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<div class="quarto-title">
<h1 class="title">MOVER dataset: EPIC complications</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<div class="cell">
<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">theme_set</span>(<span class="fu">theme_bw</span>())</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#source("01_read_clean.R")</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#save.image(file = "comps.rda")</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">load</span>(<span class="st">"comps.rda"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>The post-operative complications dataset includes 36985 patients who had 64214 surgeries.</p>
<p>The whole dataset includes 39685 patients who had 64354 surgeries, a discrepancy of 140 surgeries. Which is small considering the overall size. I wonder if these patients could have died without a recorded complication?</p>
<section id="number-of-surgeries-that-resulted-in-any-complication" class="level1">
<h1>Number of surgeries that resulted in any complication</h1>
<div class="cell">
<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>complications <span class="sc">%>%</span> </span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">count</span>(any_complication, <span class="at">name =</span> <span class="st">"n_patients"</span>) <span class="sc">%>%</span> </span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<table class="table table-sm table-striped">
<thead>
<tr class="header">
<th style="text-align: left;">any_complication</th>
<th style="text-align: right;">n_patients</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">No</td>
<td style="text-align: right;">61387</td>
</tr>
<tr class="even">
<td style="text-align: left;">Yes</td>
<td style="text-align: right;">2829</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
<section id="number-of-complications-per-surgery" class="level1">
<h1>Number of complications per surgery</h1>
<div class="cell">
<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>complications <span class="sc">%>%</span> </span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">count</span>(n_complications, <span class="at">name =</span> <span class="st">"n_patients"</span>) <span class="sc">%>%</span> </span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> knitr<span class="sc">::</span><span class="fu">kable</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<table class="table table-sm table-striped">
<thead>
<tr class="header">
<th style="text-align: right;">n_complications</th>
<th style="text-align: right;">n_patients</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: right;">0</td>
<td style="text-align: right;">61387</td>
</tr>
<tr class="even">
<td style="text-align: right;">1</td>
<td style="text-align: right;">350</td>
</tr>
<tr class="odd">
<td style="text-align: right;">2</td>
<td style="text-align: right;">1681</td>
</tr>
<tr class="even">
<td style="text-align: right;">3</td>
<td style="text-align: right;">340</td>
</tr>
<tr class="odd">
<td style="text-align: right;">4</td>
<td style="text-align: right;">182</td>
</tr>
<tr class="even">
<td style="text-align: right;">5</td>
<td style="text-align: right;">117</td>
</tr>
<tr class="odd">
<td style="text-align: right;">6</td>
<td style="text-align: right;">72</td>
</tr>
<tr class="even">
<td style="text-align: right;">7</td>
<td style="text-align: right;">60</td>
</tr>
<tr class="odd">
<td style="text-align: right;">8</td>
<td style="text-align: right;">6</td>
</tr>
<tr class="even">
<td style="text-align: right;">9</td>
<td style="text-align: right;">2</td>
</tr>
<tr class="odd">
<td style="text-align: right;">10</td>
<td style="text-align: right;">12</td>
</tr>
<tr class="even">
<td style="text-align: right;">11</td>
<td style="text-align: right;">1</td>
</tr>
<tr class="odd">
<td style="text-align: right;">12</td>
<td style="text-align: right;">2</td>
</tr>
<tr class="even">
<td style="text-align: right;">13</td>
<td style="text-align: right;">3</td>
</tr>
<tr class="odd">
<td style="text-align: right;">17</td>
<td style="text-align: right;">1</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
<section id="types-of-complications" class="level1">
<h1>Types of complications</h1>
<div class="cell">
<div class="sourceCode cell-code" 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>complications_all <span class="sc">%>%</span> </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(comp_abbr <span class="sc">!=</span> <span class="st">"None"</span>) <span class="sc">%>%</span> </span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(comp_abbr <span class="sc">!=</span> <span class="st">"Post-op AN"</span>) <span class="sc">%>%</span> </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">y =</span> <span class="fu">fct_rev</span>(<span class="fu">fct_infreq</span>(comp_abbr)))) <span class="sc">+</span></span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_bar</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="README_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<p>I have removed “AN Post-op Complications”/“Post-op AN” from the above plot as it seems to be uninformative, I wonder if it stands for “Unknown” or even something similar to an administrative entry?</p>
</section>
<section id="combinations-of-complications" class="level1">
<h1>Combinations of complications</h1>
<div class="cell">
<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>complications <span class="sc">%>%</span> </span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(complications_abbr <span class="sc">!=</span> <span class="st">"No complications"</span>) <span class="sc">%>%</span> </span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">count</span>(complications_abbr, <span class="at">sort =</span> <span class="cn">TRUE</span>) <span class="sc">%>%</span> </span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(n <span class="sc">></span> <span class="dv">20</span>) <span class="sc">%>%</span> </span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="fu">fct_reorder</span>(complications_abbr, n), n)) <span class="sc">+</span></span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>() <span class="sc">+</span></span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">coord_flip</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<p><img src="README_files/figure-html/unnamed-chunk-5-1.png" class="img-fluid" width="672"></p>
</div>
</div>
<p>Combinations of complications that occured more than 20 times.</p>
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