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    <div class="page-header toc-ignore">
      <h1 data-toc-skip>measureConditionEraCompleteness</h1>
                        <h4 data-toc-skip class="author">Maxim
Moinat</h4>
            
            <h4 data-toc-skip class="date">2024-12-24</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/OHDSI/DataQualityDashboard/blob/HEAD/vignettes/checks/measureConditionEraCompleteness.Rmd" class="external-link"><code>vignettes/checks/measureConditionEraCompleteness.Rmd</code></a></small>
      <div class="hidden name"><code>measureConditionEraCompleteness.Rmd</code></div>

    </div>

    
<div class="section level2">
<h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
</h2>
<p><strong>Level</strong>: TABLE<br><strong>Context</strong>: Validation<br><strong>Category</strong>: Completeness<br><strong>Subcategory</strong>:<br><strong>Severity</strong>: CDM convention ⚠</p>
</div>
<div class="section level2">
<h2 id="description">Description<a class="anchor" aria-label="anchor" href="#description"></a>
</h2>
<p>The number and percent of persons that does not have condition_era
built successfully, for all persons in
<code>CONDITION_OCCURRENCE</code>.</p>
</div>
<div class="section level2">
<h2 id="definition">Definition<a class="anchor" aria-label="anchor" href="#definition"></a>
</h2>
<ul>
<li>
<em>Numerator</em>: Number of unique person_ids that exist in the
<code>CONDITION_OCCURRENCE</code> table but not in the
<code>CONDITION_ERA</code> table.</li>
<li>
<em>Denominator</em>: Number of unique person_ids in the
<code>CONDITION_OCCURRENCE</code> table.</li>
<li>
<em>Related CDM Convention(s)</em>: Condition Era’s are directly
derived from Condition Occurrence.</li>
<li>
<em>CDM Fields/Tables</em>: <code>CONDITION_ERA</code>
</li>
<li>
<em>Default Threshold Value</em>: 0%</li>
</ul>
</div>
<div class="section level2">
<h2 id="user-guidance">User Guidance<a class="anchor" aria-label="anchor" href="#user-guidance"></a>
</h2>
<p>The <a href="https://ohdsi.github.io/CommonDataModel/cdm54.html#condition_era" class="external-link">Condition
Era CDM documentation</a> states that the condition era’s should be
derived by combining condition occurrences. This implies that each
person with a condition occurrence should have at least a condition era.
It does NOT clearly state that the <code>CONDITION_ERA</code> table is
required when there are condition occurrences. Still, it is has always
been a common convention in the OHDSI community to derive condition era.
There is currently no THEMIS convention on condition eras.</p>
<div class="section level3">
<h3 id="violated-rows-query">Violated rows query<a class="anchor" aria-label="anchor" href="#violated-rows-query"></a>
</h3>
<div class="sourceCode" id="cb1"><pre class="sourceCode sql"><code class="sourceCode sql"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="kw">SELECT</span> <span class="kw">DISTINCT</span> </span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>  co.person_id</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="kw">FROM</span> @cdmDatabaseSchema.condition_occurrence co</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>  <span class="kw">LEFT</span> <span class="kw">JOIN</span> @cdmDatabaseSchema.condition_era cdmTable </span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>    <span class="kw">ON</span> co.person_id <span class="op">=</span> cdmTable.person_id</span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="kw">WHERE</span> cdmTable.person_id <span class="kw">IS</span> <span class="kw">NULL</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="etl-developers">ETL Developers<a class="anchor" aria-label="anchor" href="#etl-developers"></a>
</h3>
<p>If this check fails, it is likely that there is an issue with the
condition era derivation script. Please review the ETL execution log. It
might be that this script was not executed and the condition era table
is empty, or it had issues running and the condition era table has been
partially populated. If no issues with the ETL run found, the condition
era derivation script might have bugs. Please review the code. An
example script can be found on <a href="https://ohdsi.github.io/CommonDataModel/sqlScripts.html#Condition_Eras" class="external-link">the
CDM Documentation page</a>. In both cases it is advised to truncate the
<code>CONDITION_ERA</code> table and rerun the derivation script.</p>
</div>
<div class="section level3">
<h3 id="data-users">Data Users<a class="anchor" aria-label="anchor" href="#data-users"></a>
</h3>
<p>The <code>CONDITION_ERA</code> table might seem to contain redundant
information, as for most uses the <code>CONDITION_OCCURRENCE</code>
table can be used. However, tools like FeatureExtraction use condition
eras to build some covariates and network studies might use cohorts that
are based on condition eras. It is therefore important that the
<code>CONDITION_ERA</code> table is fully populated and captures the
same persons as in condition occurrence.</p>
</div>
</div>
  </div>

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