Audit Clinical Code List Coverage — audit_code_list

Quantifies the share of records captured by the supplied code list, and identifies high-frequency omitted concepts (accounting for at least min_share of domain rows) that may cause silent under-coverage across hospital sites.

Usage

audit_code_list_coverage(
  con,
  domain,
  supplied_codes,
  concept_set_or_ancestors = NULL,
  table_name = NULL,
  by_site = TRUE,
  site_col = "site",
  min_share = 0.01
)

Arguments

con: Active DuckDB DBI connection.
domain: Clinical domain ('condition', 'drug', 'measurement', 'procedure').
supplied_codes: Character or integer vector of concept codes (ICD/RxNorm/LOINC strings) or concept IDs.
concept_set_or_ancestors: Optional integer vector of ancestor concept IDs defining the broad domain scope.
table_name: Optional custom table or view name override.
by_site: Whether to stratify results by hospital site (default TRUE).
site_col: Column name representing site (default 'site').
min_share: Minimum proportion of uncaptured rows (default 0.01 = 1 percent) to flag as an omission.

Value

A data frame with columns: site, total_rows, covered_rows, coverage_share, omitted_concept_id, omitted_code, omitted_concept_name, omitted_rows, omitted_share, flagged, reason.