Merge pull request #524 from OHDSI/gender_grp_meas_unit_test

Gender checks that use descendant concepts added + measurement unit pairs cleaned up

DESCRIPTION

@@ -46,5 +46,5 @@ Suggests:
     R.utils
 Remotes:
     ohdsi/Eunomia
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Encoding: UTF-8

R/evaluateThresholds.R

@@ -78,7 +78,29 @@
           checkResults[i, ]$cdmFieldName
         )
       } else if (checkResults[i, ]$checkLevel == "CONCEPT") {
-        if (is.na(checkResults[i, ]$unitConceptId)) {
+        if (is.na(checkResults[i, ]$unitConceptId) &&
+            grepl(",", checkResults[i, ]$conceptId)) {
+          thresholdFilter <- sprintf(
+            "conceptChecks$%s[conceptChecks$cdmTableName == '%s' &
+                                  conceptChecks$cdmFieldName == '%s' &
+                                  conceptChecks$conceptId == '%s']",
+            thresholdField,
+            checkResults[i, ]$cdmTableName,
+            checkResults[i, ]$cdmFieldName,
+            checkResults[i, ]$conceptId
+          )
+          notesFilter <- sprintf(
+            "conceptChecks$%s[conceptChecks$cdmTableName == '%s' &
+                                  conceptChecks$cdmFieldName == '%s' &
+                                  conceptChecks$conceptId == '%s']",
+            notesField,
+            checkResults[i, ]$cdmTableName,
+            checkResults[i, ]$cdmFieldName,
+            checkResults[i, ]$conceptId
+          )
+        }
+        else if (is.na(checkResults[i, ]$unitConceptId) &&
+            !grepl(",", checkResults[i, ]$conceptId)) {
           thresholdFilter <- sprintf(
             "conceptChecks$%s[conceptChecks$cdmTableName == '%s' &
                                   conceptChecks$cdmFieldName == '%s' &
@@ -97,7 +119,8 @@
             checkResults[i, ]$cdmFieldName,
             checkResults[i, ]$conceptId
           )
-        } else {
+        }
+        else {
           thresholdFilter <- sprintf(
             "conceptChecks$%s[conceptChecks$cdmTableName == '%s' &
                                   conceptChecks$cdmFieldName == '%s' &

inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv

@@ -20,8 +20,9 @@ FIELD,plausibleValueHigh,The number and percent of records with a value in the @
 FIELD,plausibleTemporalAfter,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs prior to the date in the @plausibleTemporalAfterFieldName field of the @plausibleTemporalAfterTableName table.,Verification,Plausibility,Temporal,field_plausible_temporal_after.sql,plausibleTemporalAfter=='Yes'
 FIELD,plausibleDuringLife,"If yes, the number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_during_life.sql,plausibleDuringLife=='Yes'
 FIELD,withinVisitDates,The number and percent of records not within one week on either side of the corresponding visit occurrence start and end date,Verification,Conformance,,field_within_visit_dates.sql,withinVisitDates=='Yes'
-FIELD,plausibleAfterBirth,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs prior to birth.",Verification,Plausibility,Temporal,field_plausible_after_birth.sql,plausibleAfterBirth=='Yes'
-FIELD,plausibleBeforeDeath,"The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.",Verification,Plausibility,Temporal,field_plausible_before_death.sql,plausibleBeforeDeath=='Yes'
-FIELD,plausibleStartBeforeEnd,"The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs after the date in the @plausibleStartBeforeEndFieldName.",Verification,Plausibility,Temporal,field_plausible_start_before_end.sql,plausibleStartBeforeEnd=='Yes'
+FIELD,plausibleAfterBirth,The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs prior to birth.,Verification,Plausibility,Temporal,field_plausible_after_birth.sql,plausibleAfterBirth=='Yes'
+FIELD,plausibleBeforeDeath,The number and percent of records with a date value in the @cdmFieldName field of the @cdmTableName table that occurs after death.,Verification,Plausibility,Temporal,field_plausible_before_death.sql,plausibleBeforeDeath=='Yes'
+FIELD,plausibleStartBeforeEnd,The number and percent of records with a value in the @cdmFieldName field of the @cdmTableName that occurs after the date in the @plausibleStartBeforeEndFieldName.,Verification,Plausibility,Temporal,field_plausible_start_before_end.sql,plausibleStartBeforeEnd=='Yes'
 CONCEPT,plausibleGender,"For a CONCEPT_ID @conceptId (@conceptName), the number and percent of records associated with patients with an implausible gender (correct gender = @plausibleGender).",Validation,Plausibility,Atemporal,concept_plausible_gender.sql,plausibleGender!=''
-CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN  (@plausibleUnitConceptIds)).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!=''
+CONCEPT,plausibleGenderUseDescendants,"For descendants of CONCEPT_ID @conceptId (@conceptName), the number and percent of records associated with patients with an implausible gender (correct gender = @plausibleGenderUseDescendants).",Validation,Plausibility,Atemporal,concept_plausible_gender_use_descendants.sql,plausibleGenderUseDescendants!=''
+CONCEPT,plausibleUnitConceptIds,"The number and percent of records for a given CONCEPT_ID @conceptId (@conceptName) with implausible units (i.e., UNIT_CONCEPT_ID NOT IN  (@plausibleUnitConceptIds), '-1' means unit_concept_id can be null).",Verification,Plausibility,Atemporal,concept_plausible_unit_concept_ids.sql,plausibleUnitConceptIdsThreshold!=''