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<!DOCTYPE html>
<html >
<head>
<meta charset="UTF-8">
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<title>R User Notebook</title>
<meta name="description" content="A notebook of useful R code and concepts">
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<meta property="og:title" content="R User Notebook" />
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<meta name="twitter:title" content="R User Notebook" />
<meta name="twitter:description" content="A notebook of useful R code and concepts" />
<meta name="author" content="Kieran Driscoll">
<meta name="date" content="2019-02-11">
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<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> R User Notebook</a></li>
<li class="chapter" data-level="2" data-path="basic-concepts.html"><a href="basic-concepts.html"><i class="fa fa-check"></i><b>2</b> Basic Concepts</a><ul>
<li class="chapter" data-level="2.1" data-path="basic-concepts.html"><a href="basic-concepts.html#vectors"><i class="fa fa-check"></i><b>2.1</b> Vectors</a></li>
<li class="chapter" data-level="2.2" data-path="basic-concepts.html"><a href="basic-concepts.html#matrices"><i class="fa fa-check"></i><b>2.2</b> Matrices</a></li>
<li class="chapter" data-level="2.3" data-path="basic-concepts.html"><a href="basic-concepts.html#dataframes"><i class="fa fa-check"></i><b>2.3</b> Dataframes</a></li>
<li class="chapter" data-level="2.4" data-path="basic-concepts.html"><a href="basic-concepts.html#tibbles"><i class="fa fa-check"></i><b>2.4</b> Tibbles</a></li>
<li class="chapter" data-level="2.5" data-path="basic-concepts.html"><a href="basic-concepts.html#extracting-data-from-dataframestibbles"><i class="fa fa-check"></i><b>2.5</b> Extracting data from Dataframes/Tibbles</a></li>
<li class="chapter" data-level="2.6" data-path="basic-concepts.html"><a href="basic-concepts.html#lists"><i class="fa fa-check"></i><b>2.6</b> Lists</a></li>
<li class="chapter" data-level="2.7" data-path="basic-concepts.html"><a href="basic-concepts.html#factors"><i class="fa fa-check"></i><b>2.7</b> Factors</a></li>
<li class="chapter" data-level="2.8" data-path="basic-concepts.html"><a href="basic-concepts.html#dates"><i class="fa fa-check"></i><b>2.8</b> Dates</a></li>
<li class="chapter" data-level="2.9" data-path="basic-concepts.html"><a href="basic-concepts.html#style-guide"><i class="fa fa-check"></i><b>2.9</b> Style Guide</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="importing-exporting.html"><a href="importing-exporting.html"><i class="fa fa-check"></i><b>3</b> Importing & Exporting</a><ul>
<li class="chapter" data-level="3.1" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-with-base-r"><i class="fa fa-check"></i><b>3.1</b> Importing with Base R</a></li>
<li class="chapter" data-level="3.2" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-with-other-packages"><i class="fa fa-check"></i><b>3.2</b> Importing with other packages</a><ul>
<li class="chapter" data-level="3.2.1" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-a-csv"><i class="fa fa-check"></i><b>3.2.1</b> Importing a CSV</a></li>
<li class="chapter" data-level="3.2.2" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-a-tsv"><i class="fa fa-check"></i><b>3.2.2</b> Importing a TSV</a></li>
<li class="chapter" data-level="3.2.3" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-a-r-data-file"><i class="fa fa-check"></i><b>3.2.3</b> Importing a R data file</a></li>
<li class="chapter" data-level="3.2.4" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-a-excel-file"><i class="fa fa-check"></i><b>3.2.4</b> Importing a Excel file</a></li>
<li class="chapter" data-level="3.2.5" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-a-sas-file"><i class="fa fa-check"></i><b>3.2.5</b> Importing a SAS file</a></li>
<li class="chapter" data-level="3.2.6" data-path="importing-exporting.html"><a href="importing-exporting.html#importing-json-newline-delimited-json"><i class="fa fa-check"></i><b>3.2.6</b> Importing JSON (Newline Delimited JSON)</a></li>
</ul></li>
<li class="chapter" data-level="3.3" data-path="importing-exporting.html"><a href="importing-exporting.html#exporting"><i class="fa fa-check"></i><b>3.3</b> Exporting</a><ul>
<li class="chapter" data-level="3.3.1" data-path="importing-exporting.html"><a href="importing-exporting.html#write-to-an-r-dataset"><i class="fa fa-check"></i><b>3.3.1</b> Write to an R dataset</a></li>
<li class="chapter" data-level="3.3.2" data-path="importing-exporting.html"><a href="importing-exporting.html#write-to-an-csv-file"><i class="fa fa-check"></i><b>3.3.2</b> Write to an CSV file</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="manipulating-data.html"><a href="manipulating-data.html"><i class="fa fa-check"></i><b>4</b> Manipulating data</a><ul>
<li class="chapter" data-level="4.1" data-path="manipulating-data.html"><a href="manipulating-data.html#basic-data-wrangling"><i class="fa fa-check"></i><b>4.1</b> Basic data wrangling</a></li>
<li class="chapter" data-level="4.2" data-path="manipulating-data.html"><a href="manipulating-data.html#summary-statistics"><i class="fa fa-check"></i><b>4.2</b> Summary statistics</a></li>
<li class="chapter" data-level="4.3" data-path="manipulating-data.html"><a href="manipulating-data.html#conditional-statements"><i class="fa fa-check"></i><b>4.3</b> Conditional statements</a></li>
<li class="chapter" data-level="4.4" data-path="manipulating-data.html"><a href="manipulating-data.html#recode"><i class="fa fa-check"></i><b>4.4</b> Recode</a></li>
<li class="chapter" data-level="4.5" data-path="manipulating-data.html"><a href="manipulating-data.html#appending-columns-and-rows"><i class="fa fa-check"></i><b>4.5</b> Appending columns and rows</a></li>
<li class="chapter" data-level="4.6" data-path="manipulating-data.html"><a href="manipulating-data.html#joins"><i class="fa fa-check"></i><b>4.6</b> Joins</a></li>
<li class="chapter" data-level="4.7" data-path="manipulating-data.html"><a href="manipulating-data.html#tidy-data"><i class="fa fa-check"></i><b>4.7</b> Tidy Data</a></li>
<li class="chapter" data-level="4.8" data-path="manipulating-data.html"><a href="manipulating-data.html#tibbles-1"><i class="fa fa-check"></i><b>4.8</b> tibbles</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="functions.html"><a href="functions.html"><i class="fa fa-check"></i><b>5</b> Functions</a><ul>
<li class="chapter" data-level="5.1" data-path="functions.html"><a href="functions.html#function-basics---an-example-using-str"><i class="fa fa-check"></i><b>5.1</b> Function Basics - an example using str()</a></li>
<li class="chapter" data-level="5.2" data-path="functions.html"><a href="functions.html#common-base-functions"><i class="fa fa-check"></i><b>5.2</b> Common (base) functions</a><ul>
<li class="chapter" data-level="5.2.1" data-path="functions.html"><a href="functions.html#strings"><i class="fa fa-check"></i><b>5.2.1</b> Strings</a></li>
<li class="chapter" data-level="5.2.2" data-path="functions.html"><a href="functions.html#mathematical"><i class="fa fa-check"></i><b>5.2.2</b> Mathematical</a></li>
<li class="chapter" data-level="5.2.3" data-path="functions.html"><a href="functions.html#properties-lookups"><i class="fa fa-check"></i><b>5.2.3</b> Properties & Lookups</a></li>
<li class="chapter" data-level="5.2.4" data-path="functions.html"><a href="functions.html#transformation"><i class="fa fa-check"></i><b>5.2.4</b> Transformation</a></li>
<li class="chapter" data-level="5.2.5" data-path="functions.html"><a href="functions.html#other-useful-functions"><i class="fa fa-check"></i><b>5.2.5</b> Other useful functions</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="functions.html"><a href="functions.html#stringr---more-string-functions"><i class="fa fa-check"></i><b>5.3</b> Stringr - more string functions</a></li>
<li class="chapter" data-level="5.4" data-path="functions.html"><a href="functions.html#lubridate---more-date-functions"><i class="fa fa-check"></i><b>5.4</b> Lubridate - more date functions</a></li>
<li class="chapter" data-level="5.5" data-path="functions.html"><a href="functions.html#converting-data-to-other-formats"><i class="fa fa-check"></i><b>5.5</b> Converting data to other formats</a><ul>
<li class="chapter" data-level="5.5.1" data-path="functions.html"><a href="functions.html#json"><i class="fa fa-check"></i><b>5.5.1</b> JSON</a></li>
</ul></li>
<li class="chapter" data-level="5.6" data-path="functions.html"><a href="functions.html#user-defined-functions"><i class="fa fa-check"></i><b>5.6</b> User Defined Functions</a></li>
<li class="chapter" data-level="5.7" data-path="functions.html"><a href="functions.html#chainingpiping"><i class="fa fa-check"></i><b>5.7</b> Chaining/Piping</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="loops.html"><a href="loops.html"><i class="fa fa-check"></i><b>6</b> Loops</a><ul>
<li class="chapter" data-level="6.1" data-path="loops.html"><a href="loops.html#basic-for-loop-structure"><i class="fa fa-check"></i><b>6.1</b> Basic for Loop structure</a></li>
<li class="chapter" data-level="6.2" data-path="loops.html"><a href="loops.html#looping-through-a-vector"><i class="fa fa-check"></i><b>6.2</b> Looping through a vector</a></li>
<li class="chapter" data-level="6.3" data-path="loops.html"><a href="loops.html#creating-a-list-in-a-loop"><i class="fa fa-check"></i><b>6.3</b> Creating a List in a Loop</a></li>
<li class="chapter" data-level="6.4" data-path="loops.html"><a href="loops.html#looping-with-apply-functions"><i class="fa fa-check"></i><b>6.4</b> Looping with apply functions</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="tables.html"><a href="tables.html"><i class="fa fa-check"></i><b>7</b> Tables</a><ul>
<li class="chapter" data-level="7.1" data-path="tables.html"><a href="tables.html#displaying-tables---htmltable"><i class="fa fa-check"></i><b>7.1</b> Displaying tables - htmlTable</a></li>
<li class="chapter" data-level="7.2" data-path="tables.html"><a href="tables.html#displaying-interactive-tables---dt"><i class="fa fa-check"></i><b>7.2</b> Displaying Interactive tables - DT</a></li>
<li class="chapter" data-level="7.3" data-path="tables.html"><a href="tables.html#creating-tabulations"><i class="fa fa-check"></i><b>7.3</b> Creating Tabulations</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="charts.html"><a href="charts.html"><i class="fa fa-check"></i><b>8</b> Charts</a><ul>
<li class="chapter" data-level="8.0.1" data-path="charts.html"><a href="charts.html#static-charts-with-ggplot2"><i class="fa fa-check"></i><b>8.0.1</b> Static charts with ggplot2</a></li>
<li class="chapter" data-level="8.0.2" data-path="charts.html"><a href="charts.html#changing-axes"><i class="fa fa-check"></i><b>8.0.2</b> Changing Axes</a></li>
<li class="chapter" data-level="8.0.3" data-path="charts.html"><a href="charts.html#chart-themes-styles"><i class="fa fa-check"></i><b>8.0.3</b> Chart Themes & Styles</a></li>
<li class="chapter" data-level="8.0.4" data-path="charts.html"><a href="charts.html#line-charts-geom_line"><i class="fa fa-check"></i><b>8.0.4</b> Line Charts (geom_line)</a></li>
<li class="chapter" data-level="8.0.5" data-path="charts.html"><a href="charts.html#bar-charts-geom_bar-geom_histogram"><i class="fa fa-check"></i><b>8.0.5</b> Bar Charts (geom_bar & geom_histogram)</a></li>
<li class="chapter" data-level="8.0.6" data-path="charts.html"><a href="charts.html#adding-features"><i class="fa fa-check"></i><b>8.0.6</b> Adding features</a></li>
<li class="chapter" data-level="8.0.7" data-path="charts.html"><a href="charts.html#heatmaps"><i class="fa fa-check"></i><b>8.0.7</b> Heatmaps</a></li>
<li class="chapter" data-level="8.0.8" data-path="charts.html"><a href="charts.html#boxplots"><i class="fa fa-check"></i><b>8.0.8</b> Boxplots</a></li>
<li class="chapter" data-level="8.0.9" data-path="charts.html"><a href="charts.html#combination-charts"><i class="fa fa-check"></i><b>8.0.9</b> Combination Charts</a></li>
<li class="chapter" data-level="8.0.10" data-path="charts.html"><a href="charts.html#scales"><i class="fa fa-check"></i><b>8.0.10</b> Scales</a></li>
<li class="chapter" data-level="8.0.11" data-path="charts.html"><a href="charts.html#ggplot-wizard"><i class="fa fa-check"></i><b>8.0.11</b> ggplot wizard</a></li>
<li class="chapter" data-level="8.0.12" data-path="charts.html"><a href="charts.html#interactive-charts-with-ggiraph"><i class="fa fa-check"></i><b>8.0.12</b> Interactive charts with ggiraph</a></li>
<li class="chapter" data-level="8.0.13" data-path="charts.html"><a href="charts.html#interactive-charts-with-dygraph"><i class="fa fa-check"></i><b>8.0.13</b> Interactive charts with dygraph</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="maps.html"><a href="maps.html"><i class="fa fa-check"></i><b>9</b> Maps</a><ul>
<li class="chapter" data-level="9.1" data-path="maps.html"><a href="maps.html#leaflet"><i class="fa fa-check"></i><b>9.1</b> Leaflet</a><ul>
<li class="chapter" data-level="9.1.1" data-path="maps.html"><a href="maps.html#display-a-basic-map"><i class="fa fa-check"></i><b>9.1.1</b> Display a basic map</a></li>
<li class="chapter" data-level="9.1.2" data-path="maps.html"><a href="maps.html#add-markers-shapes-and-popups-to-a-map"><i class="fa fa-check"></i><b>9.1.2</b> Add markers, shapes and popups to a map</a></li>
<li class="chapter" data-level="9.1.3" data-path="maps.html"><a href="maps.html#add-boundaries"><i class="fa fa-check"></i><b>9.1.3</b> Add Boundaries</a></li>
<li class="chapter" data-level="9.1.4" data-path="maps.html"><a href="maps.html#add-interactivity"><i class="fa fa-check"></i><b>9.1.4</b> Add Interactivity</a></li>
<li class="chapter" data-level="9.1.5" data-path="maps.html"><a href="maps.html#attach-extra-information-to-your-boundary-dataset"><i class="fa fa-check"></i><b>9.1.5</b> Attach extra information to your boundary dataset</a></li>
<li class="chapter" data-level="9.1.6" data-path="maps.html"><a href="maps.html#add-colour-based-on-area-data"><i class="fa fa-check"></i><b>9.1.6</b> Add colour based on area data</a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="maps.html"><a href="maps.html#inserting-html-javascript-directly-into-r"><i class="fa fa-check"></i><b>9.2</b> Inserting HTML & Javascript directly into R</a></li>
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<li class="chapter" data-level="10" data-path="rmarkdown-knitr.html"><a href="rmarkdown-knitr.html"><i class="fa fa-check"></i><b>10</b> RMarkdown & Knitr</a><ul>
<li class="chapter" data-level="10.1" data-path="rmarkdown-knitr.html"><a href="rmarkdown-knitr.html#knitr"><i class="fa fa-check"></i><b>10.1</b> Knitr</a></li>
<li class="chapter" data-level="10.2" data-path="rmarkdown-knitr.html"><a href="rmarkdown-knitr.html#yaml"><i class="fa fa-check"></i><b>10.2</b> YAML</a></li>
<li class="chapter" data-level="10.3" data-path="rmarkdown-knitr.html"><a href="rmarkdown-knitr.html#modular-coding"><i class="fa fa-check"></i><b>10.3</b> Modular coding</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="machine-learning-predictive-analytics.html"><a href="machine-learning-predictive-analytics.html"><i class="fa fa-check"></i><b>11</b> Machine Learning & Predictive Analytics</a><ul>
<li class="chapter" data-level="11.0.1" data-path="machine-learning-predictive-analytics.html"><a href="machine-learning-predictive-analytics.html#decision-trees"><i class="fa fa-check"></i><b>11.0.1</b> Decision Trees</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html"><i class="fa fa-check"></i><b>12</b> Text Mining & NLP</a><ul>
<li class="chapter" data-level="12.0.1" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#text-data"><i class="fa fa-check"></i><b>12.0.1</b> Text data</a></li>
<li class="chapter" data-level="12.0.2" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#tidy-text"><i class="fa fa-check"></i><b>12.0.2</b> Tidy text</a></li>
<li class="chapter" data-level="12.0.3" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#stemming"><i class="fa fa-check"></i><b>12.0.3</b> Stemming</a></li>
<li class="chapter" data-level="12.0.4" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#basic-text-stats"><i class="fa fa-check"></i><b>12.0.4</b> Basic text stats</a></li>
<li class="chapter" data-level="12.0.5" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#n-grams-analysis"><i class="fa fa-check"></i><b>12.0.5</b> N-Grams analysis</a></li>
<li class="chapter" data-level="12.0.6" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#text-preparation-with-tm"><i class="fa fa-check"></i><b>12.0.6</b> Text Preparation with <strong>tm</strong></a></li>
<li class="chapter" data-level="12.1" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#create-a-term-document-matrix"><i class="fa fa-check"></i><b>12.1</b> Create a Term Document Matrix</a><ul>
<li class="chapter" data-level="12.1.1" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#from-a-corpus-by-default-words-are-converted-to-lowercase-less-than-3-characters-are-excluded"><i class="fa fa-check"></i><b>12.1.1</b> From a Corpus (by default words are converted to lowercase less than 3 characters are excluded)</a></li>
<li class="chapter" data-level="12.1.2" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#matrix-managment"><i class="fa fa-check"></i><b>12.1.2</b> Matrix Managment</a></li>
</ul></li>
<li class="chapter" data-level="12.2" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#topic-modelling-latent-dirichlet-allocation-lda"><i class="fa fa-check"></i><b>12.2</b> Topic Modelling & Latent Dirichlet Allocation (LDA)</a></li>
<li class="chapter" data-level="12.3" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#clustering---similarity-between-topics"><i class="fa fa-check"></i><b>12.3</b> Clustering - Similarity between topics</a></li>
<li class="chapter" data-level="12.4" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#calculating-distance-between-objects"><i class="fa fa-check"></i><b>12.4</b> Calculating distance between objects</a></li>
<li class="chapter" data-level="12.5" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#non-euclidian-distances---jensen-shannon"><i class="fa fa-check"></i><b>12.5</b> Non-Euclidian Distances - Jensen Shannon</a></li>
<li class="chapter" data-level="12.6" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#scaling---principal-components"><i class="fa fa-check"></i><b>12.6</b> Scaling - Principal Components</a></li>
<li class="chapter" data-level="12.7" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#eigen-vectors"><i class="fa fa-check"></i><b>12.7</b> Eigen vectors</a></li>
<li class="chapter" data-level="12.8" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#k-means"><i class="fa fa-check"></i><b>12.8</b> K-Means</a></li>
<li class="chapter" data-level="12.9" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#naive-bayes-classifiers"><i class="fa fa-check"></i><b>12.9</b> Naive Bayes Classifiers</a></li>
<li class="chapter" data-level="12.10" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#tf-idf-classifiers-supervised"><i class="fa fa-check"></i><b>12.10</b> TF-IDF Classifiers (Supervised)</a></li>
<li class="chapter" data-level="12.11" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#sentiment-analysis"><i class="fa fa-check"></i><b>12.11</b> Sentiment Analysis</a></li>
<li class="chapter" data-level="12.12" data-path="text-mining-nlp.html"><a href="text-mining-nlp.html#word-bubble"><i class="fa fa-check"></i><b>12.12</b> Word Bubble</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="shiny.html"><a href="shiny.html"><i class="fa fa-check"></i><b>13</b> Shiny</a><ul>
<li class="chapter" data-level="13.1" data-path="shiny.html"><a href="shiny.html#basic-shiny-structure"><i class="fa fa-check"></i><b>13.1</b> Basic Shiny Structure</a></li>
<li class="chapter" data-level="13.2" data-path="shiny.html"><a href="shiny.html#user-interface"><i class="fa fa-check"></i><b>13.2</b> User Interface</a><ul>
<li class="chapter" data-level="13.2.1" data-path="shiny.html"><a href="shiny.html#layout"><i class="fa fa-check"></i><b>13.2.1</b> Layout</a></li>
<li class="chapter" data-level="13.2.2" data-path="shiny.html"><a href="shiny.html#inputs"><i class="fa fa-check"></i><b>13.2.2</b> Inputs</a></li>
<li class="chapter" data-level="13.2.3" data-path="shiny.html"><a href="shiny.html#outputs"><i class="fa fa-check"></i><b>13.2.3</b> Outputs</a></li>
</ul></li>
<li class="chapter" data-level="13.3" data-path="shiny.html"><a href="shiny.html#server"><i class="fa fa-check"></i><b>13.3</b> Server</a><ul>
<li class="chapter" data-level="13.3.1" data-path="shiny.html"><a href="shiny.html#linking-to-ui-outputs"><i class="fa fa-check"></i><b>13.3.1</b> Linking to UI outputs</a></li>
<li class="chapter" data-level="13.3.2" data-path="shiny.html"><a href="shiny.html#linking-to-ui-inputs"><i class="fa fa-check"></i><b>13.3.2</b> Linking to UI inputs</a></li>
</ul></li>
<li class="chapter" data-level="13.4" data-path="shiny.html"><a href="shiny.html#shiny-dashboard"><i class="fa fa-check"></i><b>13.4</b> Shiny Dashboard</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="bookdown.html"><a href="bookdown.html"><i class="fa fa-check"></i><b>14</b> Bookdown</a><ul>
<li class="chapter" data-level="14.1" data-path="bookdown.html"><a href="bookdown.html#set-up"><i class="fa fa-check"></i><b>14.1</b> Set-up</a></li>
<li class="chapter" data-level="14.2" data-path="bookdown.html"><a href="bookdown.html#create-the-book"><i class="fa fa-check"></i><b>14.2</b> Create the book</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="creating-packages.html"><a href="creating-packages.html"><i class="fa fa-check"></i><b>15</b> Creating Packages</a><ul>
<li class="chapter" data-level="15.1" data-path="creating-packages.html"><a href="creating-packages.html#setup-folders"><i class="fa fa-check"></i><b>15.1</b> Setup Folders</a></li>
<li class="chapter" data-level="15.2" data-path="creating-packages.html"><a href="creating-packages.html#r-folder"><i class="fa fa-check"></i><b>15.2</b> R folder</a></li>
<li class="chapter" data-level="15.3" data-path="creating-packages.html"><a href="creating-packages.html#man-folder"><i class="fa fa-check"></i><b>15.3</b> man folder</a></li>
<li class="chapter" data-level="15.4" data-path="creating-packages.html"><a href="creating-packages.html#package-details"><i class="fa fa-check"></i><b>15.4</b> Package details</a></li>
<li class="chapter" data-level="15.5" data-path="creating-packages.html"><a href="creating-packages.html#package-dependencies"><i class="fa fa-check"></i><b>15.5</b> Package Dependencies</a></li>
<li class="chapter" data-level="15.6" data-path="creating-packages.html"><a href="creating-packages.html#build-the-package"><i class="fa fa-check"></i><b>15.6</b> Build the package</a></li>
<li class="chapter" data-level="15.7" data-path="creating-packages.html"><a href="creating-packages.html#making-changes"><i class="fa fa-check"></i><b>15.7</b> Making changes</a></li>
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<li class="chapter" data-level="16" data-path="git-version-control.html"><a href="git-version-control.html"><i class="fa fa-check"></i><b>16</b> Git - Version Control</a><ul>
<li class="chapter" data-level="16.1" data-path="git-version-control.html"><a href="git-version-control.html#set-up-1"><i class="fa fa-check"></i><b>16.1</b> Set-up</a></li>
<li class="chapter" data-level="16.2" data-path="git-version-control.html"><a href="git-version-control.html#link-git-to-a-github-account"><i class="fa fa-check"></i><b>16.2</b> Link Git to a GitHub account</a></li>
<li class="chapter" data-level="16.3" data-path="git-version-control.html"><a href="git-version-control.html#starting-a-project-with-github"><i class="fa fa-check"></i><b>16.3</b> Starting a project with Github</a></li>
<li class="chapter" data-level="16.4" data-path="git-version-control.html"><a href="git-version-control.html#hosting-a-site-on-github"><i class="fa fa-check"></i><b>16.4</b> Hosting a site on Github</a></li>
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<li class="chapter" data-level="17" data-path="other-languages.html"><a href="other-languages.html"><i class="fa fa-check"></i><b>17</b> Other Languages</a><ul>
<li class="chapter" data-level="17.1" data-path="other-languages.html"><a href="other-languages.html#sql"><i class="fa fa-check"></i><b>17.1</b> SQL</a></li>
<li class="chapter" data-level="17.2" data-path="other-languages.html"><a href="other-languages.html#python"><i class="fa fa-check"></i><b>17.2</b> Python</a></li>
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<div id="manipulating-data" class="section level1">
<h1><span class="header-section-number">4</span> Manipulating data</h1>
<p>Most common data manpulation can be done using the tidyverse package, which includes <strong>dplyr</strong> and <strong>tidyr</strong>. They include functions to subset and merge and pivot dataframes/tibbles.</p>
<div id="basic-data-wrangling" class="section level2">
<h2><span class="header-section-number">4.1</span> Basic data wrangling</h2>
<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"># Keep/Drop specific columns with select()</span></a>
<a class="sourceLine" id="cb37-2" data-line-number="2">dplyr<span class="op">::</span><span class="kw">select</span>(mtcars, mpg) <span class="co"># Only keeps mpg</span></a>
<a class="sourceLine" id="cb37-3" data-line-number="3">dplyr<span class="op">::</span><span class="kw">select</span>(mtcars,<span class="op">-</span>mpg) <span class="co"># Drop mpg by prefixing with a '-' </span></a>
<a class="sourceLine" id="cb37-4" data-line-number="4"></a>
<a class="sourceLine" id="cb37-5" data-line-number="5"><span class="co"># Keep columns that meet specific conditions select_if()</span></a>
<a class="sourceLine" id="cb37-6" data-line-number="6">dplyr<span class="op">::</span><span class="kw">select_if</span>(mtcars, is.numeric)</a>
<a class="sourceLine" id="cb37-7" data-line-number="7"></a>
<a class="sourceLine" id="cb37-8" data-line-number="8"><span class="co"># Select rows that meet specific conditions using filter()</span></a>
<a class="sourceLine" id="cb37-9" data-line-number="9">dplyr<span class="op">::</span><span class="kw">filter</span>(mtcars, hp <span class="op">></span><span class="st"> </span><span class="dv">100</span> <span class="op">&</span><span class="st"> </span>hp <span class="op"><</span><span class="st"> </span><span class="dv">200</span>)</a>
<a class="sourceLine" id="cb37-10" data-line-number="10"></a>
<a class="sourceLine" id="cb37-11" data-line-number="11"><span class="co"># Rename columns using rename() </span></a>
<a class="sourceLine" id="cb37-12" data-line-number="12">dplyr<span class="op">::</span><span class="kw">rename</span>(mtcars, <span class="dt">HorsePower =</span> hp) <span class="co">#Nb. the new name is specifed first New=Old</span></a>
<a class="sourceLine" id="cb37-13" data-line-number="13"></a>
<a class="sourceLine" id="cb37-14" data-line-number="14"><span class="co"># Create new columns using mutate() or transmute()</span></a>
<a class="sourceLine" id="cb37-15" data-line-number="15">dplyr<span class="op">::</span><span class="kw">mutate</span>(mtcars, <span class="dt">kmpg =</span> mpg<span class="op">*</span><span class="fl">1.609</span>) </a>
<a class="sourceLine" id="cb37-16" data-line-number="16"><span class="co"># OR to also drop all other columns </span></a>
<a class="sourceLine" id="cb37-17" data-line-number="17">dplyr<span class="op">::</span><span class="kw">transmute</span>(mtcars, <span class="dt">kmpg =</span> mpg<span class="op">*</span><span class="fl">1.609</span>) </a>
<a class="sourceLine" id="cb37-18" data-line-number="18"></a>
<a class="sourceLine" id="cb37-19" data-line-number="19"><span class="co"># Extract a column as a vector/list</span></a>
<a class="sourceLine" id="cb37-20" data-line-number="20">dplyr<span class="op">::</span><span class="kw">pull</span>(peopletdf, Age)</a>
<a class="sourceLine" id="cb37-21" data-line-number="21"></a>
<a class="sourceLine" id="cb37-22" data-line-number="22"><span class="co"># Sort data (ascending by default)</span></a>
<a class="sourceLine" id="cb37-23" data-line-number="23">dplyr<span class="op">::</span><span class="kw">arrange</span>(mtcars, wt) <span class="co"># add desc(wt) for descending</span></a>
<a class="sourceLine" id="cb37-24" data-line-number="24"></a>
<a class="sourceLine" id="cb37-25" data-line-number="25"><span class="co"># Extract unique values</span></a>
<a class="sourceLine" id="cb37-26" data-line-number="26">dplyr<span class="op">::</span><span class="kw">distinct</span>(mtcars, cyl) </a></code></pre></div>
</div>
<div id="summary-statistics" class="section level2">
<h2><span class="header-section-number">4.2</span> Summary statistics</h2>
<p>Basic statistics about a column (eg. sum, mean, median, max, min) can be calculated using the <strong>summarise</strong> function</p>
<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">summarise</span>(mtcars, <span class="st">"mean"</span> =<span class="st"> </span><span class="kw">mean</span>(mpg),</a>
<a class="sourceLine" id="cb38-2" data-line-number="2"> <span class="st">"median"</span> =<span class="st"> </span><span class="kw">median</span>(mpg),</a>
<a class="sourceLine" id="cb38-3" data-line-number="3"> <span class="st">"max"</span> =<span class="st"> </span><span class="kw">max</span>(mpg),</a>
<a class="sourceLine" id="cb38-4" data-line-number="4"> <span class="st">"n"</span> =<span class="st"> </span><span class="kw">n</span>() )</a></code></pre></div>
<pre><code>## Warning: package 'bindrcpp' was built under R version 3.4.4</code></pre>
<pre><code>## mean median max n
## 1 20.09062 19.2 33.9 32</code></pre>
<p>Ranking can be done within the mutate function. This example adds a rank based on descending horsepower:</p>
<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">mutate</span>(mtcars, <span class="dt">rank_hp =</span> <span class="kw">rank</span>(<span class="op">-</span>hp, <span class="dt">ties.method =</span> <span class="st">"first"</span>)) <span class="co"># Other methods are "last", "random"</span></a></code></pre></div>
<pre><code>## mpg cyl disp hp drat wt qsec vs am gear carb rank_hp
## 1 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 19
## 2 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 20
## 3 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 26
## 4 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 21
## 5 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 11
## 6 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 23
## 7 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 3
## 8 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 31
## 9 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 25
## 10 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 16
## 11 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 17
## 12 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 8
## 13 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 9
## 14 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 10
## 15 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 7
## 16 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 6
## 17 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 5
## 18 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 28
## 19 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 32
## 20 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 30
## 21 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 24
## 22 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 14
## 23 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 15
## 24 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 4
## 25 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 12
## 26 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 29
## 27 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 27
## 28 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 18
## 29 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 2
## 30 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 13
## 31 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 1
## 32 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2 22</code></pre>
<p>The <strong>group_by</strong> function can be used to produce grouped statistics:</p>
<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">group_by</span>(mtcars, am) <span class="op">%>%</span></a>
<a class="sourceLine" id="cb43-2" data-line-number="2"><span class="st"> </span>dplyr<span class="op">::</span><span class="kw">summarise</span>(<span class="st">"mean"</span> =<span class="st"> </span><span class="kw">mean</span>(wt)) <span class="op">%>%</span></a>
<a class="sourceLine" id="cb43-3" data-line-number="3"><span class="st"> </span>dplyr<span class="op">::</span><span class="kw">ungroup</span>() <span class="co"># Stop grouping</span></a></code></pre></div>
<pre><code>## # A tibble: 2 x 2
## am mean
## <dbl> <dbl>
## 1 0 3.77
## 2 1.00 2.41</code></pre>
<p>The <strong>count</strong> function is a quick way of producing frequency counts by one or more variables:</p>
<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="co"># Frequency count of variable (+ optional sorting of results)</span></a>
<a class="sourceLine" id="cb45-2" data-line-number="2">dplyr<span class="op">::</span><span class="kw">count</span>(mtcars, cyl, <span class="dt">sort =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
</div>
<div id="conditional-statements" class="section level2">
<h2><span class="header-section-number">4.3</span> Conditional statements</h2>
<p>New variables can be created with conditional rules by using the <strong>case_when</strong> function:</p>
<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">mutate</span>(mtcars, <span class="dt">weight_group =</span> dplyr<span class="op">::</span><span class="kw">case_when</span>(wt <span class="op"><</span><span class="st"> </span><span class="fl">2.5</span> <span class="op">~</span><span class="st"> "low"</span>,</a>
<a class="sourceLine" id="cb46-2" data-line-number="2"> wt <span class="op"><</span><span class="st"> </span><span class="fl">3.5</span> <span class="op">~</span><span class="st"> "medium"</span>,</a>
<a class="sourceLine" id="cb46-3" data-line-number="3"> <span class="ot">TRUE</span> <span class="op">~</span><span class="st"> "high"</span>))</a></code></pre></div>
</div>
<div id="recode" class="section level2">
<h2><span class="header-section-number">4.4</span> Recode</h2>
<p>Recoding data may be useful if you have coded values and want to display a description. This is a convienience function based on case_when():</p>
<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">recode</span>(mtcars<span class="op">$</span>am, <span class="st">`</span><span class="dt">0</span><span class="st">`</span>=<span class="st">"Automatic"</span>, <span class="co"># If coded values are numeric then you need to use ``</span></a>
<a class="sourceLine" id="cb47-2" data-line-number="2"> <span class="st">`</span><span class="dt">1</span><span class="st">`</span>=<span class="st">"Manual"</span>,</a>
<a class="sourceLine" id="cb47-3" data-line-number="3"> <span class="dt">.default =</span> <span class="st">"Other"</span>,</a>
<a class="sourceLine" id="cb47-4" data-line-number="4"> <span class="dt">.missing =</span> <span class="st">"missing"</span>)</a></code></pre></div>
</div>
<div id="appending-columns-and-rows" class="section level2">
<h2><span class="header-section-number">4.5</span> Appending columns and rows</h2>
<p>Additional columns or rows can be added to a dataframe, but they must have the same number/types of elements, and be in the correct order.</p>
<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" data-line-number="1"><span class="co"># Add a column </span></a>
<a class="sourceLine" id="cb48-2" data-line-number="2"><span class="kw">cbind</span>(mtcars, mtcars<span class="op">$</span>mpg) </a>
<a class="sourceLine" id="cb48-3" data-line-number="3">dplyr<span class="op">::</span><span class="kw">bind_cols</span>(mtcars, <span class="dt">mpg2=</span>mtcars<span class="op">$</span>mpg)</a>
<a class="sourceLine" id="cb48-4" data-line-number="4"></a>
<a class="sourceLine" id="cb48-5" data-line-number="5"><span class="co"># Add a row </span></a>
<a class="sourceLine" id="cb48-6" data-line-number="6"><span class="kw">rbind</span>(mtcars, mtcars)</a>
<a class="sourceLine" id="cb48-7" data-line-number="7">dplyr<span class="op">::</span><span class="kw">bind_rows</span>(mtcars, mtcars)</a></code></pre></div>
</div>
<div id="joins" class="section level2">
<h2><span class="header-section-number">4.6</span> Joins</h2>
<p>To join dataframes together by a common id standard joins (left, inner, outer..) can be used:</p>
<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1">dplyr<span class="op">::</span><span class="kw">left_join</span>(mydf1, mydf2, <span class="dt">by =</span> <span class="st">'id'</span>)</a>
<a class="sourceLine" id="cb49-2" data-line-number="2"></a>
<a class="sourceLine" id="cb49-3" data-line-number="3"><span class="co"># Anti-Join : Only keep rows from mydf1 if they DONT match with mydf2, eg. to remove certain types of observation</span></a>
<a class="sourceLine" id="cb49-4" data-line-number="4">dplyr<span class="op">::</span><span class="kw">anti_join</span>(mydf1, mydf2, <span class="dt">by =</span> <span class="st">'id'</span>)</a></code></pre></div>
</div>
<div id="tidy-data" class="section level2">
<h2><span class="header-section-number">4.7</span> Tidy Data</h2>
<p>You can convert data to/from a tidy format with the <strong>tidyr</strong> package. Nb. tidyr includes dplyr.</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="kw">library</span>(tidyr)</a>
<a class="sourceLine" id="cb50-2" data-line-number="2">tidydf <-<span class="st"> </span>tibble<span class="op">::</span><span class="kw">tibble</span>(</a>
<a class="sourceLine" id="cb50-3" data-line-number="3"> <span class="st">'Year'</span>=<span class="kw">c</span>(<span class="dv">2016</span>,<span class="dv">2016</span>,<span class="dv">2017</span>,<span class="dv">2017</span>,<span class="dv">2018</span>,<span class="dv">2018</span>),</a>
<a class="sourceLine" id="cb50-4" data-line-number="4"> <span class="st">'Type'</span>=<span class="kw">c</span>(<span class="st">'A'</span>,<span class="st">'B'</span>,<span class="st">'A'</span>,<span class="st">'C'</span>,<span class="st">'B'</span>,<span class="st">'C'</span>),</a>
<a class="sourceLine" id="cb50-5" data-line-number="5"> <span class="st">'Amount'</span>=<span class="kw">c</span>(<span class="dv">111</span>,<span class="dv">222</span>,<span class="dv">333</span>,<span class="dv">444</span>,<span class="dv">555</span>,<span class="dv">666</span>) )</a>
<a class="sourceLine" id="cb50-6" data-line-number="6"></a>
<a class="sourceLine" id="cb50-7" data-line-number="7"><span class="co"># Pivot tidy data so that values become columns</span></a>
<a class="sourceLine" id="cb50-8" data-line-number="8">nottidy <-<span class="st"> </span>tidyr<span class="op">::</span><span class="kw">spread</span>(tidydf, <span class="dt">key=</span>Year, <span class="dt">value=</span>Amount)</a>
<a class="sourceLine" id="cb50-9" data-line-number="9"></a>
<a class="sourceLine" id="cb50-10" data-line-number="10"><span class="co"># Pivot data into a tidy format (ie. reverse spread)</span></a>
<a class="sourceLine" id="cb50-11" data-line-number="11">tidyr<span class="op">::</span><span class="kw">gather</span>(nottidy, <span class="dt">key=</span>Age, <span class="dt">value=</span>Amount, <span class="op">-</span>Type)</a></code></pre></div>
<pre><code>## # A tibble: 9 x 3
## Type Age Amount
## <chr> <chr> <dbl>
## 1 A 2016 111
## 2 B 2016 222
## 3 C 2016 NA
## 4 A 2017 333
## 5 B 2017 NA
## 6 C 2017 444
## 7 A 2018 NA
## 8 B 2018 555
## 9 C 2018 666</code></pre>
</div>
<div id="tibbles-1" class="section level2">
<h2><span class="header-section-number">4.8</span> tibbles</h2>
<p>The tibble package includes some extra functions for altering tibbles.</p>
<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1"><span class="kw">library</span>(tibble)</a>
<a class="sourceLine" id="cb52-2" data-line-number="2"></a>
<a class="sourceLine" id="cb52-3" data-line-number="3"><span class="co"># Add new column to a tibble (with value)</span></a>
<a class="sourceLine" id="cb52-4" data-line-number="4">tibble<span class="op">::</span><span class="kw">add_column</span>(mydf, <span class="dt">newcol=</span><span class="st">'2014-15'</span>)</a></code></pre></div>
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