Merge pull request #464 from dimshitc/main

fixed thresholds at the Field level:measureValueCompletenessThreshold and at the Table level: measurePersonCompletenessThreshold

inst/csv/OMOP_CDMv5.2_Field_Level.csv

@@ -298,7 +298,7 @@ CONDITION_ERA,CDM,condition_occurrence_count,No,,,integer,0,,,,No,,,No,,,,,,,,,,
 DEATH,cdm,cause_concept_id,No,,,integer,0,,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,Yes,0,,Yes,100,,Yes,5,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
 DEATH,cdm,cause_source_concept_id,No,,,integer,0,,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,No,,,Yes,100,,No,,,Yes,10,,No,,,,,,,,,,,,,,,No,,,Yes,,,
 DEATH,cdm,cause_source_value,No,,,varchar(50),0,,,"If available, put the source code representing the cause of death here. ",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,10,,CAUSE_SOURCE_CONCEPT_ID,,,,,,,,,,,,,,,Yes,,,
-DEATH,cdm,death_date,Yes,0,,date,0,,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
+DEATH,cdm,death_date,Yes,0,,date,0,,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
 DEATH,cdm,death_datetime,No,,,datetime,0,,,If not available set time to midnight (00:00:00),No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
 DEATH,cdm,death_type_concept_id,No,,,integer,0,,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Type Concept,0,,,,,Yes,0,,Yes,100,,Yes,0,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
-DEATH,cdm,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
+DEATH,cdm,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,

inst/csv/OMOP_CDMv5.2_Table_Level.csv

@@ -20,4 +20,4 @@ COST,CDM,No,,No,,,No,,,,,,
 DRUG_ERA,CDM,No,,Yes,95,,No,,,,,,
 DOSE_ERA,CDM,No,,Yes,100,,No,,,,,,
 CONDITION_ERA,CDM,No,,Yes,95,,Yes,0,,,,,
-DEATH,CDM,No,,No,,,No,,,,,,
+DEATH,CDM,No,,Yes,100,,No,,,,,,

inst/csv/OMOP_CDMv5.3_Field_Level.csv

@@ -335,7 +335,7 @@ CONDITION_ERA,cdm,condition_occurrence_count,No,,,integer,0,,,,No,,,No,,,,,,,,,,
 DEATH,cdm,cause_concept_id,No,,,integer,0,,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,Yes,0,,Yes,100,,Yes,5,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
 DEATH,cdm,cause_source_concept_id,No,,,integer,0,,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,No,,,Yes,100,,No,,,Yes,10,,No,,,,,,,,,,,,,,,No,,,Yes,,,
 DEATH,cdm,cause_source_value,No,,,varchar(50),0,,,"If available, put the source code representing the cause of death here. ",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,10,,CAUSE_SOURCE_CONCEPT_ID,,,,,,,,,,,,,,,Yes,,,
-DEATH,cdm,death_date,Yes,0,,date,0,,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
+DEATH,cdm,death_date,Yes,0,,date,0,,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
 DEATH,cdm,death_datetime,No,,,datetime,0,,,If not available set time to midnight (00:00:00),No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,,,,Yes,,,
 DEATH,cdm,death_type_concept_id,No,,,integer,0,,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Type Concept,0,,,,,Yes,0,,Yes,100,,Yes,0,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
-DEATH,cdm,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,
+DEATH,cdm,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,,,,Yes,,,

inst/csv/OMOP_CDMv5.3_Table_Level.csv

@@ -21,4 +21,4 @@ COST,CDM,No,,No,,,No,,,,,,
 DRUG_ERA,CDM,No,,Yes,95,,No,,,,,,
 DOSE_ERA,CDM,No,,Yes,100,,No,,,,,,
 CONDITION_ERA,CDM,No,,Yes,95,,Yes,0,,,,,
-DEATH,CDM,No,,No,,,No,,,,,,
+DEATH,CDM,No,,Yes,100,,No,,,,,,