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<li><a href="#genrate-recurrence-covariates" id="toc-genrate-recurrence-covariates" class="nav-link active" data-scroll-target="#genrate-recurrence-covariates"><span class="header-section-number">6.1</span> Genrate recurrence covariates</a></li>
<li><a href="#example-of-recurrence-covariates" id="toc-example-of-recurrence-covariates" class="nav-link" data-scroll-target="#example-of-recurrence-covariates"><span class="header-section-number">6.2</span> Example of recurrence covariates</a></li>
<li><a href="#recurrence-covariates-in-the-data" id="toc-recurrence-covariates-in-the-data" class="nav-link" data-scroll-target="#recurrence-covariates-in-the-data"><span class="header-section-number">6.3</span> Recurrence covariates in the data</a></li>
<li><a href="#refined-recurrence-covariates" id="toc-refined-recurrence-covariates" class="nav-link" data-scroll-target="#refined-recurrence-covariates"><span class="header-section-number">6.4</span> Refined recurrence covariates</a></li>
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<h1 class="title"><span class="chapter-number">6</span> <span class="chapter-title">Step 3: Recurrence</span></h1>
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<section id="genrate-recurrence-covariates" class="level2 page-columns page-full" data-number="6.1">
<h2 data-number="6.1" class="anchored" data-anchor-id="genrate-recurrence-covariates"><span class="header-section-number">6.1</span> Genrate recurrence covariates</h2>
<div class="no-row-height column-margin column-container"><div class="">
<p><span class="citation" data-cites="schneeweiss2009high">(<a href="references.html#ref-schneeweiss2009high" role="doc-biblioref">Schneeweiss et al. 2009</a>)</span></p>
</div></div><p>In this step, we generate <mark>3 binary recurrence covariates</mark> for each of the candidate empirical covariates identified in the previous step:</p>
<ul>
<li>occurred at least once</li>
<li>occurred sporadically (at least more than the median)</li>
<li>occurred frequently (at least more than the 75th percentile)</li>
</ul>
<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>step2 <span class="ot"><-</span> <span class="fu">get_recurrence_covariates</span>(<span class="at">df =</span> out1, </span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="at">patientIdVarname =</span> <span class="st">"idx"</span>,</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="at">eventCodeVarname =</span> <span class="st">"icd10"</span>, </span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="at">patientIdVector =</span> patientIds)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
<section id="example-of-recurrence-covariates" class="level2 page-columns page-full" data-number="6.2">
<h2 data-number="6.2" class="anchored" data-anchor-id="example-of-recurrence-covariates"><span class="header-section-number">6.2</span> Example of recurrence covariates</h2>
<style>
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background-color: #f2f2f2;
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tr:nth-child(even) td:nth-child(1){
background-color: #f2f2f2;
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<table class="caption-top table">
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<col style="width: 25%">
<col style="width: 25%">
<col style="width: 25%">
<col style="width: 25%">
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<thead>
<tr class="header">
<th>ICD-10-CM code (dimension 1)</th>
<th>code appeared at least once</th>
<th>code appeared at least more than the median</th>
<th>code appeared at least more than the 75th percentile</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><strong>D64.9</strong> Anemia</td>
<td>rec_dx_D64_once</td>
<td>rec_dx_D64_sporadic</td>
<td>rec_dx_D64_frequent</td>
</tr>
<tr class="even">
<td><strong>D75.9P</strong> Blood clots</td>
<td>rec_dx_D75_once</td>
<td>rec_dx_D75_sporadic</td>
<td>rec_dx_D75_frequent</td>
</tr>
<tr class="odd">
<td><strong>D89.9</strong> Immune disorder</td>
<td>rec_dx_D89_once</td>
<td>rec_dx_D89_sporadic</td>
<td>rec_dx_D89_frequent</td>
</tr>
<tr class="even">
<td><span class="math inline">\(\ldots\)</span></td>
<td><span class="math inline">\(\ldots\)</span></td>
<td><span class="math inline">\(\ldots\)</span></td>
<td><span class="math inline">\(\ldots\)</span></td>
</tr>
<tr class="odd">
<td><strong>E07.9</strong> Disorder of thyroid</td>
<td>rec_dx_E07_once</td>
<td>rec_dx_E07_sporadic</td>
<td>rec_dx_E07_frequent</td>
</tr>
</tbody>
</table>
<div class="no-row-height column-margin column-container"><div class="">
<p>Example of 3 binary covariates (hypothetical) created based on the candidate empirical covariates.</p>
</div></div></section>
<section id="recurrence-covariates-in-the-data" class="level2 page-columns page-full" data-number="6.3">
<h2 data-number="6.3" class="anchored" data-anchor-id="recurrence-covariates-in-the-data"><span class="header-section-number">6.3</span> Recurrence covariates in the data</h2>
<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>out2 <span class="ot"><-</span> step2<span class="sc">$</span>recurrence_data</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">ncol</span>(out2)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> [1] 92</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<div class="cell">
<div class="cell-output-display">
<div data-pagedtable="false">
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</div>
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<div class="no-row-height column-margin column-container"><div class="">
<p>Here we show <mark>binary recurrence covariates</mark> for only 2 columns</p>
</div></div></section>
<section id="refined-recurrence-covariates" class="level2 page-columns page-full" data-number="6.4">
<h2 data-number="6.4" class="anchored" data-anchor-id="refined-recurrence-covariates"><span class="header-section-number">6.4</span> Refined recurrence covariates</h2>
<p>Below you can click to see a list of all recurrence covariates obtained in our data.</p>
<button onclick="toggleTable()">
Show/Hide Table
</button>
<div class="toggle-table" style="display:none">
<table class="caption-top table">
<caption>ICD-10 Recurrence Data</caption>
<tbody>
<tr class="odd">
<td style="text-align: left;">1</td>
<td style="text-align: center;">rec_dx_A49_once</td>
<td style="text-align: center;">rec_dx_B00_once</td>
<td style="text-align: center;">rec_dx_B35_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">2</td>
<td style="text-align: center;">rec_dx_C50_once</td>
<td style="text-align: center;">rec_dx_D75_once</td>
<td style="text-align: center;">rec_dx_E03_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">3</td>
<td style="text-align: center;">rec_dx_E04_once</td>
<td style="text-align: center;">rec_dx_E07_once</td>
<td style="text-align: center;">rec_dx_E78_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">4</td>
<td style="text-align: center;">rec_dx_E87_once</td>
<td style="text-align: center;">rec_dx_F31_once</td>
<td style="text-align: center;">rec_dx_F31_frequent</td>
</tr>
<tr class="odd">
<td style="text-align: left;">5</td>
<td style="text-align: center;">rec_dx_F32_once</td>
<td style="text-align: center;">rec_dx_F39_once</td>
<td style="text-align: center;">rec_dx_F41_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">6</td>
<td style="text-align: center;">rec_dx_F43_once</td>
<td style="text-align: center;">rec_dx_F90_once</td>
<td style="text-align: center;">rec_dx_G25_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">7</td>
<td style="text-align: center;">rec_dx_G40_once</td>
<td style="text-align: center;">rec_dx_G40_frequent</td>
<td style="text-align: center;">rec_dx_G43_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">8</td>
<td style="text-align: center;">rec_dx_G47_once</td>
<td style="text-align: center;">rec_dx_H04_once</td>
<td style="text-align: center;">rec_dx_H40_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">9</td>
<td style="text-align: center;">rec_dx_H40_frequent</td>
<td style="text-align: center;">rec_dx_I10_once</td>
<td style="text-align: center;">rec_dx_I10_frequent</td>
</tr>
<tr class="even">
<td style="text-align: left;">10</td>
<td style="text-align: center;">rec_dx_I20_once</td>
<td style="text-align: center;">rec_dx_I21_once</td>
<td style="text-align: center;">rec_dx_I48_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">11</td>
<td style="text-align: center;">rec_dx_I48_frequent</td>
<td style="text-align: center;">rec_dx_I49_once</td>
<td style="text-align: center;">rec_dx_I50_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">12</td>
<td style="text-align: center;">rec_dx_I50_frequent</td>
<td style="text-align: center;">rec_dx_I51_once</td>
<td style="text-align: center;">rec_dx_I63_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">13</td>
<td style="text-align: center;">rec_dx_J30_once</td>
<td style="text-align: center;">rec_dx_J42_once</td>
<td style="text-align: center;">rec_dx_J44_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">14</td>
<td style="text-align: center;">rec_dx_J44_frequent</td>
<td style="text-align: center;">rec_dx_J45_once</td>
<td style="text-align: center;">rec_dx_J45_frequent</td>
</tr>
<tr class="odd">
<td style="text-align: left;">15</td>
<td style="text-align: center;">rec_dx_K04_once</td>
<td style="text-align: center;">rec_dx_K08_once</td>
<td style="text-align: center;">rec_dx_K21_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">16</td>
<td style="text-align: center;">rec_dx_K25_once</td>
<td style="text-align: center;">rec_dx_K27_once</td>
<td style="text-align: center;">rec_dx_K30_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">17</td>
<td style="text-align: center;">rec_dx_K59_once</td>
<td style="text-align: center;">rec_dx_K92_once</td>
<td style="text-align: center;">rec_dx_L40_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">18</td>
<td style="text-align: center;">rec_dx_L70_once</td>
<td style="text-align: center;">rec_dx_M06_once</td>
<td style="text-align: center;">rec_dx_M06_frequent</td>
</tr>
<tr class="odd">
<td style="text-align: left;">19</td>
<td style="text-align: center;">rec_dx_M10_once</td>
<td style="text-align: center;">rec_dx_M13_once</td>
<td style="text-align: center;">rec_dx_M19_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">20</td>
<td style="text-align: center;">rec_dx_M1A_once</td>
<td style="text-align: center;">rec_dx_M25_once</td>
<td style="text-align: center;">rec_dx_M54_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">21</td>
<td style="text-align: center;">rec_dx_M62_once</td>
<td style="text-align: center;">rec_dx_M79_once</td>
<td style="text-align: center;">rec_dx_M81_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">22</td>
<td style="text-align: center;">rec_dx_N28_once</td>
<td style="text-align: center;">rec_dx_N32_once</td>
<td style="text-align: center;">rec_dx_N39_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">23</td>
<td style="text-align: center;">rec_dx_N40_once</td>
<td style="text-align: center;">rec_dx_N92_once</td>
<td style="text-align: center;">rec_dx_N94_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">24</td>
<td style="text-align: center;">rec_dx_N95_once</td>
<td style="text-align: center;">rec_dx_R00_once</td>
<td style="text-align: center;">rec_dx_R05_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">25</td>
<td style="text-align: center;">rec_dx_R06_once</td>
<td style="text-align: center;">rec_dx_R07_once</td>
<td style="text-align: center;">rec_dx_R09_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">26</td>
<td style="text-align: center;">rec_dx_R10_once</td>
<td style="text-align: center;">rec_dx_R11_once</td>
<td style="text-align: center;">rec_dx_R12_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">27</td>
<td style="text-align: center;">rec_dx_R25_once</td>
<td style="text-align: center;">rec_dx_R32_once</td>
<td style="text-align: center;">rec_dx_R35_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">28</td>
<td style="text-align: center;">rec_dx_R39_once</td>
<td style="text-align: center;">rec_dx_R41_once</td>
<td style="text-align: center;">rec_dx_R42_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">29</td>
<td style="text-align: center;">rec_dx_R51_once</td>
<td style="text-align: center;">rec_dx_R52_once</td>
<td style="text-align: center;">rec_dx_R60_once</td>
</tr>
<tr class="even">
<td style="text-align: left;">30</td>
<td style="text-align: center;">rec_dx_R73_once</td>
<td style="text-align: center;">rec_dx_T14_once</td>
<td style="text-align: center;">rec_dx_T78_once</td>
</tr>
<tr class="odd">
<td style="text-align: left;">31</td>
<td style="text-align: center;">rec_dx_Z79_once</td>
<td style="text-align: center;"></td>
<td style="text-align: center;"></td>
</tr>
</tbody>
</table>
</div>
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<div class="callout callout-style-default callout-tip callout-titled">
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Tip
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<ul>
<li>Given that we had one dimension of proxy data, <span class="math inline">\(p=1\)</span>, at most <span class="math inline">\(n=200\)</span> most prevalent codes (with the restriction that minimum number of patients in each code = 20), and <span class="math inline">\(3\)</span> intensity, we could theoretically have at most <span class="math inline">\(p \times n \times 3 = 1 \times 200 \times \ 3 = 600\)</span> recurrence covariates.</li>
</ul>
</div>
</div>
<ul>
<li>Based on all of the restrictions, we created <mark>143 distinct recurrence covariates</mark>.</li>
<li>The merged data (analytic and proxies) size is now 7,585.</li>
</ul>
<div class="no-row-height column-margin column-container"><div class="">
<ul>
<li>If 2 or all 3 recurrence covariates are identical, only <mark>one distinct recurrence covariate</mark> is returned. This is why you do not see any sporadic recurrence covariate here.</li>
<li>Recurrence covariate creation is for each patient, and it is possible to have same code occur multiple time because we are working with a 3 digit granularity (possible to have medications from other codes within same ICD-10 3 digit granularity).</li>
</ul>
</div></div><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list" style="display: none">
<div id="ref-schneeweiss2009high" class="csl-entry" role="listitem">
Schneeweiss, Sebastian, Jeremy A Rassen, Robert J Glynn, Jerry Avorn, Helen Mogun, and M Alan Brookhart. 2009. <span>“High-Dimensional Propensity Score Adjustment in Studies of Treatment Effects Using Health Care Claims Data.”</span> <em>Epidemiology (Cambridge, Mass.)</em> 20 (4): 512.
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