├── .gitignore ├── Data ├── DQACatalog │ ├── AA-001_Value_set_Violation.csv │ ├── AA-002_invalid_concept_id.csv │ ├── AA-003_PK_sourcevalue_inconsistency.csv │ ├── AA-004_Unexpected_Fact.csv │ ├── AA-005_incorrect_concept_id_vocab.csv │ ├── AA-006_Violate_inclusion_Criteria.csv │ ├── AA-007_incorrect_mapping.csv │ ├── AA-008_illegal_concept_class.csv │ ├── AA-009_inconsistent_datetime.csv │ ├── AA-010_invalid_format.csv │ ├── BA-001_Missing_data.csv │ ├── BA-002_no_matching_concept.csv │ ├── BA-003_missing_expected_concept.csv │ ├── BA-004_insuff_fact_visits.csv │ ├── BA-005_insuff_fact_visit_type.csv │ ├── CA-001_Future_Event.csv │ ├── CA-002_Past_Event.csv │ ├── CA-003_Pre_birth_fact.csv │ ├── CA-004_Post_Death_fact.csv │ ├── CA-005_unexpected_change_records_num.csv │ ├── CA-006_change_missingness.csv │ ├── CA-007_entity_outliers.csv │ ├── CA-008_temporal_outliers.csv │ ├── CA-009_temp_distribution.csv │ ├── CA-011_implausible_numerical_values.csv │ ├── CA-012_unexpected_distribution.csv │ ├── CA-013_inconsistent_visit_type.csv │ ├── CA-014_inconsistent_null_values.csv │ ├── CA-015_unexpected_change_facttype.csv │ ├── CA-016_start_date_after_end_date.csv │ ├── CA-017_date_align.csv │ ├── CA-018_procedure_visit_date.csv │ ├── CB-001_unexpected_fact_pt_ratio.csv │ ├── CB-002_unexpected_freq_values.csv │ ├── CB-003_lab_range.csv │ ├── CB-004_drug_class.csv │ ├── DQA_Check_Type_Inventory.csv │ ├── Mapping_old_new_catalog.csv │ └── old_dictionary │ │ └── DCC_DQA_Dictionary.csv ├── PreviousDataSummary │ ├── #top50_inpatient_conditions_ranked.csv# │ ├── .#top50_inpatient_conditions_ranked.csv │ └── holder.txt └── ValueSets │ ├── adt_occurrence │ ├── adt_type_concept_id.txt │ ├── adt_type_concept_id_dplyr.txt │ ├── service_concept_id.txt │ └── service_concept_id_dplyr.txt │ ├── care_site │ ├── place_of_service.csv │ ├── place_of_service_dplyr.txt │ ├── specialty.csv │ ├── specialty.txt │ └── specialty_dplyr.txt │ ├── condition_occurrence │ ├── condition_status_concept_id.csv │ ├── condition_type_concept_id.txt │ ├── condition_type_concept_id_dplyr.txt │ └── poa_concept_id.csv │ ├── death │ ├── death_impute.txt │ ├── death_impute_dplyr.txt │ ├── death_type.txt │ └── death_type_dplyr.txt │ ├── device_exposure │ ├── device_concept_id.txt │ └── device_concept_id_dplyr.txt │ ├── drug_exposure │ ├── dispense_as_written_concept_id.csv │ ├── dose_unit_concept_id.txt │ ├── dose_unit_concept_id_dplyr.txt │ ├── drug_type_concept_id.csv │ ├── route_concept_id.txt │ └── route_concept_id_dplyr.txt │ ├── fact_relationship │ ├── domain_id.txt │ ├── domain_id_dplyr.txt │ ├── relationship_concept_id.txt │ └── relationship_concept_id_dplyr.txt │ ├── immunization │ ├── imm_body_site_concept_id_dplyr.txt │ ├── imm_dose_unit_concept_id.txt │ ├── imm_dose_unit_concept_id_dplyr.txt │ ├── imm_route_concept_id.txt │ ├── imm_route_concept_id_dplyr.txt │ └── immunization_type_concept_id.csv │ ├── location │ └── zip.csv │ ├── measurement │ ├── fev_list.csv │ ├── lab_list.csv │ ├── measurement_type_concept_id.csv │ ├── operator_concept_id.csv │ ├── patient_reported_list.csv │ ├── priority_concept_id.txt │ ├── priority_concept_id_dplyr.txt │ ├── specimen_concept_id.txt │ ├── specimen_concept_id_dplyr.txt │ ├── unit_concept_id.txt │ ├── unit_concept_id_dplyr.txt │ ├── value_as_concept_id.txt │ ├── value_as_concept_id_dplyr.txt │ └── vital_list.csv │ ├── measurement_organism │ ├── organism_concept_id.txt │ └── organism_concept_id_dplyr.txt │ ├── observation │ ├── observation_concept_id.csv │ ├── observation_type_concept_id.csv │ ├── qualifier_concept_id.txt │ ├── qualifier_concept_id_dplyr.txt │ ├── unit_concept_id.txt │ ├── unit_concept_id_dplyr.txt │ ├── value_as_concept_id.txt │ └── value_as_concept_id_dplyr.txt │ ├── person │ ├── day_of_birth.csv │ ├── ethnicity.txt │ ├── ethnicity_dplyr.txt │ ├── gender.csv │ ├── gender.txt │ ├── gender_dplyr.txt │ ├── language.csv │ ├── month_of_birth.csv │ ├── race.csv │ ├── race.txt │ └── race_dplyr.txt │ ├── procedure_occurrence │ ├── gender.txt │ ├── gender_dplyr.txt │ ├── modifier_concept_id.txt │ ├── modifier_concept_id_dplyr.txt │ └── procedure_type_concept_id.csv │ ├── provider │ ├── gender.txt │ ├── gender_dplyr.txt │ ├── specialty.csv │ ├── specialty.csv~ │ ├── specialty.txt │ └── specialty_dplyr.txt │ ├── visit_occurrence │ ├── admitted_from_concept_id.csv │ ├── discharge_to_concept_id.csv │ ├── visit_concept_id.csv │ ├── visit_concept_id.txt │ ├── visit_concept_id_dplyr.txt │ ├── visit_type.csv │ ├── visit_type.txt │ └── visit_type_dplyr.txt │ └── visit_payer │ ├── plan_class.csv │ ├── plan_type.csv │ └── visit_payer_type_concept_id.csv ├── Doc ├── DQA-HowtoexecuteDQAonaPEDSnetSiteDataset.pdf └── PEDSnet_DQA_Documentation.md ├── Infrastructure ├── GlobalConstants.R ├── LibraryImports.R ├── LoggingFunctions.R └── ReportImports.R ├── LICENSE ├── Library ├── CheckFunctions.R ├── CheckType.R ├── CreatePlots.R ├── DDL_RxNorm_Tables.sql ├── DateAlign.R ├── DocumentationModules.R ├── DrugClass.R ├── ImplEvent.R ├── ImplFutureDate.R ├── InconCohort.R ├── InconDateTime.R ├── InconPK.R ├── InconSource.R ├── InconVisitType.R ├── InvalidConID.R ├── InvalidFormat.R ├── InvalidValue.R ├── InvalidVocab.R ├── Issue.R ├── LabRange.R ├── MissConID.R ├── MissData.R ├── MissFact.R ├── MissVisitFact.R ├── MissVisitTypeFact.R ├── NumOutlier.R ├── Oracle_LowerCaseViews.sql ├── PEDSnet_Data_Specifications_blank.xlsx ├── PerformDatabaseOperations.R ├── PostDeath.R ├── PreBirth.R ├── ProcedureVisitDate.R ├── TempOutlier.R ├── UnexDiff.R ├── UnexDiffFactType.R ├── UnexTop.R └── new_utils.R ├── Main ├── Level1 │ ├── Execute_Level1_PEDSnet_DQA.R │ ├── scripts │ │ ├── GenerateADT_OccurrenceReport.R │ │ ├── GenerateCare_SiteReport.R │ │ ├── GenerateCondition_OccurrenceReport_QueryWise.R │ │ ├── GenerateDeathReport.R │ │ ├── GenerateDevice_ExposureReport_QueryWise.R │ │ ├── GenerateDrug_ExposureReport_QueryWise.R │ │ ├── GenerateFact_RelationshipReport_QueryWise.R │ │ ├── GenerateHashReport.R │ │ ├── GenerateImmunizationReport_QueryWise.R │ │ ├── GenerateLocationHistoryReport.R │ │ ├── GenerateLocationReport.R │ │ ├── GenerateMeasurementReport_QueryWise.R │ │ ├── GenerateMeasurement_OrganismReport_QueryWise.R │ │ ├── GenerateObservationReport_QueryWise.R │ │ ├── GeneratePersonReport_QueryWise.R │ │ ├── GenerateProcedure_OccurrenceReport_QueryWise.R │ │ ├── GenerateProviderReport.R │ │ ├── GenerateVisit_OccurrenceReport_QueryWise.R │ │ └── GenerateVisit_PayerReport_QueryWise.R │ └── v2 │ │ └── scripts │ │ └── GenerateMeasurementReport_QueryWise.R~ └── Level2 │ ├── Execute_Level2_PEDSnet_DQA.R │ ├── Level2_queries.md │ └── scripts │ ├── .Rapp.history │ ├── GenerateLevel2ADT_Occurrence.R │ ├── GenerateLevel2Condition.R │ ├── GenerateLevel2Death.R │ ├── GenerateLevel2Drug.R │ ├── GenerateLevel2Measurement.R │ ├── GenerateLevel2Measurement_Organism.R │ ├── GenerateLevel2Observation.R │ ├── GenerateLevel2Patient.R │ ├── GenerateLevel2Procedure.R │ ├── GenerateLevel2Visit.R │ └── Utility_Functions.R ├── ReadMe.md ├── Resources ├── PEDSnet_config_sample.yml └── site_info.R ├── Run_DQA.R └── Tools ├── ConflictResolution ├── conflict_associations.csv ├── resolve.py └── resolvers │ ├── aa_001.py │ ├── aa_003.py │ ├── ba_001.py │ ├── ba_002.py │ ├── ba_003.py │ ├── ca_001.py │ ├── ca_003.py │ ├── ca_004.py │ ├── ca_008.py │ ├── ca_011.py │ ├── ca_013.py │ ├── ca_014.py │ ├── ca_016.py │ └── cb_002.py ├── dqa ├── Makefile ├── README.md ├── feedback │ ├── cmd.go │ └── github.go ├── generate │ └── cmd.go ├── glide.lock ├── glide.yaml ├── issues │ ├── cmd.go │ └── github.go ├── main.go ├── migrate │ └── cmd.go ├── query │ ├── cmd.go │ ├── db.go │ └── db_test.go ├── rank │ └── cmd.go ├── results │ ├── file.go │ ├── io.go │ ├── io_test.go │ ├── model.go │ ├── report.go │ └── report_test.go ├── rules │ ├── condition.go │ ├── parser.go │ ├── rules.go │ └── rules_test.go ├── uni │ └── 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