes as an argument the data frame you wish to render, and it will automatically convert that value into a Markdown table:</p>
<pre class="rmd"><code>```{r echo=FALSE}
library(knitr) # make sure you load this library (once per doc)
# make a data frame
letters <- c("a", "b", "c")
numbers <- 1:3
df <- data.frame(letters = letters, numbers = numbers)
# render the table
kable(df)
```</code></pre>
<ul>
<li><code>kable()</code> supports a number of other arguments that can be used to customize how it outputs a table.</li>
<li>And of courrse, if the values in the dataframe are strings that contain Markdown syntax (e.g., bold, itaic, or hyperlinks), they will be rendered as such in the table!</li>
</ul>
<p>So while you may need to do a little bit of work to manually generate the Markdown syntax, it is possible to dynamically produce complex documents based on dynamic data sources</p>
</div>
</div>
<div id="resources-11" class="section level2 unnumbered">
<h2>Resources</h2>
<ul>
<li><a href="http://rmarkdown.rstudio.com/">R Markdown Homepage</a></li>
<li><a href="https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf">R Markdown Cheatsheet</a> (really useful!)</li>
<li><a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference</a> (really useful!)</li>
<li><a href="https://yihui.name/knitr/"><code>knitr</code></a></li>
</ul>
</div>
</div>
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