added cleaned up measurement-unit checks, aggregated gender concepts,

to do: update the documentation

Author: Dmitry Dymshyts

inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv

@@ -20,8 +20,6 @@ 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'
 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!=''

inst/csv/OMOP_CDMv5.2_Concept_Level.csv

@@ -20,8 +20,6 @@ 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'
 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!=''