Package index • ndq

Data Quality Checks

The primary functions used to execute each data quality analysis

check_bmc(): Best Mapped Concepts

check_cfd(): Clinical Fact Documentation

check_dc(): Data Cycle Changes

check_dcon(): Domain Concordance

check_dp(): Date Plausibility

check_ecp(): Expected Concepts Present

check_fot(): Facts Over Time

check_mf_visitid(): Missing Field: Visit ID

check_uc(): Unmapped Concepts

check_vc(): Vocabulary Conformance

check_vs(): Valueset Conformance

Data Quality Processing

Post-processing functions to be applied to output after the primary analyses have been executed on all network institutions.

process_bmc(): Best Mapped Concepts – Processing

process_cfd(): Clinical Fact Documentation – Processing

process_dc(): Data Cycle Changes – Processing

process_dcon(): Domain Concordance – Processing

process_dp(): Date Plausibility – Processing

process_ecp(): Expected Concepts Present – Processing

process_fot(): Facts Over Time – Processing

process_mf_visitid(): Missing Field: Visit ID – Processing

process_uc(): Unmapped Concepts – Processing

process_vc(): Vocabulary Conformance – Processing

process_vs(): Valueset Conformance – Processing

Helper Functions

Miscellaneous helper functions to supplement the analyses

attach_anon_id(): Add an anonymized site identifier to all tables

create_check_metadata(): Create informational metadata file

summarize_large_n(): Add summary columns for a large N of sites

Example Function Inputs

Examples of all the tables that should be used as input to each of the check_* functions. There are specific examples for both OMOP and PCORnet configurations.

bmc_input_omop: Best Mapped Concepts Input File (OMOP)

bmc_input_pcornet: Best Mapped Concepts Input File (PCORnet)

cfd_input_omop: Clinical Fact Documentation Input File (OMOP)

cfd_input_pcornet: Clinical Fact Documentation Input File (PCORnet)

cfd_visit_types_omop: Clinical Fact Documentation Visit Type Input File (OMOP)

cfd_visit_types_pcornet: Clinical Fact Documentation Visit Type Input File (PCORnet)

dc_input_omop: Data Cycle Changes Input File (OMOP)

dc_input_pcornet: Data Cycle Changes Input File (PCORnet)

dcon_input_omop: Domain Concordance Input File (OMOP)

dcon_input_pcornet: Domain Concordance Input File (PCORnet)

dp_input_omop: Date Plausibility Input File (OMOP)

dp_input_pcornet: Date Plausibility Input File (PCORnet)

ecp_input_omop: Expected Concepts Present Input File (OMOP)

ecp_input_pcornet: Expected Concepts Present Input File (PCORnet)

fot_input_omop: Facts Over Time Input File (OMOP)

fot_input_pcornet: Facts Over Time Input File (PCORnet)

mf_input_omop: Missing Field: Visit ID Input File (OMOP)

mf_input_pcornet: Missing Field: Visit ID Input File (PCORnet)

uc_input_omop: Unmapped Concepts Input File (OMOP)

uc_input_pcornet: Unmapped Concepts Input File (PCORnet)

vc_input_omop: Vocabulary Conformance Input File (OMOP)

vc_input_pcornet: Vocabulary Conformance Input File (PCORnet)

vs_input_omop: Valueset Conformance Input File (OMOP)

vs_input_pcornet: Valueset Conformance Input File (PCORnet)