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edward-burn committed Jun 15, 2024
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268 changes: 227 additions & 41 deletions _book/ch_1_getting_started.html
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455 changes: 334 additions & 121 deletions _book/ch_2_cdm_reference.html
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219 changes: 105 additions & 114 deletions _book/ch_3_exploring_the_cdm.html
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277 changes: 139 additions & 138 deletions _book/ch_4_adding_features.html
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4 changes: 2 additions & 2 deletions _book/ch_5_creating_cohorts.html
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Expand Up @@ -163,13 +163,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_2_cdm_reference.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to the OMOP common data model</span></span></a>
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to data in the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_3_exploring_the_cdm.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the CDM</span></span></a>
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
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21 changes: 14 additions & 7 deletions _book/ch_6_working_with_cohorts.html
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Expand Up @@ -155,13 +155,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_2_cdm_reference.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to the OMOP common data model</span></span></a>
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to data in the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_3_exploring_the_cdm.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the CDM</span></span></a>
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
Expand Down Expand Up @@ -219,6 +219,7 @@ <h2 id="toc-title">Table of contents</h2>
<li><a href="#date-and-times" id="toc-date-and-times" class="nav-link" data-scroll-target="#date-and-times"><span class="header-section-number">6.3.3</span> Date and times</a></li>
</ul></li>
<li><a href="#intersection-between-a-cohort-and-tables-with-patient-data" id="toc-intersection-between-a-cohort-and-tables-with-patient-data" class="nav-link" data-scroll-target="#intersection-between-a-cohort-and-tables-with-patient-data"><span class="header-section-number">6.4</span> Intersection between a cohort and tables with patient data</a></li>
<li><a href="#further-reading" id="toc-further-reading" class="nav-link" data-scroll-target="#further-reading"><span class="header-section-number">7</span> Further reading</a></li>
</ul>
</nav>
</div>
Expand Down Expand Up @@ -266,12 +267,12 @@ <h2 data-number="6.3" class="anchored" data-anchor-id="set-up"><span class="head
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> <span class="at">write_schema =</span> <span class="st">"main"</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a>cdm <span class="ot">&lt;-</span> cdm <span class="sc">%&gt;%</span> </span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a>cdm <span class="ot">&lt;-</span> cdm <span class="sc">|&gt;</span> </span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">generate_concept_cohort_set</span>(<span class="at">concept_set =</span> <span class="fu">list</span>(<span class="st">"gi_bleed"</span> <span class="ot">=</span> <span class="dv">192671</span>), </span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a> <span class="at">limit =</span> <span class="st">"all"</span>, </span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a> <span class="at">end =</span> <span class="dv">30</span>,</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a> <span class="at">name =</span> <span class="st">"gi_bleed"</span>,</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a> <span class="at">overwrite =</span> <span class="cn">TRUE</span>) <span class="sc">%&gt;%</span> </span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a> <span class="at">overwrite =</span> <span class="cn">TRUE</span>) <span class="sc">|&gt;</span> </span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">generate_concept_cohort_set</span>(<span class="at">concept_set =</span> <span class="fu">list</span>(<span class="st">"acetaminophen"</span> <span class="ot">=</span> <span class="fu">c</span>(<span class="dv">1125315</span>,</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a> <span class="dv">1127078</span>,</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a> <span class="dv">1127433</span>,</span>
Expand All @@ -287,14 +288,14 @@ <h2 data-number="6.3" class="anchored" data-anchor-id="set-up"><span class="head
<section id="flag" class="level3" data-number="6.3.1">
<h3 data-number="6.3.1" class="anchored" data-anchor-id="flag"><span class="header-section-number">6.3.1</span> Flag</h3>
<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>cdm<span class="sc">$</span>gi_bleed <span class="ot">&lt;-</span> cdm<span class="sc">$</span>gi_bleed <span class="sc">%&gt;%</span> </span>
<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>cdm<span class="sc">$</span>gi_bleed <span class="ot">&lt;-</span> cdm<span class="sc">$</span>gi_bleed <span class="sc">|&gt;</span> </span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">addCohortIntersectFlag</span>(<span class="at">targetCohortTable =</span> <span class="st">"acetaminophen"</span>,</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="at">window =</span> <span class="fu">list</span>(<span class="fu">c</span>(<span class="sc">-</span><span class="cn">Inf</span>, <span class="sc">-</span><span class="dv">1</span>), <span class="fu">c</span>(<span class="dv">0</span>,<span class="dv">0</span>), <span class="fu">c</span>(<span class="dv">1</span>, <span class="cn">Inf</span>)))</span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>cdm<span class="sc">$</span>gi_bleed <span class="sc">%&gt;%</span> </span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>cdm<span class="sc">$</span>gi_bleed <span class="sc">|&gt;</span> </span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(<span class="at">acetaminophen_prior =</span> <span class="fu">sum</span>(acetaminophen_minf_to_m1), </span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="at">acetaminophen_index =</span> <span class="fu">sum</span>(acetaminophen_0_to_0),</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="at">acetaminophen_post =</span> <span class="fu">sum</span>(acetaminophen_1_to_inf)) <span class="sc">%&gt;%</span> </span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> <span class="at">acetaminophen_post =</span> <span class="fu">sum</span>(acetaminophen_1_to_inf)) <span class="sc">|&gt;</span> </span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">collect</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 3
Expand All @@ -313,6 +314,12 @@ <h3 data-number="6.3.3" class="anchored" data-anchor-id="date-and-times"><span c
</section>
<section id="intersection-between-a-cohort-and-tables-with-patient-data" class="level2" data-number="6.4">
<h2 data-number="6.4" class="anchored" data-anchor-id="intersection-between-a-cohort-and-tables-with-patient-data"><span class="header-section-number">6.4</span> Intersection between a cohort and tables with patient data</h2>
</section>
<section id="further-reading" class="level1" data-number="7">
<h1 data-number="7"><span class="header-section-number">7</span> Further reading</h1>
<ul>
<li>…</li>
</ul>


</section>
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16 changes: 2 additions & 14 deletions _book/ch_7_summarising_cohorts.html
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Expand Up @@ -121,13 +121,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_2_cdm_reference.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to the OMOP common data model</span></span></a>
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to data in the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_3_exploring_the_cdm.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the CDM</span></span></a>
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
Expand Down Expand Up @@ -159,18 +159,6 @@
<a href="./ch_8_comparing_cohorts.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_9_organising_study_code.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Organising study code</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_10_efficient_study_code.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Efficient study code</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
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22 changes: 5 additions & 17 deletions _book/ch_8_comparing_cohorts.html
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<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./ch_9_organising_study_code.html" rel="next">
<link href="./references.html" rel="next">
<link href="./ch_7_summarising_cohorts.html" rel="prev">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
Expand Down Expand Up @@ -121,13 +121,13 @@
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_2_cdm_reference.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to the OMOP common data model</span></span></a>
<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Creating a reference to data in the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_3_exploring_the_cdm.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the CDM</span></span></a>
<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Exploring the OMOP CDM</span></span></a>
</div>
</li>
<li class="sidebar-item">
Expand Down Expand Up @@ -159,18 +159,6 @@
<a href="./ch_8_comparing_cohorts.html" class="sidebar-item-text sidebar-link active">
<span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Comparing cohorts</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_9_organising_study_code.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Organising study code</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./ch_10_efficient_study_code.html" class="sidebar-item-text sidebar-link">
<span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Efficient study code</span></span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
Expand Down Expand Up @@ -628,8 +616,8 @@ <h1 class="title"><span class="chapter-number">8</span>&nbsp; <span class="chapt
</a>
</div>
<div class="nav-page nav-page-next">
<a href="./ch_9_organising_study_code.html" class="pagination-link" aria-label="Organising study code">
<span class="nav-page-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Organising study code</span></span> <i class="bi bi-arrow-right-short"></i>
<a href="./references.html" class="pagination-link" aria-label="References">
<span class="nav-page-text">References</span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
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