added male specific procedures, cleaned up concept_plausible_gender_u…

…se_descendants.sql, added missing check_description

DESCRIPTION

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

inst/csv/OMOP_CDMv5.2_Check_Descriptions.csv

@@ -23,3 +23,6 @@ FIELD,withinVisitDates,The number and percent of records not within one week on
 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,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!=''
+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'

inst/csv/OMOP_CDMv5.2_Concept_Level.csv

@@ -335,6 +335,7 @@ CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45772671,Nodular prostate without urin
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4090861, 4025213","Male genitalia finding, Male reproductive finding",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4095793 , 443343, 4024004 , 4172857, 444094 , 197810, 4158481","Female genitalia finding, Disorder of intrauterine contraceptive device, Menopause finding, Disorder of female genital system, Malignant neoplasm of uterine adnexa, Finding related to pregnancy, Female reproductive finding",,,,,,,,,,Female,,2,,,,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4041261,Procedure on female genital system,,,,,,,,,,Female,,2,,,,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,"4250917, 4077750, 4043199, 4040577","Operation on prostate, Operation on scrotum, Procedure on penis, Procedure on testis",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3006315,Basophils [#/volume] in Blood,,,,,,,,,,,,,,,,,,,,,,,"8784,8848,8961,9444",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,3004410,Hemoglobin A1c/Hemoglobin.total in Blood,,,,,,,,,,,,,,,,,,,,,,,"8554,8737,9225,9579",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID
 MEASUREMENT,MEASUREMENT_CONCEPT_ID,40487382,Total lymphocyte count,,,,,,,,,,,,,,,,,,,,,,,"8784,8848,8961",5,Approved UNIT_CONCEPT_IDs for the given MEASUREMENT_CONCEPT_ID

inst/csv/OMOP_CDMv5.3_Check_Descriptions.csv

@@ -23,3 +23,6 @@ FIELD,withinVisitDates,The number and percent of records not within one week on
 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,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!=''
+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'

inst/csv/OMOP_CDMv5.3_Concept_Level.csv

@@ -335,6 +335,7 @@ CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45772671,Nodular prostate without urin
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4090861, 4025213","Male genitalia finding, Male reproductive finding",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4095793 , 443343, 4024004 , 4172857, 444094 , 197810, 4158481","Female genitalia finding, Disorder of intrauterine contraceptive device, Menopause finding, Disorder of female genital system, Malignant neoplasm of uterine adnexa, Finding related to pregnancy, Female reproductive finding",,,,,,,,,,Female,,2,,,,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4041261,Procedure on female genital system,,,,,,,,,,Female,,2,,,,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,"4250917, 4077750, 4043199, 4040577","Operation on prostate, Operation on scrotum, Procedure on penis, Procedure on testis",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37393449,Plasma total cholesterol level,8840,milligram per deciliter,50,5,,500,5,,,,,,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37393449,Plasma total cholesterol level,8753,millimole per liter,1,5,,15,5,,,,,,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37397989,Serum total cholesterol level,8840,milligram per deciliter,50,5,,500,5,,,,,,,,,,,,,,,,,,

inst/csv/OMOP_CDMv5.4_Check_Descriptions.csv

@@ -23,3 +23,6 @@ FIELD,withinVisitDates,The number and percent of records not within one week on
 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,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!=''
+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'

inst/csv/OMOP_CDMv5.4_Concept_Level.csv

@@ -335,6 +335,7 @@ CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,45772671,Nodular prostate without urin
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4090861, 4025213","Male genitalia finding, Male reproductive finding",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 CONDITION_OCCURRENCE,CONDITION_CONCEPT_ID,"4095793 , 443343, 4024004 , 4172857, 444094 , 197810, 4158481","Female genitalia finding, Disorder of intrauterine contraceptive device, Menopause finding, Disorder of female genital system, Malignant neoplasm of uterine adnexa, Finding related to pregnancy, Female reproductive finding",,,,,,,,,,Female,,2,,,,,,,,,,,,,
 PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,4041261,Procedure on female genital system,,,,,,,,,,Female,,2,,,,,,,,,,,,,
+PROCEDURE_OCCURRENCE,PROCEDURE_CONCEPT_ID,"4250917, 4077750, 4043199, 4040577","Operation on prostate, Operation on scrotum, Procedure on penis, Procedure on testis",,,,,,,,,,Male,,2,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37393449,Plasma total cholesterol level,8840,milligram per deciliter,50,5,,500,5,,,,,,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37393449,Plasma total cholesterol level,8753,millimole per liter,1,5,,15,5,,,,,,,,,,,,,,,,,,
 OBSERVATION,OBSERVATION_CONCEPT_ID,37397989,Serum total cholesterol level,8840,milligram per deciliter,50,5,,500,5,,,,,,,,,,,,,,,,,,

inst/sql/sql_server/concept_plausible_gender_use_descendants.sql

@@ -33,14 +33,14 @@ FROM
 		/*violatedRowsBegin*/
 		SELECT cdmTable.* 
 		FROM @cdmDatabaseSchema.@cdmTableName cdmTable
-			INNER JOIN @cdmDatabaseSchema.person p
-			ON cdmTable.person_id = p.person_id
-			INNER JOIN @vocabDatabaseSchema.concept_ancestor ca
-			ON ca.descendant_concept_id = cdmTable.@cdmFieldName
+			JOIN @cdmDatabaseSchema.person p
+			  ON cdmTable.person_id = p.person_id
+			JOIN @vocabDatabaseSchema.concept_ancestor ca
+			  ON ca.descendant_concept_id = cdmTable.@cdmFieldName
 			{@cohort}?{
-      	JOIN @cohortDatabaseSchema.@cohortTableName c
-      	  ON cdmTable.person_id = c.subject_id
-      	  AND c.cohort_definition_id = @cohortDefinitionId
+      JOIN @cohortDatabaseSchema.@cohortTableName c
+      	ON cdmTable.person_id = c.subject_id
+      	AND c.cohort_definition_id = @cohortDefinitionId
     	}
 		WHERE ca.ancestor_concept_id in (@conceptId)
 		AND p.gender_concept_id <> {@plausibleGenderUseDescendants == 'Male'} ? {8507} : {8532} 
@@ -51,10 +51,10 @@ FROM
 	SELECT 
 	  COUNT_BIG(*) AS num_rows
 	FROM @cdmDatabaseSchema.@cdmTableName cdmTable
-	INNER JOIN @vocabDatabaseSchema.concept_ancestor ca
+	JOIN @vocabDatabaseSchema.concept_ancestor ca
 	ON ca.descendant_concept_id = cdmTable.@cdmFieldName
   	{@cohort}?{
-    	JOIN @cohortDatabaseSchema.@cohortTableName c
+  	JOIN @cohortDatabaseSchema.@cohortTableName c
       	ON cdmTable.person_id = c.subject_id
       	AND c.cohort_definition_id = @cohortDefinitionId
   	}