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<h1 class="quarto-secondary-nav-title">Practice Session: Collaborative Report</h1>
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<li><a href="#about-the-data" id="toc-about-the-data" class="nav-link active" data-scroll-target="#about-the-data">About the data</a></li>
<li><a href="#explore-clean-and-wrangle-data" id="toc-explore-clean-and-wrangle-data" class="nav-link" data-scroll-target="#explore-clean-and-wrangle-data"><span class="header-section-number">1</span> Explore, clean and wrangle data</a></li>
<li><a href="#create-visually-appealing-and-informative-data-visualization" id="toc-create-visually-appealing-and-informative-data-visualization" class="nav-link" data-scroll-target="#create-visually-appealing-and-informative-data-visualization"><span class="header-section-number">2</span> Create visually appealing and informative data visualization</a></li>
<li><a href="#collaborate-on-a-report-and-publish-using-github-pages" id="toc-collaborate-on-a-report-and-publish-using-github-pages" class="nav-link" data-scroll-target="#collaborate-on-a-report-and-publish-using-github-pages"><span class="header-section-number">3</span> Collaborate on a report and publish using GitHub pages</a></li>
<li><a href="#bonus-add-marine-protected-area-mpa-designation-to-the-data" id="toc-bonus-add-marine-protected-area-mpa-designation-to-the-data" class="nav-link" data-scroll-target="#bonus-add-marine-protected-area-mpa-designation-to-the-data"><span class="header-section-number">4</span> Bonus: Add marine protected area (MPA) designation to the data</a></li>
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Learning Objectives
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<ul>
<li>Practice using common cleaning and wrangling functions</li>
<li>Practice creating plots using common visualization functions in <code>ggplot</code></li>
<li>Practice saving and sharing data visualizations</li>
<li>Practice Git and GitHub workflow and collaborating with a collegue</li>
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Acknowledgements
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<p>These exercises are adapted from Allison Horst’s EDS 221: Scientific Programming Essentials Course for the Bren School’s Master of Environmental Data Science program.</p>
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<section id="about-the-data" class="level2 unnumbered">
<h2 class="unnumbered anchored" data-anchor-id="about-the-data">About the data</h2>
<p>These exercises will be using data on abundance, size, and trap counts (fishing pressure) of California spiny lobster (<em>Panulirus interruptus</em>) and were collected along the mainland coast of the Santa Barbara Channel by Santa Barbara Coastal LTER researchers [CITATION].</p>
<p>Your task: Collaborate on an analysis and create a report to publish using GitHub Pages.</p>
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Setup
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<ol type="1">
<li>Create a new repository with a partner
<ol type="a">
<li>Determine who is the Owner and who is the Collaborator</li>
<li>The Owner creates a repository on GitHub titled with both your names (i.e. If Casey and Camila were partners, and Casey is the Owner, she would create a repo called <code>casey-camila</code>)
<ol type="i">
<li>When creating the repository, add a brief description (i.e. R Practice Session: Collaborating on, Wrangling & Visualizing Data), keep the repo Public, and Initialize the repo with a <code>README</code> file and an R <code>.gitignore</code> template.</li>
</ol></li>
<li>The Owner adds the Collaborator to the repo</li>
<li>Both the Collaborator and the Owner clone the repo into their RStudio <!-- e. Both the Collaborator and the Owner run ```git config pull.rebase false``` in the Terminal to set the `Git` default strategy for `Pull`ing --></li>
</ol></li>
</ol>
<p>**Step 2 and Step 3 are meant <u>to be completed at the same time</u>. - Collaborator completes Step 2 - Owner completes Step 3</p>
<ol start="2" type="1">
<li><strong>Collaborator</strong> creates new files for exercise
<ol type="a">
<li>The Collaborator creates the following directory (folder):
<ol type="i">
<li><code>analysis</code></li>
</ol></li>
<li>After creating the directories, create the following Quarto Documents and store them in the listed folders:
<ol type="i">
<li>Title it: “Owner Analysis”, save it as: <code>owner-analysis.qmd</code>, and store in <code>analysis</code> folder</li>
<li>Title it: “Collaborator Analysis”, save it as: <code>collaborator-analysis.qmd</code>, and store in <code>analysis</code> folder</li>
<li>Title it: “Lobster Report” and save it as: <code>lobster-report.qmd</code> and store in <code>analysis</code> folder</li>
</ol></li>
<li>After creating the files, the Collaborator will <code>stage (add)</code>, <code>commit</code>, write a commit message, <code>pull</code>, and <code>push</code> the files to the remote repository (on GitHub)</li>
<li>The Owner <code>pull</code>s the changes and Quarto Documents into their local repository (their workspace)</li>
</ol></li>
<li><strong>Owner</strong> downloads data from the EDI Data Portal <a href="https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-sbc.77.8">SBC LTER: Reef: Abundance, size and fishing effort for California Spiny Lobster (Panulirus interruptus), ongoing since 2012</a>.
<ol type="a">
<li>Create two new directories one called <code>data</code> and one called <code>figs</code>
<ol type="i">
<li><em>Note: Git does not track empty directories, so you won’t see <code>figs</code> when you push to GitHub</em></li>
</ol></li>
<li>Download the following data and upload them to the <code>data</code> folder:
<ol type="i">
<li>Time-series of lobster abundance and size</li>
<li>Time-series of lobster trap buoy counts</li>
</ol></li>
<li>After creating the <code>data</code> folder and adding the data, the Owner will <code>stage (add)</code>, <code>commit</code>, write a commit message,<code>pull</code>, and <code>push</code> the files to the remote repository (on GitHub)</li>
<li>The Collaborator <code>pull</code>s the changes and data into their local repository (their workspace)</li>
</ol></li>
</ol>
</div>
</div>
</section>
<section id="explore-clean-and-wrangle-data" class="level2" data-number="1">
<h2 data-number="1" class="anchored" data-anchor-id="explore-clean-and-wrangle-data"><span class="header-section-number">1</span> Explore, clean and wrangle data</h2>
<p>For this portion of the exercise, the - <u>Owner</u> will be working with the <strong>lobster abundance and size data</strong> - <u>Collaborator</u> will be working with the <strong>lobster trap buoy counts data</strong></p>
<p>Questions 1-3 you will be working independently since you’re working with different data frames, but you’re welcome to check in with each other.</p>
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Setup
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<li>Open the Quarto Document <code>owner-analysis.qmd</code>
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<li>Check the <code>YAML</code> and add your name to the <code>author</code> field</li>
<li>Create a new section with a level 2 header and title it “Exercise: Explore, Clean, and Wrangle Data”</li>
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<li>Load the following libraries at the top of your Quarto Document</li>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(readr)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(here)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<li>Read in the data and store the data frame as <code>lobster_abundance</code></li>
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<div class="sourceCode" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>lobster_abundance <span class="ot"><-</span> <span class="fu">read_csv</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data/Lobster_Abundance_All_Years_20220829.csv"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<li><p>Look at your data. Take a minute to explore what your data structure looks like, what data types are in the data frame, or use a function to get a high-level summary of the data you’re working with.</p></li>
<li><p>Use the Git workflow: <code>Stage (add) -> Commit -> Pull -> Push</code></p>
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<li><strong>Note:</strong> You also want to <code>Pull</code> when you first open a project</li>
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<section id="convert-missing-values-using-mutate-and-na_if" class="level4" data-number="1.0.1">
<h4 data-number="1.0.1" class="anchored" data-anchor-id="convert-missing-values-using-mutate-and-na_if"><span class="header-section-number">1.0.1</span> Convert missing values using <code>mutate()</code> and <code>na_if()</code></h4>
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Exercise 1 - Question 1
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<p>The variable <code>SIZE_MM</code> uses -99999 as the code for missing values (see metadata or use <code>unique()</code>). This has the potential to cause conflicts with our analyses, so let’s convert -99999 to an <code>NA</code> value. Do this using <code>mutate()</code> and <code>na_if()</code>. Look up the help page to see how to use <code>na_if()</code>. Check your output data using <code>unique()</code>.</p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>lobster_abundance <span class="ot"><-</span> lobster_abundance <span class="sc">%>%</span> </span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">SIZE_MM =</span> <span class="fu">na_if</span>(SIZE_MM, <span class="sc">-</span><span class="dv">99999</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</section>
<section id="filter-practice" class="level4" data-number="1.0.2">
<h4 data-number="1.0.2" class="anchored" data-anchor-id="filter-practice"><span class="header-section-number">1.0.2</span> <code>filter()</code> practice</h4>
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Exercise 2 - Question 2
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<p>Create and store a subset that does NOT include observations from Naples Reef (<code>NAPL</code>). Check your output data frame to ensure that <code>NAPL</code> is NOT in the data frame.</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>not_napl <span class="ot"><-</span> lobster_abundance <span class="sc">%>%</span> </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(SITE <span class="sc">!=</span> <span class="st">"NAPL"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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Exercise 3 - Question 3
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<p>Create and store a subset with lobsters at Arroyo Quemado (<code>AQUE</code>) AND with a carapace length greater than 70 mm. Check your output.</p>
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<div class="sourceCode" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>aque_70mm <span class="ot"><-</span> lobster_abundance <span class="sc">%>%</span> </span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(SITE <span class="sc">==</span> <span class="st">"AQUE"</span> <span class="sc">&</span> SIZE_MM <span class="sc">>=</span> <span class="dv">70</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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Exercise 4 - Question 4
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<p>Find the maximum carapace length using <code>max()</code> and group by <code>SITE</code> and <code>MONTH</code>. Think about how you want to treat the NA values in <code>SIZE_MM</code> (Hint: check the arguments in <code>max()</code>). Check your output.</p>
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<div class="sourceCode" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># `group_by() %>% summarize()` practice</span></span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>max_lobster <span class="ot"><-</span> lobster_abundance <span class="sc">%>%</span> </span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(SITE, MONTH) <span class="sc">%>%</span> </span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarize</span>(<span class="at">MAX_LENGTH =</span> <span class="fu">max</span>(SIZE_MM, <span class="at">na.rm =</span> <span class="cn">TRUE</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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Save your work and don’t forget the Git and GitHub workflow!
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<p>After you’ve completed the exercises or reached a significant stopping point, use the workflow: <code>Stage (add) -> Commit -> Pull -> Push</code></p>
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Setup
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