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Fix data type mismatches #685

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Fix data type mismatches #685

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24 changes: 12 additions & 12 deletions inst/csv/OMOP_CDMv5.2_Field_Level.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,8 @@ VISIT_OCCURRENCE,CDM,admitting_source_value,No,,,varchar(50),0,,,"This informati
VISIT_OCCURRENCE,CDM,discharge_to_concept_id,No,,,integer,0,,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example.","If available, map the discharge_to_source_value to a standard concept in the visit domain.",No,,,Yes,0,,CONCEPT,CONCEPT_ID,Visit,0,,,,,Yes,0,,Yes,100,,Yes,100,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
VISIT_OCCURRENCE,CDM,discharge_to_source_value,No,,,varchar(50),0,,,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,100,,DISCHARGE_TO_CONCEPT_ID,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
VISIT_OCCURRENCE,CDM,preceding_visit_occurrence_id,No,,,integer,0,,Use this field to find the visit that occured for the person prior to the given visit. There could be a few days or a few years in between.,"The preceding_visit_id can be used to link a visit immediately preceding the current visit. Note this is not symmetrical, and there is no such thing as a ""following_visit_id"".",No,,,Yes,0,,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_occurrence_id,Yes,0,,bigint,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,person_id,Yes,0,,bigint,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_occurrence_id,Yes,0,,integer,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_concept_id,Yes,0,,integer,0,,"The CONDITION_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies",,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Condition,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_start_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,CONDITION_END_DATE,1,,Yes,1,,Yes,1,,Yes,Yes,5,
CONDITION_OCCURRENCE,CDM,condition_start_datetime,No,,,datetime,0,,,,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,CONDITION_END_DATETIME,1,,Yes,1,,Yes,1,,Yes,,,
Expand All @@ -63,8 +63,8 @@ CONDITION_OCCURRENCE,CDM,visit_occurrence_id,No,,,integer,0,,,,No,,,Yes,0,,VISIT
CONDITION_OCCURRENCE,CDM,condition_source_value,No,,,varchar(50),0,,"This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Condition necessary for a given analytic use case. Consider using CONDITION_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. ",This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,10,,CONDITION_CONCEPT_ID,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_source_concept_id,No,,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,No,,,Yes,100,,No,,,Yes,10,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_OCCURRENCE,CDM,condition_status_source_value,No,,,varchar(50),0,,,This code is mapped to a Standard Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,100,,CONDITION_STATUS_CONCEPT_ID,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,drug_exposure_id,Yes,0,,bigint,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,person_id,Yes,0,,bigint,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,drug_exposure_id,Yes,0,,integer,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,drug_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Drug,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_EXPOSURE,CDM,drug_exposure_start_date,Yes,0,,date,0,,,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration procedure was recorded.",No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DRUG_EXPOSURE_END_DATE,1,,Yes,1,,Yes,1,,Yes,Yes,5,
DRUG_EXPOSURE,CDM,drug_exposure_start_datetime,No,,,datetime,0,,,,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DRUG_EXPOSURE_END_DATETIME,1,,Yes,1,,Yes,1,,Yes,,,
Expand Down Expand Up @@ -98,8 +98,8 @@ PROCEDURE_OCCURRENCE,CDM,visit_occurrence_id,No,,,integer,0,,,,No,,,Yes,0,,VISIT
PROCEDURE_OCCURRENCE,CDM,procedure_source_value,No,,,varchar(50),0,,,"This code is mapped to a standard procedure Concept in the Standardized Vocabularies and the original code is, stored here for reference. Procedure source codes are typically ICD-9-Proc, CPT-4, HCPCS or OPCS-4 codes.",No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,10,,PROCEDURE_CONCEPT_ID,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
PROCEDURE_OCCURRENCE,CDM,procedure_source_concept_id,No,,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,,,,,,,No,,,Yes,100,,No,,,Yes,10,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
PROCEDURE_OCCURRENCE,CDM,qualifier_source_value,No,,,varchar(50),0,,,,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,Yes,100,,MODIFIER_CONCEPT_ID,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,device_exposure_id,Yes,0,,bigint,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,person_id,Yes,0,,bigint,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,device_exposure_id,Yes,0,,integer,0,,,,Yes,0,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,device_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Device,0,,,,,Yes,0,,Yes,0,,Yes,5,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DEVICE_EXPOSURE,CDM,device_exposure_start_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,No,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DEVICE_EXPOSURE_END_DATE,1,,Yes,1,,Yes,1,,Yes,Yes,5,
DEVICE_EXPOSURE,CDM,device_exposure_start_datetime,No,,,datetime,0,,,,No,,,No,,,,,,,,,,,No,,,Yes,100,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DEVICE_EXPOSURE_END_DATETIME,1,,Yes,1,,Yes,1,,Yes,,,
Expand Down Expand Up @@ -275,8 +275,8 @@ COST,CDM,drg_source_value,No,,,VARCHAR(3),0,,Diagnosis Related Groups are US cod
DRUG_ERA,CDM,drug_era_id,Yes,0,,integer,0,,,,Yes,0,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_ERA,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_ERA,CDM,drug_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Drug,0,,Ingredient,0,,Yes,0,,Yes,0,,Yes,0,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DRUG_ERA,CDM,drug_era_start_date,Yes,0,,datetime,0,,,The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient. (NOT RIGHT),No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DRUG_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
DRUG_ERA,CDM,drug_era_end_date,Yes,0,,datetime,0,,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
DRUG_ERA,CDM,drug_era_start_date,Yes,0,,date,0,,,The Drug Era Start Date is the start date of the first Drug Exposure for a given ingredient. (NOT RIGHT),No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DRUG_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
DRUG_ERA,CDM,drug_era_end_date,Yes,0,,date,0,,,"The Drug Era End Date is the end date of the last Drug Exposure. The End Date of each Drug Exposure is either taken from the field drug_exposure_end_date or, as it is typically not available, inferred using the following rules:
For pharmacy prescription data, the date when the drug was dispensed plus the number of days of supply are used to extrapolate the End Date for the Drug Exposure. Depending on the country-specific healthcare system, this supply information is either explicitly provided in the day_supply field or inferred from package size or similar information.
For Procedure Drugs, usually the drug is administered on a single date (i.e., the administration date).
A standard Persistence Window of 30 days (gap, slack) is permitted between two subsequent such extrapolated DRUG_EXPOSURE records to be considered to be merged into a single Drug Era. (ARENT WE REQUIRING TO USE DRUG_EXPOSURE_END_DATE NOW????)",No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,DRUG_ERA,DRUG_ERA_START_DATE,1,,No,,,,,,,Yes,1,,Yes,1,,Yes,,,
Expand All @@ -287,13 +287,13 @@ DOSE_ERA,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,,,
DOSE_ERA,CDM,drug_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Drug,0,,Ingredient,0,,Yes,0,,Yes,0,,Yes,0,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DOSE_ERA,CDM,unit_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Unit,0,,,,,Yes,0,,Yes,0,,Yes,0,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DOSE_ERA,CDM,dose_value,Yes,0,,float,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,0,1,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
DOSE_ERA,CDM,dose_era_start_date,Yes,0,,datetime,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DOSE_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
DOSE_ERA,CDM,dose_era_end_date,Yes,0,,datetime,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,No,,,,,,,Yes,1,,Yes,1,,Yes,,,
DOSE_ERA,CDM,dose_era_start_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,DOSE_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
DOSE_ERA,CDM,dose_era_end_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,No,,,,,,,Yes,1,,Yes,1,,Yes,,,
CONDITION_ERA,CDM,condition_era_id,Yes,0,,integer,0,,,,Yes,0,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_ERA,CDM,person_id,Yes,0,,integer,0,,,,No,,,Yes,0,,PERSON,PERSON_ID,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_ERA,CDM,condition_concept_id,Yes,0,,integer,0,,,,No,,,Yes,0,,CONCEPT,CONCEPT_ID,Condition,0,,,,,Yes,0,,Yes,0,,Yes,0,,No,,,No,,,,,,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
CONDITION_ERA,CDM,condition_era_start_date,Yes,0,,datetime,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,CONDITION_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
CONDITION_ERA,CDM,condition_era_end_date,Yes,0,,datetime,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,No,,,,,,,Yes,1,,Yes,1,,Yes,,,
CONDITION_ERA,CDM,condition_era_start_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,Yes,1,,Yes,CONDITION_ERA_END_DATE,1,,Yes,1,,Yes,1,,Yes,,,
CONDITION_ERA,CDM,condition_era_end_date,Yes,0,,date,0,,,,No,,,No,,,,,,,,,,,,,,Yes,0,,No,,,No,,,No,,,,'19500101',1,,"DATEADD(dd,1,GETDATE())",1,,Yes,PERSON,BIRTH_DATETIME,1,,No,,,,,,,Yes,1,,Yes,1,,Yes,,,
CONDITION_ERA,CDM,condition_occurrence_count,No,,,integer,0,,,,No,,,No,,,,,,,,,,,,,,Yes,100,,No,,,No,,,No,,,,1,1,,,,,,,,,,No,,,,,,,,,,,,,Yes,,,
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,,,
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