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<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>
</ul></li>
<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>
<li class="chapter" data-level="" data-path="git-basics.html"><a href="git-basics.html#resources-3"><i class="fa fa-check"></i>Resources</a></li>
</ul></li>
<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 &amp; 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>
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<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>
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<div id="functions" class="section level1">
<h1><span class="header-section-number">Chapter 6</span> Functions</h1>
<p>This chapter will explore how to use <strong>functions</strong> in R to perform advanced capabilities and actually ask questions about data. After considering a function in an abstract sense, it will discuss using built-in R functions, accessing additional functions by loading R packages, and writing your own functions.</p>
<div id="what-are-functions" class="section level2">
<h2><span class="header-section-number">6.1</span> What are Functions?</h2>
<p>In a broad sense, a <strong>function</strong> is a named sequence of instructions
(lines of code) that you may want to perform one or more times
throughout a program. They provide a way of <em>encapsulating</em> multiple
instructions into a single “unit” that can be used in a variety of
different contexts. So rather than needing to repeatedly write down all
the individual instructions for “make a sandwich” every time you’re
hungry, you can define a <code>make_sandwich()</code> function once and then just
<strong>call</strong> (execute) that function when you want to perform those steps.
Typically, functions also accept <em>inputs</em> so you can make the things
slightly differently from time to time. For instance, sometimes you may
want to call <code>make_sandwich(cheese)</code> while another time <code>make_sandwich(chicken)</code>.</p>
<p>In addition to grouping instructions, functions in programming languages
also allow to model the mathematical definition of function,
i.e. perform certain operations on a number of inputs that lead to an
<em>output</em>. For instance, look at the
function <code>max()</code> that finds the largest value among numbers:</p>
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw">max</span>(<span class="dv">1</span>,<span class="dv">2</span>,<span class="dv">3</span>)  <span class="co"># 3</span></a></code></pre></div>
<p>The inputs are numbers <code>1</code>, <code>2</code>, and <code>3</code> in parenthesis, usually called
<strong>arguments</strong> or <strong>parameters</strong>, and we say that these arguments are
<strong>passed</strong> to a function (like a football). We say that a function then
<strong>returns</strong> a value, number “3” in this example, which we can either
print or assign to a variable and use later.</p>
<p>Finally, the functions may also have <strong>side effects</strong>. An example case
is the <code>cat()</code> function that just prints it’s arguments. For instance,
in case of the following line of code</p>
<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" data-line-number="1"><span class="kw">cat</span>(<span class="st">&quot;The answer is&quot;</span>, <span class="dv">1</span><span class="op">+</span><span class="dv">1</span>, <span class="st">&quot;</span><span class="ch">\n</span><span class="st">&quot;</span>)</a></code></pre></div>
<p>we call function <code>cat()</code> with three arguments: <code>&quot;The answer is&quot;</code>, <code>2</code>
(note: <code>1+1</code> will be evaluated to 2),
and <code>&quot;\n&quot;</code> (the line break symbol). However, here we may not care about the return value but in the side effect—the message being printed on the screen.</p>
</div>
<div id="how-to-use-functions" class="section level2">
<h2><span class="header-section-number">6.2</span> How to Use Functions</h2>
<p>R functions are referred to by name (technically, they are values like
any other variable, just not atomic values). As in many programming
languages, we <strong>call</strong> a function by writing the name of the function
followed immediately (no space) by parentheses <code>()</code>. Sometimes this is
enough, for instance</p>
<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" data-line-number="1"><span class="kw">Sys.Date</span>()</a></code></pre></div>
<p>gives us the current date and that’s it.</p>
<p>But often we want the function to do something with our inputs. In this
case we put the <strong>arguments</strong> (inputs) inside the parenthesis, separated
by commas (<strong><code>,</code></strong>). Thus computer functions look just like
multi-variable mathematical functions, although usually with fancier names than <code>f()</code>.</p>
<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1"><span class="co"># call the sqrt() function, passing it 25 as an argument</span></a>
<a class="sourceLine" id="cb37-2" data-line-number="2"><span class="kw">sqrt</span>(<span class="dv">25</span>)  <span class="co"># 5, square root of 25</span></a>
<a class="sourceLine" id="cb37-3" data-line-number="3"></a>
<a class="sourceLine" id="cb37-4" data-line-number="4"><span class="co"># count number of characters in &quot;Hello world&quot; as an argument</span></a>
<a class="sourceLine" id="cb37-5" data-line-number="5"><span class="kw">nchar</span>(<span class="st">&quot;Hello world&quot;</span>)  <span class="co"># 11, note: space is a character too</span></a>
<a class="sourceLine" id="cb37-6" data-line-number="6"></a>
<a class="sourceLine" id="cb37-7" data-line-number="7"><span class="co"># call the min() function, pass it 1, 6/8, AND 4/3 as arguments</span></a>
<a class="sourceLine" id="cb37-8" data-line-number="8"><span class="co"># this is an example of a function that takes multiple args</span></a>
<a class="sourceLine" id="cb37-9" data-line-number="9"><span class="kw">min</span>(<span class="dv">1</span>, <span class="dv">6</span><span class="op">/</span><span class="dv">8</span>, <span class="dv">4</span><span class="op">/</span><span class="dv">3</span>)  <span class="co"># 0.75, (6/8 is the smallest value)</span></a></code></pre></div>
<p>To keep functions and ordinary variables distinct, we include empty parentheses <code>()</code> when referring to a function by name. This does not mean that the function takes no arguments, it is just a useful shorthand for indicating that something is a function.</p>
<p class="alert alert-info">
<strong>Note:</strong> You always need to supply the
parenthesis if you want to <em>call</em> the function (force it to do what it
is supposed to do). If you leave the parenthesis out, you get the
function definition printed on screen instead. So <code>cat()</code> is actually a <em>function call</em> while <code>cat</code> is the function. You can see that it is a function if you just print it as <code>print(cat)</code>.
However, we ignore this distinction here.
</p>
<p>If you call any of these functions interactively, R will display the <strong>returned value</strong> (the output) in the console. However, the computer is not able to “read” what is written in the console—that’s for humans to view! If you want the computer to be able to <em>use</em> a returned value, you will need to give that value a name so that the computer can refer to it. That is, you need to store the returned value in a variable:</p>
<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" data-line-number="1"><span class="co"># store min value in smallest.number variable</span></a>
<a class="sourceLine" id="cb38-2" data-line-number="2">smallest_number &lt;-<span class="st"> </span><span class="kw">min</span>(<span class="dv">1</span>, <span class="dv">6</span><span class="op">/</span><span class="dv">8</span>, <span class="dv">4</span><span class="op">/</span><span class="dv">3</span>)</a>
<a class="sourceLine" id="cb38-3" data-line-number="3"></a>
<a class="sourceLine" id="cb38-4" data-line-number="4"><span class="co"># we can then use the variable as normal, such as for a comparison</span></a>
<a class="sourceLine" id="cb38-5" data-line-number="5">min_is_big &lt;-<span class="st"> </span>smallest_number <span class="op">&gt;</span><span class="st"> </span><span class="dv">1</span>  <span class="co"># FALSE</span></a>
<a class="sourceLine" id="cb38-6" data-line-number="6"></a>
<a class="sourceLine" id="cb38-7" data-line-number="7"><span class="co"># we can also use functions directly when doing computations</span></a>
<a class="sourceLine" id="cb38-8" data-line-number="8">phi &lt;-<span class="st"> </span><span class="fl">.5</span> <span class="op">+</span><span class="st"> </span><span class="kw">sqrt</span>(<span class="dv">5</span>)<span class="op">/</span><span class="dv">2</span>  <span class="co"># 1.618...</span></a>
<a class="sourceLine" id="cb38-9" data-line-number="9"></a>
<a class="sourceLine" id="cb38-10" data-line-number="10"><span class="co"># we can even pass the result of a function as an argument to another!</span></a>
<a class="sourceLine" id="cb38-11" data-line-number="11"><span class="co"># watch out for where the parentheses close!</span></a>
<a class="sourceLine" id="cb38-12" data-line-number="12"><span class="kw">print</span>(<span class="kw">min</span>(<span class="fl">1.5</span>, <span class="kw">sqrt</span>(<span class="dv">3</span>)))  <span class="co"># prints 1.5</span></a></code></pre></div>
<ul>
<li>In the last example, the resulting <em>value</em> of the “inner” function
(e.g., <code>sqrt()</code>) is immediately used as an argument for the middle
function (i.e. <code>min()</code>), value of which is fed in turn to the outer
function <code>print()</code>. Because that value is used immediately, we don’t
have to assign it a separate variable name. It is known as an
<strong>anonymous variable</strong>.</li>
<li>note also that in the last example, we are solely interested in the
side effect of the <code>print()</code> function. It also returns it’s argument
(<code>min(1.5, sqrt(3))</code> here) but we do not store it in a variable.</li>
</ul>
<p>R functions take two types of arguments: <strong>positional arguments</strong> and
<strong>named arguments</strong>: the function has to know how to treat each of it’s
arguments. For instance, we can round number <em>e</em> to 3
digits by <code>round(2.718282, 3)</code>. But in order to do this, the <code>round()</code> function must know that <code>2.718282</code> is the number
and <code>3</code> is the requested number of digits, and not the other way around. It understands this because
it requires the number to be the first argument, and digits
the second argument. This approach works well in case of known small
number of inputs. However, this is not an option for functions with
<strong>variable number of arguments</strong>, such as <code>cat()</code>. <code>cat()</code> just prints
out all of it’s (potentially a large number of) inputs, except a limited number of special named
arguments. One of these is <code>sep</code>, the string to be placed between the other pieces
of output (by default just a space is printed). Note the difference in output
between</p>
<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1"><span class="kw">cat</span>(<span class="dv">1</span>, <span class="dv">2</span>, <span class="st">&quot;-&quot;</span>, <span class="st">&quot;</span><span class="ch">\n</span><span class="st">&quot;</span>)  <span class="co"># 1 2 - </span></a>
<a class="sourceLine" id="cb39-2" data-line-number="2"><span class="kw">cat</span>(<span class="dv">1</span>, <span class="dv">2</span>, <span class="dt">sep=</span><span class="st">&quot;-&quot;</span>, <span class="st">&quot;</span><span class="ch">\n</span><span class="st">&quot;</span>)  <span class="co"># 1-2-</span></a></code></pre></div>
<p>In the first case <code>cat()</code> prints <code>1</code>, <code>2</code>, <code>&quot;-&quot;</code>, and the line break
<code>&quot;\n&quot;</code>, all separated by a space. In the second case the name <code>sep</code>
ensures that <code>&quot;-&quot;</code> is not
printed out but instead treated as the separator between <code>1</code>, <code>2</code> and <code>&quot;\n&quot;</code>.</p>
</div>
<div id="built-in-r-functions" class="section level2">
<h2><span class="header-section-number">6.3</span> Built-in R Functions</h2>
<p>As you have likely noticed, R comes with a variety of functions that are built into the language. In the above example, we used the <code>print()</code> function to print a value to the console, the <code>min()</code> function to find the smallest number among the arguments, and the <code>sqrt()</code> function to take the square root of a number. Here is a <em>very</em> limited list of functions you can experiment with (or see a few more <a href="http://www.statmethods.net/management/functions.html">here</a>).</p>
<!-- TODO: Fix the formatting for this? -->
<table>
<colgroup>
<col width="20%" />
<col width="33%" />
<col width="46%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Function Name</th>
<th align="left">Description</th>
<th align="left">Example</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><code>sum(a,b,...)</code></td>
<td align="left">Calculates the sum of all input values</td>
<td align="left"><code>sum(1, 5)</code> returns <code>6</code></td>
</tr>
<tr class="even">
<td align="left"><code>round(x,digits)</code></td>
<td align="left">Rounds the first argument to the given number of digits</td>
<td align="left"><code>round(3.1415, 3)</code> returns <code>3.142</code></td>
</tr>
<tr class="odd">
<td align="left"><code>toupper(str)</code></td>
<td align="left">Returns the characters in uppercase</td>
<td align="left"><code>toupper(&quot;hi there&quot;)</code> returns <code>&quot;HI THERE&quot;</code></td>
</tr>
<tr class="even">
<td align="left"><code>paste(a,b,...)</code></td>
<td align="left"><em>Concatenate</em> (combine) characters into one value</td>
<td align="left"><code>paste(&quot;hi&quot;, &quot;there&quot;)</code> returns <code>&quot;hi there&quot;</code></td>
</tr>
<tr class="odd">
<td align="left"><code>nchar(str)</code></td>
<td align="left">Counts the number of characters in a string</td>
<td align="left"><code>nchar(&quot;hi there&quot;)</code> returns <code>8</code> (space is a character!)</td>
</tr>
<tr class="even">
<td align="left"><code>c(a,b,...)</code></td>
<td align="left"><em>Concatenate</em> (combine) multiple items into a <em>vector</em> (see <a href="vectors.html#vectors">chapter 7</a>)</td>
<td align="left"><code>c(1, 2)</code> returns <code>1, 2</code></td>
</tr>
<tr class="odd">
<td align="left"><code>seq(a,b)</code></td>
<td align="left">Return a sequence of numbers from a to b</td>
<td align="left"><code>seq(1, 5)</code> returns <code>1, 2, 3, 4, 5</code></td>
</tr>
</tbody>
</table>
<p>To learn more about any individual function, look them up in the R documentation by using <code>?FunctionName</code> account as described in the previous chapter.</p>
<!-- TODO: Make this a link to the chapter?? Why won't it work? -->
<p class="alert alert-info">
“Knowing” how to program in a language is to some extent simply “knowing” what provided functions are available in that language. Thus you should look around and become familiar with these functions… but <strong>do not</strong> feel that you need to memorize them! It’s enough to simply be aware “oh yeah, there was a function that sums up numbers”, and then be able to look up the name and argument for that function.
</p>
</div>
<div id="loading-functions" class="section level2">
<h2><span class="header-section-number">6.4</span> Loading Functions</h2>
<p>Although R comes with lots of built-in functions, you can always use
more! <strong>Packages</strong> (also known as <strong>libraries</strong>) are additional sets of
R functions (and data and variables) that are written and published by the R community. Because
many R users encounter the same data management/analysis challenges,
programmers are able to use these libraries and thus benefit from the
work of others (this is the amazing thing about the open-source
community—people solve problems and then make those solutions
available to others). Popular packages include <em>dplyr</em> for
manipulating data, <em>ggplot2</em> for visualizations, and <em>data.table</em> for
handling large datasets.</p>
<p>Most of the R packages <strong>do not</strong> ship with the R
software by default, and need to be downloaded (once) and then loaded
into your interpreter’s environment (each time you wish to use
them). While this may seem cumbersome, it is a necessary trade-off
between speed and size. R software would be huge and slow if it would
include <em>all</em> available packages.</p>
<p>Luckily, it is quite simple to install and load R packages from within
R. To do so, you’ll need to use the <em>built-in</em> R functions
<code>install.packages</code> and <code>library</code>. Below is an example of installing and
loading the <code>stringr</code> package (which contains many handy functions for working with character strings):</p>
<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1"><span class="co"># Install the `stringr` package. Only needs to be done once on your machine</span></a>
<a class="sourceLine" id="cb40-2" data-line-number="2"><span class="kw">install.packages</span>(<span class="st">&quot;stringr&quot;</span>)</a></code></pre></div>
<p class="alert alert-warning">
We stress here that you need to install each package only once per computer.
As installation may be slow and and resource-demanding, you <strong>should not
do it repeatedly inside your script!</strong>. Even more, if your script is
also run by other users on their computers, you should get their
explicit consent before installing additional software for them!
The easiest remedy is to solely rely on manual installation.
</p>
<p>Exactly the same syntax—<code>install.packages(&quot;stringr&quot;)</code>—is
also used for re-installing it. You may want to re-install it if a
newer version comes out, of if you upgrade your R and receive warnings
about the package being built under a previous version of R.</p>
<p>After installation, the easiest way to get access to the functions is by
<em>loading the package</em>:</p>
<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" data-line-number="1"><span class="co"># Load the package (make stringr() functions available in this R session/program)</span></a>
<a class="sourceLine" id="cb41-2" data-line-number="2"><span class="kw">library</span>(<span class="st">&quot;stringr&quot;</span>) <span class="co"># quotes optional here</span></a></code></pre></div>
<p>This makes all functions in the <em>stringr</em> package available for R (see <a href="https://cran.r-project.org/web/packages/stringr/stringr.pdf">the documentation</a> for a list of functions included with the <code>stringr</code> library). For
instance, if we want to pad the word “justice” from left with tildes to create a
width-10 string, we can do</p>
<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1"><span class="kw">str_pad</span>(<span class="st">&quot;justice&quot;</span>, <span class="dv">10</span>, <span class="st">&quot;left&quot;</span>, <span class="st">&quot;~&quot;</span>)  <span class="co"># &quot;~~~justice&quot;</span></a></code></pre></div>
<p>We can use <code>str_pad</code> function without any additional hassle because <code>library()</code> command made it
available.</p>
<p>This is an easy and popular approach. However, what happens if more than one package call a function by the same name? For
instance, many packages implement function <code>filter()</code>. In this case
the more recent package will <em>mask</em> the function as defined by the
previous package. You will also see related warnings when you load the
library. In case you want to use a masked
function you can write something like <code>package::function()</code> in order to
call it. For instance, we can do the example above with</p>
<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">stringr<span class="op">::</span><span class="kw">str_pad</span>(<span class="st">&quot;justice&quot;</span>, <span class="dv">10</span>, <span class="st">&quot;left&quot;</span>, <span class="st">&quot;~&quot;</span>)  <span class="co"># &quot;~~~justice&quot;</span></a></code></pre></div>
<p>This approach—specifying <em>namespace</em> in front of the
function—ensures we access the function in the right package. If
we call all functions in this way, we don’t even need to load the
package with <code>library()</code> command. This is the preferred approach if you
only need few functions from a large library.</p>
</div>
<div id="writing-functions" class="section level2">
<h2><span class="header-section-number">6.5</span> Writing Functions</h2>
<p>Even more exciting than loading other peoples’ functions is writing your
own. Any time you have a task that you may repeat throughout a
script—or sometimes when you just want to organize your code
better—it’s a good practice to write a function to perform that task. This will limit repetition and reduce the likelihood of errors as well as make things easier to read and understand (and thus identify flaws in your analysis).</p>
Functions are values like numbers and characters, so we use the <em>assignment
operator</em> (<strong><code>&lt;-</code></strong>) to store a function into a variable.<br />

<p class="alert alert-info">
Although “values” (more precisely <em>objects</em>), functions are not <a href="#basic-data-strucures">atomic
objects</a>. But they can still be stored and
manipulated in many ways like other objects.
</p>
<p><a href="http://style.tidyverse.org/functions.html">Tidyverse style guide</a> we
follow in this books suggests to use verbs as function names,
written in <strong>snake_case</strong> just like other variables.</p>
<p>The best way to understand the syntax for defining a function is to look at an example:</p>
<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="co"># A function named `make_full_name` that takes two arguments</span></a>
<a class="sourceLine" id="cb44-2" data-line-number="2"><span class="co"># and returns the &quot;full name&quot; made from them</span></a>
<a class="sourceLine" id="cb44-3" data-line-number="3">make_full_name &lt;-<span class="st"> </span><span class="cf">function</span>(first_name, last_name) {</a>
<a class="sourceLine" id="cb44-4" data-line-number="4">  <span class="co"># Function body: perform tasks in here</span></a>
<a class="sourceLine" id="cb44-5" data-line-number="5">  full_name &lt;-<span class="st"> </span><span class="kw">paste</span>(first_name, last_name)</a>
<a class="sourceLine" id="cb44-6" data-line-number="6">                           <span class="co"># paste joins first and last name into a</span></a>
<a class="sourceLine" id="cb44-7" data-line-number="7">                           <span class="co"># single string</span></a>
<a class="sourceLine" id="cb44-8" data-line-number="8">  <span class="co"># Return: what you want the function to output</span></a>
<a class="sourceLine" id="cb44-9" data-line-number="9">  <span class="kw">return</span>(full_name)</a>
<a class="sourceLine" id="cb44-10" data-line-number="10">}</a>
<a class="sourceLine" id="cb44-11" data-line-number="11"></a>
<a class="sourceLine" id="cb44-12" data-line-number="12"><span class="co"># Call the `make_full_name` function with the values &quot;Alice&quot; and &quot;Kim&quot;</span></a>
<a class="sourceLine" id="cb44-13" data-line-number="13">my_name &lt;-<span class="st"> </span><span class="kw">make_full_name</span>(<span class="st">&quot;Alice&quot;</span>, <span class="st">&quot;Kim&quot;</span>)  <span class="co"># &quot;Alice Kim&quot;</span></a></code></pre></div>
<p>Function definition contains several important pieces:</p>
<ul>
<li><p>The value assigned to the function variable uses the
syntax <code>function(....)</code> to indicate that you are creating a function
(as opposed to a number or character string).</p></li>
<li><p>If you want to feed your function with certain
inputs, these must be referred somehow inside of your function.
You list these names between the parentheses in the <code>function(....)</code>
declaration. These are called <strong>formal arguments</strong>. Formal arguments <em>will
contain</em> the values passed in when calling the function (called
<strong>actual arguments</strong>). For example, when we
call <code>make_full_name(&quot;Alice&quot;, &quot;Kim&quot;)</code>, the value of the first
actual argument (<code>&quot;Alice&quot;</code>) will be assigned to the first formal argument
(<code>first_name</code>), and the value of the second actual argument (<code>&quot;Kim&quot;</code>) will
be assigned to the second formal argument (<code>last_name</code>). Inside the
function’s body, both of these formal arguments behave exactly as
ordinary variables with values “Alice” and “Kim” respectively.</p>
<p>Importantly, we could have made the formal argument names anything
we wanted (<code>name_first</code>, <code>xyz</code>, etc.), just as long as we then use
<em>these formal argument names</em> to refer to the argument while inside
the function.</p>
<p>Moreover, the formal argument names <em>only apply</em> while inside the function. You can think of them like “nicknames” for the values. The variables <code>first_name</code>, <code>last_name</code>, and <code>full_name</code> only exist within this particular function.</p></li>
<li><p><strong>Body</strong>: The body of the function is a <strong>block</strong> of code that falls between curly braces <strong><code>{}</code></strong> (a “block” is represented by curly braces surrounding code statements). Note that cleanest style is to put the opening <code>{</code> immediately after the arguments list, and the closing <code>}</code> on its own line.</p>
<p>The function body specifies all the instructions (lines of code)
that your function will perform. A function can contain as many
lines of code as you want—you’ll usually want more than 1 to
make it worth while, but if you have more than 20 you might want to
break it up into separate functions. You can use the formal
arguments here as any other variables, you can create new variables,
call other functions, you can even declare functions inside
functions… basically any code that you would write outside of a
function can be written inside of one as well!</p>
<p>All the variables you create in the function body are <strong>local
variables</strong>. These are only visible from within the function and
“will be forgotten” as soon as you return from the function. However,
variables defined outside of the function are still visible from
within.</p></li>
<li><p><strong>Return value</strong> is what your function produces. You can specify this
by calling the <code>return()</code> function and passing that the value that
you wish <em>your function</em> to return. It is typically the last line
of the function. Note that even though we returned a variable
called <code>full_name</code>, that variable was <em>local</em> to the function and so
doesn’t exist outside of it; thus we have to store the returned
value into another variable if we want to use it later (as with
<code>name &lt;- make_full_name(&quot;Alice&quot;, &quot;Kim&quot;)</code>).</p></li>
</ul>
<p><code>return()</code> statement is usually unnecessary as R implicitly returns
the last object it evaluated anyway. So we may shorten the function
definition into</p>
<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1">make_full_name &lt;-<span class="st"> </span><span class="cf">function</span>(first_name, last_name) {</a>
<a class="sourceLine" id="cb45-2" data-line-number="2">  full_name &lt;-<span class="st"> </span><span class="kw">paste</span>(first_name, last_name)</a>
<a class="sourceLine" id="cb45-3" data-line-number="3">}</a></code></pre></div>
<p>or even not store the concatenated names into <code>full_name</code>:</p>
<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1">make_full_name &lt;-<span class="st"> </span><span class="cf">function</span>(first_name, last_name) {</a>
<a class="sourceLine" id="cb46-2" data-line-number="2">   <span class="kw">paste</span>(first_name, last_name)</a>
<a class="sourceLine" id="cb46-3" data-line-number="3">}</a></code></pre></div>
<p>The last evaluation was concatenating the first and last name, and
hence the full name will be implicitly returned.</p>
<p>We can call (execute) a function we defined exactly in the same way we
call built-in functions. When we do so, R will take the <em>actual
arguments</em> we passed in (e.g., <code>&quot;Alice&quot;</code> and <code>&quot;Kim&quot;</code>) and assign them to
the <em>formal arguments</em>. Then it executes each line of code in the <em>function body</em> one at a time. When it gets to the <code>return()</code> call, it will end the function and return the given value, which can then be assigned to a different variable outside of the function.</p>
</div>
<div id="conditional-statements" class="section level2">
<h2><span class="header-section-number">6.6</span> Conditional Statements</h2>
<p>Functions are one way to organize and control the flow of execution
(e.g., what lines of code get run in what order). There are other
ways. In all languages, we can specify that different instructions will
be run based on a different set of conditions. These are <strong>Conditional
statements</strong> which specify which chunks of code will run
depending on which conditions are true. This is valuable both within
and outside of functions.</p>
<p>In an abstract sense, an conditional statement is saying:</p>
<pre><code>IF something is true
  do some lines of code
OTHERWISE
  do some other lines of code</code></pre>
<p>In R, we write these conditional statements using the keywords <strong><code>if</code></strong> and <strong><code>else</code></strong> and the following syntax:</p>
<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" data-line-number="1"><span class="cf">if</span> (condition) {</a>
<a class="sourceLine" id="cb48-2" data-line-number="2">  <span class="co"># lines of code to run if condition is TRUE</span></a>
<a class="sourceLine" id="cb48-3" data-line-number="3">} <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb48-4" data-line-number="4">  <span class="co"># lines of code to run if condition is FALSE</span></a>
<a class="sourceLine" id="cb48-5" data-line-number="5">}</a></code></pre></div>
<p>(Note that the the <code>else</code> needs to be on the same line as the closing <code>}</code> of the <code>if</code> block. It is also possible to omit the <code>else</code> and its block).</p>
<p>The <code>condition</code> can be any variable or expression that resolves to a logical value (<code>TRUE</code> or <code>FALSE</code>). Thus both of the conditional statements below are valid:</p>
<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1">porridge_temp &lt;-<span class="st"> </span><span class="dv">115</span> <span class="co"># in degrees F</span></a>
<a class="sourceLine" id="cb49-2" data-line-number="2"><span class="cf">if</span> (porridge_temp <span class="op">&gt;</span><span class="st"> </span><span class="dv">120</span>) {</a>
<a class="sourceLine" id="cb49-3" data-line-number="3">  <span class="kw">print</span>(<span class="st">&quot;This porridge is too hot!&quot;</span>)</a>
<a class="sourceLine" id="cb49-4" data-line-number="4">}</a>
<a class="sourceLine" id="cb49-5" data-line-number="5"></a>
<a class="sourceLine" id="cb49-6" data-line-number="6">too_cold &lt;-<span class="st"> </span>porridge_temp <span class="op">&lt;</span><span class="st"> </span><span class="dv">70</span></a>
<a class="sourceLine" id="cb49-7" data-line-number="7"><span class="co"># a logical value</span></a>
<a class="sourceLine" id="cb49-8" data-line-number="8"><span class="cf">if</span> (too_cold) {</a>
<a class="sourceLine" id="cb49-9" data-line-number="9">  <span class="kw">print</span>(<span class="st">&quot;This porridge is too cold!&quot;</span>)</a>
<a class="sourceLine" id="cb49-10" data-line-number="10">}</a></code></pre></div>
<p>Note, we can extend the set of conditions evaluated using an <code>else if</code> statement. For example:</p>
<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" data-line-number="1"><span class="co"># Function to determine if you should eat porridge</span></a>
<a class="sourceLine" id="cb50-2" data-line-number="2">test_food_temp &lt;-<span class="st"> </span><span class="cf">function</span>(temp) {</a>
<a class="sourceLine" id="cb50-3" data-line-number="3">  <span class="cf">if</span> (temp <span class="op">&gt;</span><span class="st"> </span><span class="dv">120</span>) {</a>
<a class="sourceLine" id="cb50-4" data-line-number="4">    status &lt;-<span class="st"> &quot;This porridge is too hot!&quot;</span></a>
<a class="sourceLine" id="cb50-5" data-line-number="5">  } <span class="cf">else</span> <span class="cf">if</span> (temp <span class="op">&lt;</span><span class="st"> </span><span class="dv">70</span>) {</a>
<a class="sourceLine" id="cb50-6" data-line-number="6">    status &lt;-<span class="st"> &quot;This porridge is too cold!&quot;</span></a>
<a class="sourceLine" id="cb50-7" data-line-number="7">  } <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb50-8" data-line-number="8">    status &lt;-<span class="st"> &quot;This porridge is just right!&quot;</span></a>
<a class="sourceLine" id="cb50-9" data-line-number="9">  }</a>
<a class="sourceLine" id="cb50-10" data-line-number="10">  <span class="kw">return</span>(status)</a>
<a class="sourceLine" id="cb50-11" data-line-number="11">}</a>
<a class="sourceLine" id="cb50-12" data-line-number="12"><span class="co"># Use function on different temperatures</span></a>
<a class="sourceLine" id="cb50-13" data-line-number="13"><span class="kw">test_food_temp</span>(<span class="dv">119</span>)  <span class="co"># &quot;This porridge is just right!&quot;</span></a>
<a class="sourceLine" id="cb50-14" data-line-number="14"><span class="kw">test_food_temp</span>(<span class="dv">60</span>)   <span class="co"># &quot;This porridge is too cold!&quot;</span></a>
<a class="sourceLine" id="cb50-15" data-line-number="15"><span class="kw">test_food_temp</span>(<span class="dv">150</span>)  <span class="co"># &quot;This porridge is too hot!&quot;</span></a></code></pre></div>
<p>See more about <code>if</code>, <code>else</code> and other related constructs in <a href="control-structures.html#control-structures">Appendix C</a>.</p>
</div>
<div id="resources-5" class="section level2 unnumbered">
<h2>Resources</h2>
<ul>
<li><a href="https://cran.r-project.org/doc/contrib/Short-refcard.pdf">R Function Cheatsheet</a></li>
<li><a href="http://www.statmethods.net/management/userfunctions.html">User Defined R Functions</a></li>
</ul>

</div>
</div>
            </section>

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