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<!DOCTYPE html>
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<title>R User Notebook</title>
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<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>
</ul></li>
<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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<section class="normal" id="section-">
<div id="maps" class="section level1">
<h1><span class="header-section-number">9</span> Maps</h1>
<div id="leaflet" class="section level2">
<h2><span class="header-section-number">9.1</span> Leaflet</h2>
<p>To create interactive maps you need the <strong>leaflet</strong> library. This provides various functions that will be transalated into Javascript.</p>
<div id="display-a-basic-map" class="section level3">
<h3><span class="header-section-number">9.1.1</span> Display a basic map</h3>
<div class="sourceCode" id="cb149"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb149-1" data-line-number="1"><span class="kw">library</span>(leaflet)</a></code></pre></div>
<pre><code>## Warning: package 'leaflet' was built under R version 3.4.4</code></pre>
<div class="sourceCode" id="cb151"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb151-1" data-line-number="1">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">leaflet</span>() <span class="co"># This initiates a map; it is possible to change the width and height here</span></a>
<a class="sourceLine" id="cb151-2" data-line-number="2"></a>
<a class="sourceLine" id="cb151-3" data-line-number="3">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">setView</span>(mymap,</a>
<a class="sourceLine" id="cb151-4" data-line-number="4"> <span class="dt">lng =</span> <span class="fl">-0.12481</span>, <span class="co"># The initial longitude + latitude </span></a>
<a class="sourceLine" id="cb151-5" data-line-number="5"> <span class="dt">lat =</span> <span class="fl">51.50811</span>,</a>
<a class="sourceLine" id="cb151-6" data-line-number="6"> <span class="dt">zoom =</span> <span class="dv">10</span>) <span class="co"># The initial zoom level</span></a>
<a class="sourceLine" id="cb151-7" data-line-number="7"></a>
<a class="sourceLine" id="cb151-8" data-line-number="8">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addTiles</span>(mymap) <span class="co"># This add tiles to the map; by default it uses OpenStreetMap</span></a>
<a class="sourceLine" id="cb151-9" data-line-number="9"></a>
<a class="sourceLine" id="cb151-10" data-line-number="10">mymap <span class="co"># this will display the map</span></a></code></pre></div>
<div id="htmlwidget-daa3d759b5ef741e8042" style="width:672px;height:480px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-daa3d759b5ef741e8042">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"setView":[[51.50811,-0.12481],10,[]],"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]}]},"evals":[],"jsHooks":[]}</script>
</div>
<div id="add-markers-shapes-and-popups-to-a-map" class="section level3">
<h3><span class="header-section-number">9.1.2</span> Add markers, shapes and popups to a map</h3>
<div class="sourceCode" id="cb152"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb152-1" data-line-number="1">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addMarkers</span>(mymap, <span class="dt">lng=</span><span class="op">-</span><span class="fl">0.126965</span>, <span class="dt">lat=</span><span class="fl">51.501555</span>, <span class="dt">popup=</span><span class="st">"HMRC"</span>) <span class="co">#Use longitude and latitude to place a marker. The default blue marker is used.</span></a>
<a class="sourceLine" id="cb152-2" data-line-number="2"></a>
<a class="sourceLine" id="cb152-3" data-line-number="3">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addCircles</span>(mymap, <span class="dt">lng=</span><span class="op">-</span><span class="fl">0.021002</span>, <span class="dt">lat=</span><span class="fl">51.504475</span>,<span class="dt">radius=</span><span class="dv">10</span>, <span class="dt">popup=</span><span class="st">"HMRC"</span>) <span class="co">#Use longitude and latitude to place a circle, and radius (in metres) for its size. </span></a>
<a class="sourceLine" id="cb152-4" data-line-number="4"></a>
<a class="sourceLine" id="cb152-5" data-line-number="5">mymap</a></code></pre></div>
<div id="htmlwidget-26e1836bc9f9ccf9c4c2" style="width:672px;height:480px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-26e1836bc9f9ccf9c4c2">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"setView":[[51.50811,-0.12481],10,[]],"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addMarkers","args":[51.501555,-0.126965,null,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":false,"riseOffset":250},"HMRC",null,null,null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]},{"method":"addCircles","args":[51.504475,-0.021002,10,null,null,{"interactive":true,"className":"","stroke":true,"color":"#03F","weight":5,"opacity":0.5,"fill":true,"fillColor":"#03F","fillOpacity":0.2},"HMRC",null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null,null]}],"limits":{"lat":[51.501555,51.504475],"lng":[-0.126965,-0.021002]}},"evals":[],"jsHooks":[]}</script>
</div>
<div id="add-boundaries" class="section level3">
<h3><span class="header-section-number">9.1.3</span> Add Boundaries</h3>
<p>To add boundaries you need geojson or topojson. This needs to be converted into a format the R understands using functions in the geojsonio library.</p>
<div class="sourceCode" id="cb153"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb153-1" data-line-number="1"><span class="kw">library</span>(geojsonio)</a>
<a class="sourceLine" id="cb153-2" data-line-number="2">la <-<span class="st"> </span>geojsonio<span class="op">::</span><span class="kw">topojson_read</span>(<span class="st">'~/R/Local_Auths_Dec16_Gen_Clip_GB.json'</span>)</a></code></pre></div>
<p>R converts this geojson into a Spatial Polygon Dataframe (SPD). This should consist of 2 main attributes: <strong>data</strong> which has descriptive information about the polygon such as a name, and <strong>polygons</strong> and contains all the coordinates for each polygon. To see what the contain you can us the following:</p>
<div class="sourceCode" id="cb154"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb154-1" data-line-number="1">la<span class="op">@</span>data</a>
<a class="sourceLine" id="cb154-2" data-line-number="2">la<span class="op">@</span>polygons</a>
<a class="sourceLine" id="cb154-3" data-line-number="3"><span class="co"># The @ symbol is used to access different 'slots' in the SPD. </span></a></code></pre></div>
<p>The boundary data can now be attached to the map when it is first initialized.</p>
<div class="sourceCode" id="cb155"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb155-1" data-line-number="1">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">leaflet</span>(la)</a>
<a class="sourceLine" id="cb155-2" data-line-number="2">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">setView</span>(mymap,<span class="dt">lng=</span><span class="op">-</span><span class="fl">3.332291</span>,<span class="dt">lat=</span><span class="fl">54.978353</span>,<span class="dt">zoom=</span><span class="dv">5</span>)</a>
<a class="sourceLine" id="cb155-3" data-line-number="3">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addPolygons</span>(mymap, <span class="dt">color=</span><span class="st">'black'</span>,<span class="dt">weight=</span><span class="dv">1</span>, <span class="dt">fillColor=</span><span class="st">'white'</span>,<span class="dt">fillOpacity =</span> <span class="fl">0.8</span>) <span class="co">#This draws the boundary lines</span></a>
<a class="sourceLine" id="cb155-4" data-line-number="4">mymap</a></code></pre></div>
</div>
<div id="add-interactivity" class="section level3">
<h3><span class="header-section-number">9.1.4</span> Add Interactivity</h3>
<p>Highlights can be added when you hover over an area.</p>
<div class="sourceCode" id="cb156"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb156-1" data-line-number="1">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addPolygons</span>(mymap,</a>
<a class="sourceLine" id="cb156-2" data-line-number="2"> <span class="dt">color=</span><span class="st">'black'</span>,</a>
<a class="sourceLine" id="cb156-3" data-line-number="3"> <span class="dt">weight=</span><span class="dv">1</span>,</a>
<a class="sourceLine" id="cb156-4" data-line-number="4"> <span class="dt">fillColor=</span><span class="st">'white'</span>,</a>
<a class="sourceLine" id="cb156-5" data-line-number="5"> <span class="dt">fillOpacity =</span> <span class="fl">0.8</span> ,</a>
<a class="sourceLine" id="cb156-6" data-line-number="6"> <span class="dt">highlight =</span> <span class="kw">highlightOptions</span>(</a>
<a class="sourceLine" id="cb156-7" data-line-number="7"> <span class="dt">weight =</span> <span class="dv">2</span>,</a>
<a class="sourceLine" id="cb156-8" data-line-number="8"> <span class="dt">color =</span> <span class="st">"red"</span>,</a>
<a class="sourceLine" id="cb156-9" data-line-number="9"> <span class="dt">bringToFront =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb156-10" data-line-number="10"> )</a></code></pre></div>
<p>Popup info can also be added when you hover over an area. This requires using the sprintf function, which includes HTML.</p>
<div class="sourceCode" id="cb157"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb157-1" data-line-number="1">mylabel <-<span class="st"> </span><span class="kw">sprintf</span>(<span class="st">"<strong>%s</strong><br/>%s"</span>, la<span class="op">$</span>lad16nm, la<span class="op">$</span>lad16cd ) <span class="op">%>%</span><span class="st"> </span><span class="kw">lapply</span>(htmltools<span class="op">::</span>HTML)</a>
<a class="sourceLine" id="cb157-2" data-line-number="2"></a>
<a class="sourceLine" id="cb157-3" data-line-number="3"><span class="co"># These can can now be assigned to the label attribute</span></a>
<a class="sourceLine" id="cb157-4" data-line-number="4">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addPolygons</span>(mymap, <span class="dt">color=</span><span class="st">'black'</span>,<span class="dt">weight=</span><span class="dv">1</span>, <span class="dt">fillColor=</span><span class="st">'white'</span>,<span class="dt">fillOpacity =</span> <span class="fl">0.8</span>,</a>
<a class="sourceLine" id="cb157-5" data-line-number="5"> <span class="dt">highlight =</span> <span class="kw">highlightOptions</span>(</a>
<a class="sourceLine" id="cb157-6" data-line-number="6"> <span class="dt">weight =</span> <span class="dv">2</span>,</a>
<a class="sourceLine" id="cb157-7" data-line-number="7"> <span class="dt">color =</span> <span class="st">"red"</span>,</a>
<a class="sourceLine" id="cb157-8" data-line-number="8"> <span class="dt">bringToFront =</span> <span class="ot">TRUE</span>),</a>
<a class="sourceLine" id="cb157-9" data-line-number="9"> <span class="dt">label =</span> mylabel)</a></code></pre></div>
<p>The code that is written in the <strong>sprintf</strong> function rquires a special format. The first argument defines what and how text willl be dispalayed. It includes placeholders (eg. %s) that can have differnet types. All subsequent arguments represent the data variables that will are represented by the placeholders (in the order they occur).For more info see <a href="https://www.rdocumentation.org/packages/base/versions/3.4.3/topics/sprintf" class="uri">https://www.rdocumentation.org/packages/base/versions/3.4.3/topics/sprintf</a>.</p>
</div>
<div id="attach-extra-information-to-your-boundary-dataset" class="section level3">
<h3><span class="header-section-number">9.1.5</span> Attach extra information to your boundary dataset</h3>
<p>You will usually want to add additional data/statistics to the boundary file, so that you can improve visualition/interactivity.
You can merge a regular dataframe wih an SPD provided they have a common variable (eg. ONS Id’s).</p>
<div class="sourceCode" id="cb158"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb158-1" data-line-number="1"><span class="co"># First create a dataframe with test data</span></a>
<a class="sourceLine" id="cb158-2" data-line-number="2">mydf <-<span class="st"> </span><span class="kw">data.frame</span>(<span class="st">'lad16cd'</span>=<span class="kw">c</span>(<span class="st">'E06000001'</span>,<span class="st">'E06000002'</span>,<span class="st">'E06000003'</span>),</a>
<a class="sourceLine" id="cb158-3" data-line-number="3"> <span class="st">'extraStat'</span>=<span class="kw">c</span>(<span class="dv">25000</span>,<span class="dv">34000</span>,<span class="dv">38000</span>) )</a>
<a class="sourceLine" id="cb158-4" data-line-number="4"></a>
<a class="sourceLine" id="cb158-5" data-line-number="5"><span class="co"># Merge extra data into the SPD</span></a>
<a class="sourceLine" id="cb158-6" data-line-number="6"><span class="kw">require</span>(sp) <span class="co"># Need for the following merge to work correctly</span></a>
<a class="sourceLine" id="cb158-7" data-line-number="7">la <-<span class="st"> </span>sp<span class="op">::</span><span class="kw">merge</span>(la, mydf, <span class="dt">by.x =</span> <span class="st">"lad16cd"</span>, <span class="dt">by.y =</span> <span class="st">"lad16cd"</span>)</a>
<a class="sourceLine" id="cb158-8" data-line-number="8"></a>
<a class="sourceLine" id="cb158-9" data-line-number="9"><span class="co">#Check that merge has worked</span></a>
<a class="sourceLine" id="cb158-10" data-line-number="10">la<span class="op">@</span>data <span class="co"># A new column should appear with the extra data </span></a></code></pre></div>
</div>
<div id="add-colour-based-on-area-data" class="section level3">
<h3><span class="header-section-number">9.1.6</span> Add colour based on area data</h3>
<p>First you will need to define a colour pallete, and the range of values (bins) they will apply to. This is done using the colorBin function.</p>
<div class="sourceCode" id="cb159"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb159-1" data-line-number="1">pal <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">colorBin</span>(<span class="st">"YlOrRd"</span>, <span class="dt">bins =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">24999</span>, <span class="dv">34000</span>, <span class="dv">38000</span>, <span class="ot">Inf</span>))</a>
<a class="sourceLine" id="cb159-2" data-line-number="2"></a>
<a class="sourceLine" id="cb159-3" data-line-number="3"><span class="co"># 'YlorRd' is a particular color scale. See http://colorbrewer2.org for alternatives. You could also create a user defined list of colours using Hexadecimal eg. #fcbba1 instead. </span></a></code></pre></div>
<p>Now the colour pallete can be assigned to the <strong>fillColor</strong> attribute, allomg with the variable name that will be used .</p>
<div class="sourceCode" id="cb160"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb160-1" data-line-number="1">mymap <-<span class="st"> </span>leaflet<span class="op">::</span><span class="kw">addPolygons</span>(mymap,</a>
<a class="sourceLine" id="cb160-2" data-line-number="2"> <span class="dt">color=</span><span class="st">'black'</span>,</a>
<a class="sourceLine" id="cb160-3" data-line-number="3"> <span class="dt">weight=</span><span class="dv">1</span>,</a>
<a class="sourceLine" id="cb160-4" data-line-number="4"> <span class="dt">fillColor=</span><span class="op">~</span><span class="kw">pal</span>(extraStat), <span class="co">#Nb. the ~ indicates that the variable is contained with the la SPD </span></a>
<a class="sourceLine" id="cb160-5" data-line-number="5"> <span class="dt">fillOpacity =</span> <span class="fl">0.8</span>,</a>
<a class="sourceLine" id="cb160-6" data-line-number="6"> <span class="dt">highlight =</span> <span class="kw">highlightOptions</span>(</a>
<a class="sourceLine" id="cb160-7" data-line-number="7"> <span class="dt">weight =</span> <span class="dv">4</span>,</a>
<a class="sourceLine" id="cb160-8" data-line-number="8"> <span class="dt">color =</span> <span class="st">"red"</span>,</a>
<a class="sourceLine" id="cb160-9" data-line-number="9"> <span class="dt">bringToFront =</span> <span class="ot">TRUE</span>))</a></code></pre></div>
</div>
</div>
<div id="inserting-html-javascript-directly-into-r" class="section level2">
<h2><span class="header-section-number">9.2</span> Inserting HTML & Javascript directly into R</h2>
<p>Instead of using packages to create javavscript, you can insert javascript directly into Rmarkdown, and it should be displayed correctly when it Knitr is used.</p>
<div class="sourceCode" id="cb161"><pre class="sourceCode js"><code class="sourceCode javascript"><a class="sourceLine" id="cb161-1" data-line-number="1"><span class="op"><</span>link rel<span class="op">=</span><span class="st">"stylesheet"</span> href<span class="op">=</span><span class="st">"https://unpkg.com/leaflet@1.0.0-rc.3/dist/leaflet.css"</span> /> </a>
<a class="sourceLine" id="cb161-2" data-line-number="2"><span class="op"><</span>script src<span class="op">=</span><span class="st">"https://unpkg.com/leaflet@1.0.0-rc.3/dist/leaflet.js"</span><span class="op">></span></script<span class="op">></span></a>
<a class="sourceLine" id="cb161-3" data-line-number="3"><span class="op"><</span>script type<span class="op">=</span><span class="st">"text/javascript"</span> src<span class="op">=</span><span class="st">"https://stamen-maps.a.ssl.fastly.net/js/tile.stamen.js"</span><span class="op">></span></script<span class="op">></span></a>
<a class="sourceLine" id="cb161-4" data-line-number="4"><span class="op"><</span>div id<span class="op">=</span><span class="st">"mapid"</span><span class="op">></span></div<span class="op">></span></a>
<a class="sourceLine" id="cb161-5" data-line-number="5"></a>
<a class="sourceLine" id="cb161-6" data-line-number="6"><span class="co">// Define Map area/position and any background tiles </span></a>
<a class="sourceLine" id="cb161-7" data-line-number="7"> <span class="kw">var</span> map <span class="op">=</span> <span class="kw">new</span> <span class="va">L</span>.<span class="at">Map</span>(<span class="st">'mapid'</span><span class="op">,</span> <span class="op">{</span> <span class="dt">center</span><span class="op">:</span> <span class="kw">new</span> <span class="va">L</span>.<span class="at">LatLng</span>(<span class="fl">53.10</span><span class="op">,</span> <span class="fl">-1.26</span>)<span class="op">,</span><span class="dt">zoom</span><span class="op">:</span> <span class="dv">7</span> <span class="op">}</span>)<span class="op">;</span></a>
<a class="sourceLine" id="cb161-8" data-line-number="8"> <span class="kw">var</span> layer <span class="op">=</span> <span class="kw">new</span> <span class="va">L</span>.<span class="at">StamenTileLayer</span>(<span class="st">"terrain"</span>)<span class="op">;</span></a>
<a class="sourceLine" id="cb161-9" data-line-number="9"> <span class="va">map</span>.<span class="at">addLayer</span>(layer)<span class="op">;</span></a></code></pre></div>
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