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Lesson5.html
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<a href="Lesson1.html">Lesson 1</a>
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<p><br />
<!-- install packages --></p>
<!-- ____________________________________________________________________________ -->
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<!-- start body -->
<div id="lesson-5-turning-code-into-reproducible-documents-with-rmarkdown" class="section level1">
<h1>Lesson 5: Turning code into reproducible documents with <code>Rmarkdown</code></h1>
<p> </p>
<p>Functions for Lesson 5<br />
<code>here</code>, <code>summarise</code>, <code>set_here</code>, <code>dr_here</code><br />
</p>
<p>Packages for Lesson 5<br />
<code>here</code>, <code>dplyr</code>, <code>readr</code>,<code>rmarkdown</code><br />
</p>
</div>
<div id="agenda" class="section level1">
<h1>Agenda</h1>
<p>Create reproducible HTML, PDF, and Word documents from R using <code>RMarkdown</code>.<br />
* <strong><a href="https://github.com/darwinanddavis/EmoRyCodingClub/raw/master/Lesson5_rmd.Rmd">Download the <code>RMarkdown</code> template (right click > Save As)</a>.</strong> Save this in the same folder as your coding club files. The file should have a <em>.Rmd</em> extension, e.g. <strong>Lesson5_rmd.Rmd</strong>.<br />
* Open <code>RStudio</code> and run the following code to install the necessary packages:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">packages <-<span class="st"> </span><span class="kw">c</span>(<span class="st">"pacman"</span>, <span class="st">"rmarkdown"</span>, <span class="st">"here"</span>)
<span class="kw">install.packages</span>(packages, <span class="dt">dependencies =</span> T)
<span class="kw">lapply</span>(packages, require, <span class="dt">character.only =</span> T)</code></pre></div>
<p> </p>
<!-- end yaml template------------------------------------------------------- -->
</div>
<div id="do-first" class="section level1">
<h1>Do First</h1>
<p>Recreate the below plot using the larger NYC Airbnb dataset. Here's the code to add the title and labels.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">url <-<span class="st"> "http://data.insideairbnb.com/united-states/ny/new-york-city/2021-04-07/data/listings.csv.gz"</span>
nyc_full <-<span class="st"> </span>readr<span class="op">::</span><span class="kw">read_csv</span>(url) <span class="co"># reads in data</span>
ttl <-<span class="st"> "NYC Airbnb availability"</span>
subttl <-<span class="st"> "for room types across neighbourhoods"</span>
xlab <-<span class="st"> "Availability of property in next 30 days"</span>
ylab <-<span class="st"> "Count"</span>
<span class="co"># append this to your ggplot function with a `+`</span>
<span class="kw">labs</span>(<span class="dt">title =</span> ttl, <span class="dt">subtitle =</span> subttl, <span class="dt">x =</span> xlab, <span class="dt">y =</span> ylab)</code></pre></div>
<pre><code> [1] "id" "listing_url"
[3] "scrape_id" "last_scraped"
[5] "name" "description"
[7] "neighborhood_overview" "picture_url"
[9] "host_id" "host_url"
[11] "host_name" "host_since"
[13] "host_location" "host_about"
[15] "host_response_time" "host_response_rate"
[17] "host_acceptance_rate" "host_is_superhost"
[19] "host_thumbnail_url" "host_picture_url"
[21] "host_neighbourhood" "host_listings_count"
[23] "host_total_listings_count" "host_verifications"
[25] "host_has_profile_pic" "host_identity_verified"
[27] "neighbourhood" "neighbourhood_cleansed"
[29] "neighbourhood_group_cleansed" "latitude"
[31] "longitude" "property_type"
[33] "room_type" "accommodates"
[35] "bathrooms" "bathrooms_text"
[37] "bedrooms" "beds"
[39] "amenities" "price"
[41] "minimum_nights" "maximum_nights"
[43] "minimum_minimum_nights" "maximum_minimum_nights"
[45] "minimum_maximum_nights" "maximum_maximum_nights"
[47] "minimum_nights_avg_ntm" "maximum_nights_avg_ntm"
[49] "calendar_updated" "has_availability"
[51] "availability_30" "availability_60"
[53] "availability_90" "availability_365"
[55] "calendar_last_scraped" "number_of_reviews"
[57] "number_of_reviews_ltm" "number_of_reviews_l30d"
[59] "first_review" "last_review"
[61] "review_scores_rating" "review_scores_accuracy"
[63] "review_scores_cleanliness" "review_scores_checkin"
[65] "review_scores_communication" "review_scores_location"
[67] "review_scores_value" "license"
[69] "instant_bookable" "calculated_host_listings_count"
[71] "calculated_host_listings_count_entire_homes" "calculated_host_listings_count_private_rooms"
[73] "calculated_host_listings_count_shared_rooms" "reviews_per_month" </code></pre>
<p><img src="Lesson5_files/figure-html/unnamed-chunk-4-1.png" width="100%" /></p>
</div>
<div id="setting-your-working-directory" class="section level1">
<h1>Setting your working directory</h1>
<p>Using <code>here</code> to set your working directory</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(here) <span class="co"># load the here package if not already</span>
<span class="kw">set_here</span>() <span class="co"># set current working directory </span>
<span class="kw">dr_here</span>() <span class="co"># print current working directory where .here is located</span></code></pre></div>
<p><strong>Example 1</strong><br />
1. Create a folder in your local directory called <strong>'lookhere'</strong>.<br />
2. Open a new file in TextEdit (Mac) or Notepad (Windows), type in something like " <em>We found the here file!</em> ", then save the file as <strong>"heretest.txt"</strong>.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(readr)
<span class="co"># example 1</span>
<span class="kw">list.files</span>() <span class="co"># print files in your current working dir. the 'heretest.txt' file is not here, but one folder below in the new 'lookhere' folder</span>
<span class="kw">here</span>(<span class="st">"lookhere"</span>, <span class="st">"heretest.txt"</span>) <span class="co"># using here to forage for the file</span>
<span class="kw">here</span>(<span class="st">"lookhere"</span>, <span class="st">"heretest.txt"</span>) <span class="op">%>%</span><span class="st"> </span>read_lines <span class="co"># print the contents in R</span></code></pre></div>
<p> </p>
<p><strong>Example 2</strong><br />
1. Create another folder within the <strong>lookhere</strong> folder called <strong>lookheretoo</strong><br />
2. Create another .txt file called <strong>heretesttoo.txt</strong> and save it.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># example 2 create two folders</span>
folder1 <-<span class="st"> "lookhere"</span>
folder2 <-<span class="st"> "lookheretoo"</span>
file <-<span class="st"> "heretesttoo.txt"</span>
<span class="co"># navigate to the /lookheretoo folder and open the heretesttoo file using 'here'</span>
<span class="kw">here</span>(folder1, folder2, file) <span class="op">%>%</span><span class="st"> </span>read_lines
<span class="kw">read_lines</span>(<span class="kw">here</span>(folder1, folder2, file)) <span class="co"># non-tidy version</span></code></pre></div>
<p><br />
Why is <code>here</code> useful?<br />
* You can step through sub folders by defining them individually as function inputs<br />
* You can user define these subfolders as variables at the beginning of your <code>R</code> script and refer to them throughout your script without pasting, e.g. <code>paste(folder1,folder2,sep="/")</code>.</p>
</div>
<div id="creating-an-r-project-rproj-file" class="section level1">
<h1>Creating an <code>R</code> project (<code>Rproj</code>) file</h1>
<p><strong>Option 1:</strong> Create an RProject new directory:<br />
* <em>File > New Project</em><br />
* <em>Create New Project</em><br />
* Choose a name for your RProj folder. Fill out <em>Directory name:</em> (make it machine-friendly, i.e. no spaces)<br />
* Choose a place for the RProj to live. <em>Browse</em><br />
* Select <em>Open in new session</em></p>
<p> </p>
<p><strong>Option 2:</strong> If you already have a folder <em>just</em> for Emory Coding Club:<br />
* <em>File > New Project</em><br />
* <em>Existing directory > Browse</em><br />
* Select <em>Open in new session</em></p>
<p> </p>
<ul>
<li>Open the 'Lesson5_rmd.Rmd' file within this project and save it as 'Lesson5_rmd.Rmd'.<br />
</li>
<li>Open another <em>.R</em> file within this project and save it.<br />
</li>
<li>Now repeat the above steps with a second <em>Rproj</em> file. Save this in another directory somewhere on your computer.<br />
</li>
<li>Now check the working directory within both <em>Rproj</em> files using the <code>here</code> package. What do you see?</li>
</ul>
</div>
<div id="navigating-the-rmarkdown-interface" class="section level1">
<h1>Navigating the <code>Rmarkdown</code> interface</h1>
<p>Have a look through each section of the raw <code>.Rmd</code> file to see what the code does. You'll be using this template to create your own files, such as creating personal notes for future sessions in this coding club.</p>
<!-- ----------------------- image --------------------------- -->
<div align="center" ;="" text-align:center="">
<p><img src="img/rmd.jpg" style=width:100%></p>
</div>
<!-- ----------------------- image --------------------------- -->
</div>
<div id="exercises" class="section level1">
<h1>Exercises</h1>
<ul>
<li>Knit an HTML document. Use the hotkey <code>Cmd/Ctrl + Shift + K</code><br />
</li>
<li>Create a 'EmoRy Coding Club notes' document<br />
</li>
<li>Create your own parameter in the yaml<br />
</li>
<li>Create a code chunk that shows the code and output, but masks any warnings<br />
</li>
<li>Create a code chunk with a plot of your own data or from the Airbnb data. Here's the NYC Airbnb data:</li>
</ul>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># large Airbnb dataset (106 cols)</span>
<span class="kw">require</span>(readr, dplyr)
url <-<span class="st"> "http://data.insideairbnb.com/united-states/ny/new-york-city/2021-04-07/data/listings.csv.gz"</span>
nyc_full <-<span class="st"> </span><span class="kw">read_csv</span>(url) <span class="co"># reads in data</span>
nyc_full <span class="op">%>%</span><span class="st"> </span>glimpse</code></pre></div>
<ul>
<li>Change the above figure dimensions in the knitted document<br />
</li>
<li>Create a table with the title in bold, one of the columns set to right justified text, and one of the rows italicised<br />
</li>
<li>Write an inline equation and an indented equation</li>
</ul>
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