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<title>Lab 1</title>
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<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#part-1-data-exploration-and-wrangling-review" id="toc-part-1-data-exploration-and-wrangling-review" class="nav-link active" data-scroll-target="#part-1-data-exploration-and-wrangling-review">Part 1: data exploration and wrangling review</a>
<ul class="collapse">
<li><a href="#example-1" id="toc-example-1" class="nav-link" data-scroll-target="#example-1">Example 1:</a>
<ul class="collapse">
<li><a href="#pseudocode" id="toc-pseudocode" class="nav-link" data-scroll-target="#pseudocode">Pseudocode</a></li>
</ul></li>
<li><a href="#example-2" id="toc-example-2" class="nav-link" data-scroll-target="#example-2">Example 2</a>
<ul class="collapse">
<li><a href="#pseudocode-1" id="toc-pseudocode-1" class="nav-link" data-scroll-target="#pseudocode-1">Pseudocode</a></li>
<li><a href="#functional-code" id="toc-functional-code" class="nav-link" data-scroll-target="#functional-code">Functional code</a></li>
</ul></li>
<li><a href="#example-3" id="toc-example-3" class="nav-link" data-scroll-target="#example-3">Example 3</a>
<ul class="collapse">
<li><a href="#pseudocode-2" id="toc-pseudocode-2" class="nav-link" data-scroll-target="#pseudocode-2">Pseudocode</a></li>
<li><a href="#functional-code-1" id="toc-functional-code-1" class="nav-link" data-scroll-target="#functional-code-1">Functional code</a></li>
</ul></li>
<li><a href="#example-4" id="toc-example-4" class="nav-link" data-scroll-target="#example-4">Example 4</a></li>
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<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Lab 1</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Casey </p>
</div>
</div>
</div>
</header>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" 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>(tidyverse)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(here)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(sf)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tmap)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" 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>sfo_trees_df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="fu">here</span>(<span class="st">'data'</span>, <span class="st">'sfo_trees'</span>, <span class="st">'sfo_trees.csv'</span>)) <span class="sc">%>%</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> janitor<span class="sc">::</span><span class="fu">clean_names</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<section id="part-1-data-exploration-and-wrangling-review" class="level1">
<h1>Part 1: data exploration and wrangling review</h1>
<section id="example-1" class="level2">
<h2 class="anchored" data-anchor-id="example-1">Example 1:</h2>
<p>Find counts of observations by <code>legal_status</code>, then select the statuses with the five highest tree counts.</p>
<section id="pseudocode" class="level3">
<h3 class="anchored" data-anchor-id="pseudocode">Pseudocode</h3>
<p>grouping by legal status each observation into its own variable column, so counts are separate summarize by tree count</p>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" 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>sfo_trees_df <span class="sc">%>%</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(legal_status) <span class="sc">%>%</span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarize</span>(<span class="at">tree_count =</span> <span class="fu">n</span>())</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 13 × 2
legal_status tree_count
<chr> <int>
1 DPW Maintained 143537
2 Landmark tree 243
3 Permitted Site 40201
4 Planning Code 138.1 required 1148
5 Private 336
6 Property Tree 362
7 Prune Opt Out 178
8 Section 143 131
9 Section 806 (d) 619
10 Significant Tree 1978
11 Street Tree Maintenance Opt Out 58
12 Undocumented 8770
13 <NA> 57</code></pre>
</div>
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" 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>top_5_status <span class="ot"><-</span> sfo_trees_df <span class="sc">%>%</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(<span class="sc">!</span><span class="fu">is.na</span>(legal_status)) <span class="sc">%>%</span></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(legal_status) <span class="sc">%>%</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarize</span>(<span class="at">tree_count =</span> <span class="fu">n</span>()) <span class="sc">%>%</span></span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">ungroup</span>() <span class="sc">%>%</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">slice_max</span>(tree_count, <span class="at">n =</span> <span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<p>Make a ggplot of the top 5 observations from above:</p>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" 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="fu">ggplot</span>(top_5_status, </span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">y =</span> <span class="fu">fct_reorder</span>(legal_status, tree_count), </span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> tree_count)) <span class="sc">+</span></span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>(<span class="at">fill =</span> <span class="st">'blue'</span>) <span class="sc">+</span></span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">y =</span> <span class="st">'Legal status'</span>, <span class="at">x =</span> <span class="st">'tree count'</span>) <span class="sc">+</span></span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="lab_1_cco_files/figure-html/unnamed-chunk-2-1.png" class="img-fluid" width="672"></p>
</div>
</div>
</section>
</section>
<section id="example-2" class="level2">
<h2 class="anchored" data-anchor-id="example-2">Example 2</h2>
<p>Only keep observations where legal status is “Permitted Site” and caretaker is “MTA” or “DPW”. Store as “permitted_mta_dpw”</p>
<section id="pseudocode-1" class="level3">
<h3 class="anchored" data-anchor-id="pseudocode-1">Pseudocode</h3>
<p>filter to keep the observations with Permitted Site, and also for the caretaker categories - logic of “and”? mutate or select?</p>
</section>
<section id="functional-code" class="level3">
<h3 class="anchored" data-anchor-id="functional-code">Functional code</h3>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>permitted_mta_dpw <span class="ot"><-</span> sfo_trees_df <span class="sc">%>%</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(legal_status <span class="sc">%in%</span> <span class="st">'Permitted Site'</span> <span class="sc">&</span> caretaker <span class="sc">%in%</span> <span class="fu">c</span>(<span class="st">'MTA'</span>, <span class="st">'DPW'</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
</section>
</section>
<section id="example-3" class="level2">
<h2 class="anchored" data-anchor-id="example-3">Example 3</h2>
<p>Only keep observations of oak and pine trees then only keep columns “species”, “legal_status”, “plant_date”, and “latitude” and “longitude” For each tree, note whether it’s an oak or a pine!</p>
<section id="pseudocode-2" class="level3">
<h3 class="anchored" data-anchor-id="pseudocode-2">Pseudocode</h3>
<p>Filter oak and pine trees, but the species are complicated! find by a search string? if the column <em>contains</em> pine or oak, and then subset select columns as needed mutate a new column for oak vs pine</p>
</section>
<section id="functional-code-1" class="level3">
<h3 class="anchored" data-anchor-id="functional-code-1">Functional code</h3>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>oak_pine_df <span class="ot"><-</span> sfo_trees_df <span class="sc">%>%</span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(<span class="fu">str_detect</span>(species, <span class="st">"Oak"</span>) <span class="sc">|</span> <span class="fu">str_detect</span>(species, <span class="st">'Pine'</span>)) <span class="sc">%>%</span></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(species, legal_status, plant_date, latitude, longitude) <span class="sc">%>%</span></span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">type =</span> <span class="fu">ifelse</span>(<span class="fu">str_detect</span>(species, <span class="st">'Oak'</span>), <span class="st">'oak'</span>, <span class="st">'pine'</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> oak_pine_df, <span class="fu">aes</span>(<span class="at">x =</span> longitude, <span class="at">y =</span> latitude, <span class="at">color =</span> type)) <span class="sc">+</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.title =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">color =</span> <span class="st">'Tree type'</span>,</span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a> <span class="at">caption =</span> <span class="st">'Location of oaks and pines in San Francisco'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output-display">
<p><img src="lab_1_cco_files/figure-html/unnamed-chunk-5-1.png" class="img-fluid" width="672"></p>
</div>
</div>
</section>
</section>
<section id="example-4" class="level2">
<h2 class="anchored" data-anchor-id="example-4">Example 4</h2>
<p>load a list of CA native species</p>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>ca_native_df <span class="ot"><-</span> <span class="fu">read_csv</span>(<span class="fu">here</span>(<span class="st">'data/sfo_trees/ca_native_spp.csv'</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
</div>
<p>How can we compare the CA native species to thos in our SF trees database? Add a column noting whether a tree is native or not. We’ll need the common and scientific names separated!</p>
<div class="cell">
<details>
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>sfo_trees_native <span class="ot"><-</span> sfo_trees_df <span class="sc">%>%</span></span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">separate</span>(species, <span class="at">into =</span> <span class="fu">c</span>(<span class="st">'spp_sci'</span>, <span class="st">'spp_common'</span>), <span class="at">sep =</span> <span class="st">' :: '</span>) <span class="sc">%>%</span></span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="fu">starts_with</span>(<span class="st">'spp'</span>), <span class="st">'plant_date'</span>, <span class="st">'legal_status'</span>, <span class="st">'longitude'</span>, <span class="st">'latitude'</span>) <span class="sc">%>%</span></span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">ca_native =</span> (spp_sci <span class="sc">%in%</span> ca_native_df<span class="sc">$</span>scientific_name))</span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a>sfo_native_status <span class="ot"><-</span> sfo_trees_native <span class="sc">%>%</span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(legal_status, ca_native) <span class="sc">%>%</span></span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarize</span>(<span class="at">n_trees =</span> <span class="fu">n</span>(),</span>
<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a> <span class="at">n_species =</span> <span class="fu">n_distinct</span>(spp_sci))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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