From 4a2e2aabe7abc7677946ac72e706b26426eb4b28 Mon Sep 17 00:00:00 2001
From: Katy Sadowski <katy.sadowski@gmail.com>
Date: Thu, 24 Oct 2024 10:35:31 -0400
Subject: [PATCH] minor fixes

---
 .../checks/plausibleGenderUseDescendants.html     | 15 +++++++--------
 docs/articles/checks/plausibleUnitConceptIds.html | 12 ++++++------
 docs/articles/index.html                          |  2 +-
 docs/pkgdown.yml                                  |  2 +-
 .../checks/plausibleGenderUseDescendants.Rmd      |  6 +++---
 vignettes/checks/plausibleUnitConceptIds.Rmd      |  8 ++++----
 6 files changed, 22 insertions(+), 23 deletions(-)

diff --git a/docs/articles/checks/plausibleGenderUseDescendants.html b/docs/articles/checks/plausibleGenderUseDescendants.html
index 985ffb09..82fae2b0 100644
--- a/docs/articles/checks/plausibleGenderUseDescendants.html
+++ b/docs/articles/checks/plausibleGenderUseDescendants.html
@@ -5,13 +5,13 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>plausibleGender • DataQualityDashboard</title>
+<title>plausibleGenderUseDescendants • DataQualityDashboard</title>
 <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet">
-<script src="../../pkgdown.js"></script><meta property="og:title" content="plausibleGender">
+<script src="../../pkgdown.js"></script><meta property="og:title" content="plausibleGenderUseDescendants">
 <meta property="og:description" content="DataQualityDashboard">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -186,7 +186,7 @@
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>plausibleGender</h1>
+      <h1 data-toc-skip>plausibleGenderUseDescendants</h1>
                         <h4 data-toc-skip class="author">Katy Sadowski
 and Dmytry Dymshyts</h4>
             
@@ -270,14 +270,13 @@ <h3 id="violated-rows-query">Violated rows query<a class="anchor" aria-label="an
 person has the incorrect gender, or that the finding is a true data
 anomaly. Examples of true anomalies include:</p>
 <ul>
-<li>Occasional stray code (e.g., due to typo in EHR). This gives an idea
-how noisy the data is.</li>
+<li>Occasional stray code (e.g., due to typo in EHR).</li>
 <li>Newborn codes recorded in the mother’s record (e.g.,
 circumcision).</li>
 <li>Gender reassignment procedures (e.g., penectomy and prostatectomy in
-patients with acquired (female) gender). <strong>NOTE</strong> that this
-is technically a violation of the OMOP CDM specification, since the CDM
-actually requires that the <code>gender_concept_id</code> represents the
+patients with acquired female gender). <strong>NOTE</strong> that this
+scenario is technically a violation of the OMOP CDM specification, since
+the CDM requires that the <code>gender_concept_id</code> represents a
 person’s sex at birth. For more information on this convention, see <a href="https://ohdsi.github.io/Themis/populate_gender_concept_id.html" class="external-link uri">https://ohdsi.github.io/Themis/populate_gender_concept_id.html</a>
 </li>
 </ul>
diff --git a/docs/articles/checks/plausibleUnitConceptIds.html b/docs/articles/checks/plausibleUnitConceptIds.html
index 72e249dd..1c4f8d02 100644
--- a/docs/articles/checks/plausibleUnitConceptIds.html
+++ b/docs/articles/checks/plausibleUnitConceptIds.html
@@ -202,7 +202,7 @@ <h4 data-toc-skip class="date">2024-10-24</h4>
 <div class="section level2">
 <h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
-<p><strong>Level</strong>: CONCEPT<br><strong>Context</strong>: Verification<br><strong>Category</strong>: Plausibility<br><strong>Subcategory</strong>: Atemporal<br><strong>Severity</strong>: Characterization ✔</p>
+<p><strong>Level</strong>: CONCEPT<br><strong>Context</strong>: Validation<br><strong>Category</strong>: Plausibility<br><strong>Subcategory</strong>: Atemporal<br><strong>Severity</strong>: Characterization ✔</p>
 </div>
 <div class="section level2">
 <h2 id="description">Description<a class="anchor" aria-label="anchor" href="#description"></a>
@@ -251,7 +251,7 @@ <h2 id="user-guidance">User Guidance<a class="anchor" aria-label="anchor" href="
 <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>
-<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>    m.unit_concept_id,</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>  m.unit_concept_id,</span>
 <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>  m.unit_source_concept_id,</span>
 <span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>  m.unit_source_value,</span>
 <span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a>  <span class="fu">COUNT</span>(<span class="op">*</span>)</span>
@@ -265,9 +265,9 @@ <h3 id="violated-rows-query">Violated rows query<a class="anchor" aria-label="an
 <code>unit_source_concept_id</code> are populated, check them against
 the list of plausible unit concept IDs to understand if they should have
 been mapped to one of the plausible standard concepts. If the
-<code>unit_source_value</code> is NULL but the list of plausible unit
-concept IDs includes -1, then you may need to check your source data to
-undersand whether or not a unit is available in the source.</p>
+<code>unit_source_value</code> is NULL and the list of plausible unit
+concept IDs does not include -1, then you may need to check your source
+data to undersand whether or not a unit is available in the source.</p>
 </div>
 <div class="section level3">
 <h3 id="etl-developers">ETL Developers<a class="anchor" aria-label="anchor" href="#etl-developers"></a>
@@ -287,7 +287,7 @@ <h3 id="etl-developers">ETL Developers<a class="anchor" aria-label="anchor" href
 <div class="section level3">
 <h3 id="data-users">Data Users<a class="anchor" aria-label="anchor" href="#data-users"></a>
 </h3>
-<p>It is generally recommended not to use measurements with implausible
+<p>It is generally not recommended to use measurements with implausible
 units in analyses as it is impossible to determine whether the unit is
 wrong; the value is wrong; and/or the measurement code is wrong in the
 source data. If a measurement is missing a <code>unit_concept_id</code>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 5958ef1d..d9262bf3 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -206,7 +206,7 @@ <h3>All vignettes</h3>
         <dd>
         </dd><dt><a href="checks/plausibleBeforeDeath.html">plausibleBeforeDeath</a></dt>
         <dd>
-        </dd><dt><a href="checks/plausibleGenderUseDescendants.html">plausibleGender</a></dt>
+        </dd><dt><a href="checks/plausibleGenderUseDescendants.html">plausibleGenderUseDescendants</a></dt>
         <dd>
         </dd><dt><a href="checks/plausibleStartBeforeEnd.html">plausibleStartBeforeEnd</a></dt>
         <dd>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 2aa6f2b6..df0d4847 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -34,7 +34,7 @@ articles:
   standardConceptRecordCompleteness: checks/standardConceptRecordCompleteness.html
   Thresholds: Thresholds.html
   withinVisitDates: checks/withinVisitDates.html
-last_built: 2024-10-24T13:49Z
+last_built: 2024-10-24T14:34Z
 urls:
   reference: https://ohdsi.github.io/DataQualityDashboard/reference
   article: https://ohdsi.github.io/DataQualityDashboard/articles
diff --git a/vignettes/checks/plausibleGenderUseDescendants.Rmd b/vignettes/checks/plausibleGenderUseDescendants.Rmd
index d9d79400..16c4923c 100644
--- a/vignettes/checks/plausibleGenderUseDescendants.Rmd
+++ b/vignettes/checks/plausibleGenderUseDescendants.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "plausibleGender"
+title: "plausibleGenderUseDescendants"
 author: "Katy Sadowski and Dmytry Dymshyts"
 date: "`r Sys.Date()`"
 output:
@@ -54,9 +54,9 @@ GROUP BY 1,2,3
 ```
 The above query should help to identify if a mapping issue is the cause of the failure.  If the source value and source concept ID are correctly mapped to a standard concept, then the issue may be that the person has the incorrect gender, or that the finding is a true data anomaly.  Examples of true anomalies include:
 
-- Occasional stray code (e.g., due to typo in EHR). This gives an idea how noisy the data is. 
+- Occasional stray code (e.g., due to typo in EHR). 
 - Newborn codes recorded in the mother’s record (e.g., circumcision). 
-- Gender reassignment procedures (e.g., penectomy and prostatectomy in patients with acquired (female) gender). **NOTE** that this is technically a violation of the OMOP CDM specification, since the CDM actually requires that the `gender_concept_id` represents the person's sex at birth. For more information on this convention, see https://ohdsi.github.io/Themis/populate_gender_concept_id.html
+- Gender reassignment procedures (e.g., penectomy and prostatectomy in patients with acquired female gender). **NOTE** that this scenario is technically a violation of the OMOP CDM specification, since the CDM requires that the `gender_concept_id` represents a person's sex at birth. For more information on this convention, see https://ohdsi.github.io/Themis/populate_gender_concept_id.html
 
 ### ETL Developers
 
diff --git a/vignettes/checks/plausibleUnitConceptIds.Rmd b/vignettes/checks/plausibleUnitConceptIds.Rmd
index df4ba14a..14585070 100644
--- a/vignettes/checks/plausibleUnitConceptIds.Rmd
+++ b/vignettes/checks/plausibleUnitConceptIds.Rmd
@@ -11,7 +11,7 @@ output:
 ## Summary
 
 **Level**: CONCEPT\
-**Context**: Verification\
+**Context**: Validation\
 **Category**: Plausibility\
 **Subcategory**: Atemporal\
 **Severity**: Characterization &#10004;
@@ -43,7 +43,7 @@ The above issues could either be due to incorrect data in the source system or i
 ### Violated rows query
 ```sql
 SELECT 
-	m.unit_concept_id,
+  m.unit_concept_id,
   m.unit_source_concept_id,
   m.unit_source_value,
   COUNT(*)
@@ -54,7 +54,7 @@ WHERE m.@cdmFieldName = @conceptId
 GROUP BY 1,2,3
 ```
 
-Inspect the output of the violated rows query to identify the root cause of the issue.  If the `unit_source_value` and/or `unit_source_concept_id` are populated, check them against the list of plausible unit concept IDs to understand if they should have been mapped to one of the plausible standard concepts.  If the `unit_source_value` is NULL but the list of plausible unit concept IDs includes -1, then you may need to check your source data to undersand whether or not a unit is available in the source. 
+Inspect the output of the violated rows query to identify the root cause of the issue.  If the `unit_source_value` and/or `unit_source_concept_id` are populated, check them against the list of plausible unit concept IDs to understand if they should have been mapped to one of the plausible standard concepts.  If the `unit_source_value` is NULL and the list of plausible unit concept IDs does not include -1, then you may need to check your source data to undersand whether or not a unit is available in the source. 
 
 ### ETL Developers
 
@@ -62,4 +62,4 @@ Ensure that all units available in the source data are being pulled into the CDM
 
 ### Data Users
 
-It is generally recommended not to use measurements with implausible units in analyses as it is impossible to determine whether the unit is wrong; the value is wrong; and/or the measurement code is wrong in the source data.  If a measurement is missing a `unit_concept_id` due to an ETL issue, and the `unit_source_value` or `unit_source_concept_id` is available, you can utilize these values to perform your analysis.  If `unit_source_value` and `unit_source_concept_id` are missing, you may consider consulting with your data provider as to if and when you may be able to infer what the missing unit should be. 
\ No newline at end of file
+It is generally not recommended to use measurements with implausible units in analyses as it is impossible to determine whether the unit is wrong; the value is wrong; and/or the measurement code is wrong in the source data.  If a measurement is missing a `unit_concept_id` due to an ETL issue, and the `unit_source_value` or `unit_source_concept_id` is available, you can utilize these values to perform your analysis.  If `unit_source_value` and `unit_source_concept_id` are missing, you may consider consulting with your data provider as to if and when you may be able to infer what the missing unit should be. 
\ No newline at end of file