minor fixes

OHDSI · Oct 24, 2024 · 4a2e2aa · 4a2e2aa
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diff --git a/docs/articles/checks/plausibleGenderUseDescendants.html b/docs/articles/checks/plausibleGenderUseDescendants.html
diff --git a/docs/articles/checks/plausibleUnitConceptIds.html b/docs/articles/checks/plausibleUnitConceptIds.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git 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
@@ -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
@@ -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(*)
@@ -54,12 +54,12 @@ 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
 
 Ensure that all units available in the source data are being pulled into the CDM and mapped correctly to a standard concept ID.  If a unit is available in the source and is being correctly populated & mapped in your ETL but is *not* present on the list of plausible unit concept IDs, you should verify whether or not the unit is actually plausible - you may need to consult a clinician to do so.  If the unit is plausible for the given measurement, please report this as a DataQualityDashboard bug here: https://github.com/OHDSI/DataQualityDashboard/issues.  If the unit is not plausible, do not change it!  Instead, you should document the issue for users of the CDM and discuss with your data provider how to handle the data.
 
 ### 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. 
+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.