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)
bmc_best_notbest: Best Mapped Concepts Best/Not Best File
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)