plausibleGender
- +Katy Sadowski +and Dmytry Dymshyts
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleGenderUseDescendants.Rmd
plausibleGenderUseDescendants.Rmd2024-07-12
Summary
-Level: CONCEPT
Context: Validation
Category: Plausibility
Subcategory: Atemporal
Severity:
Level: CONCEPT
Context: Validation
Category: Plausibility
Subcategory: Atemporal
Severity: Characterization ✔
Description
-For a CONCEPT_ID @conceptId (@conceptName), the number and percent of records -associated with patients with an implausible gender (correct gender = -@plausibleGender).
+For descendants of CONCEPT_ID conceptId (conceptName), the number and +percent of records associated with patients with an implausible gender +(correct gender = plausibleGenderUseDescendants).
Definition
+This check will count the number of records for which the person’s +gender is implausible given the concept for the record. For a given +gender-specific concept (e.g., prostate cancer) and its descendants, the +check will identify records for which the associated person has an +implausible gender (e.g., a female with prostate cancer). There are +currently 4 instances of this check - female condition concepts; male +condition concepts; female procedure concepts; and male procedure +concepts.
- -Numerator: +Numerator: The number of rows with a gender-specific +concept whose associated person has an implausible gender.
- -Denominator: +Denominator: The number of rows with a gender-specific +concept.
- -Related CDM Convention(s): +Related CDM Convention(s): https://ohdsi.github.io/Themis/populate_gender_concept_id.html +
- -CDM Fields/Tables: +CDM Fields/Tables:
- -Default Threshold Value: +Default Threshold Value: 5%
CONDITION_OCURRENCE,
+PROCEDURE_OCCURRENCE
+
User Guidance
+A failure of this check indicates one of the following scenarios:
+-
+
- The person’s gender is wrong +
- The gender-specific concept is wrong +
- The person changed genders and the concept was plausible at the time +it was recorded +
Violated rows query
-SELECT
+ cdmTable.@cdmFieldName,
+ cdmTable.@sourceConceptIdField, -- x_source_concept_id for the table of interest (condition_occurrence or procedure_occurrence)
+ cdmTable.@sourceValueField, -- x_source_value for the table of interest
+ COUNT(*)
+FROM @cdmDatabaseSchema.@cdmTableName cdmTable
+ JOIN @cdmDatabaseSchema.person p ON cdmTable.person_id = p.person_id
+ JOIN @vocabDatabaseSchema.concept_ancestor ca ON ca.descendant_concept_id = cdmTable.@cdmFieldName
+WHERE ca.ancestor_concept_id IN (@conceptId)
+ AND p.gender_concept_id <> {@plausibleGenderUseDescendants == 'Male'} ? {8507} : {8532}
+GROUP BY 1,2,3The 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. +
- 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_idrepresents the +person’s sex at birth. For more information on this convention, see https://ohdsi.github.io/Themis/populate_gender_concept_id.html +
+
plausibleStartBeforeEnd
Maxim Moinat
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleStartBeforeEnd.Rmd
plausibleStartBeforeEnd.RmdplausibleTemporalAfter
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleTemporalAfter.Rmd
plausibleTemporalAfter.RmdplausibleUnitConceptIds
- +Katy +Sadowski
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleUnitConceptIds.Rmd
plausibleUnitConceptIds.Rmd2024-07-12
Summary
-Level: CONCEPT
Context: Verification
Category: Plausibility
Subcategory: Atemporal
Severity:
Level: CONCEPT
Context: Verification
Category: Plausibility
Subcategory: Atemporal
Severity: Characterization ✔
Description
@@ -208,32 +215,88 @@ Definition
User Guidance
+A failure of this check indicates one of the following:
+
+- A measurement record has the incorrect unit
+- A measurement record has no unit when it should have one
+- A measurement record has a unit when it should not have one
+- The list of plausible unit concept IDs in the threshold file is
+incomplete (please report this as a DataQualityDashboard bug!)
+
+The above issues could either be due to incorrect data in the source
+system or incorrect mapping of the unit concept IDs in the ETL
+process.
Violated rows query
-
+SELECT
+ m.unit_concept_id,
+ m.unit_source_concept_id,
+ m.unit_source_value,
+ COUNT(*)
+FROM @cdmDatabaseSchema.@cdmTableName m
+WHERE m.@cdmFieldName = @conceptId
+ AND COALESCE (m.unit_concept_id, -1) NOT IN (@plausibleUnitConceptIds) -- '-1' stands for the cases when unit_concept_id is null
+ AND m.value_as_number IS NOT NULL
+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.
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.
User Guidance
+A failure of this check indicates one of the following:
+-
+
- A measurement record has the incorrect unit +
- A measurement record has no unit when it should have one +
- A measurement record has a unit when it should not have one +
- The list of plausible unit concept IDs in the threshold file is +incomplete (please report this as a DataQualityDashboard bug!) +
The above issues could either be due to incorrect data in the source +system or incorrect mapping of the unit concept IDs in the ETL +process.
Violated rows query
-SELECT
+ m.unit_concept_id,
+ m.unit_source_concept_id,
+ m.unit_source_value,
+ COUNT(*)
+FROM @cdmDatabaseSchema.@cdmTableName m
+WHERE m.@cdmFieldName = @conceptId
+ AND COALESCE (m.unit_concept_id, -1) NOT IN (@plausibleUnitConceptIds) -- '-1' stands for the cases when unit_concept_id is null
+ AND m.value_as_number IS NOT NULL
+GROUP BY 1,2,3Inspect 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.
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.
plausibleValueHigh
Dymytry Dymshyts
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleValueHigh.Rmd
plausibleValueHigh.RmdplausibleValueLow
Dymytry Dymshyts
-2024-07-12
+2024-10-24
Source:vignettes/checks/plausibleValueLow.Rmd
plausibleValueLow.RmdsourceConceptRecordCompleteness
Katy Sadowski
-2024-07-12
+2024-10-24
Source:vignettes/checks/sourceConceptRecordCompleteness.Rmd
sourceConceptRecordCompleteness.RmdsourceValueCompleteness
Jared Houghtaling, Clair Blacketer
-2024-07-12
+2024-10-24
Source:vignettes/checks/sourceValueCompleteness.Rmd
sourceValueCompleteness.RmdstandardConceptRecordCompleteness
Katy Sadowski
-2024-07-12
+2024-10-24
Source:vignettes/checks/standardConceptRecordCompleteness.Rmd
standardConceptRecordCompleteness.RmdwithinVisitDates
Clair Blacketer
-2024-07-12
+2024-10-24
Source:vignettes/checks/withinVisitDates.Rmd
withinVisitDates.Rmd-
-
+ hadesLogo
-
diff --git a/docs/reference/dot-calculateNotApplicableStatus.html b/docs/reference/dot-calculateNotApplicableStatus.html
index 5e15185d..5d20d366 100644
--- a/docs/reference/dot-calculateNotApplicableStatus.html
+++ b/docs/reference/dot-calculateNotApplicableStatus.html
@@ -131,12 +131,18 @@
- measureConditionEraCompleteness
+- + plausibleUnitConceptIds +
+- + plausibleGenderUseDescendants +
-
-
+ hadesLogo
-
diff --git a/docs/reference/dot-containsNAchecks.html b/docs/reference/dot-containsNAchecks.html
index aa5fb1c7..ee1fdb9b 100644
--- a/docs/reference/dot-containsNAchecks.html
+++ b/docs/reference/dot-containsNAchecks.html
@@ -131,12 +131,18 @@
- measureConditionEraCompleteness
+- + plausibleUnitConceptIds +
+- + plausibleGenderUseDescendants +
-
-
+ hadesLogo
-
diff --git a/docs/reference/dot-evaluateThresholds.html b/docs/reference/dot-evaluateThresholds.html
index 1fe4a5cf..f880b017 100644
--- a/docs/reference/dot-evaluateThresholds.html
+++ b/docs/reference/dot-evaluateThresholds.html
@@ -131,6 +131,12 @@
- measureConditionEraCompleteness
+- + plausibleUnitConceptIds +
+- + plausibleGenderUseDescendants +
-
-
+ hadesLogo
-
diff --git a/docs/reference/dot-processCheck.html b/docs/reference/dot-processCheck.html
index e680356c..89d1fa01 100644
--- a/docs/reference/dot-processCheck.html
+++ b/docs/reference/dot-processCheck.html
@@ -131,6 +131,12 @@
- measureConditionEraCompleteness
+- + plausibleUnitConceptIds +
+- + plausibleGenderUseDescendants +