Force Study Cohort Index Stays from an External List — cohort_from_index

Maps source patient and encounter identifiers to standard OMOP person_id and visit_occurrence_id, producing a compliant OMOP cohort table while reporting match/unmatched diagnostic tallies.

Usage

cohort_from_index_stays(
  con,
  stays,
  id_type = "person_source_value",
  person_source_col = "person_source_value",
  visit_source_col = "visit_source_value",
  index_date_col = "index_date",
  end_date_col = "end_date",
  cohort_definition_id = 1L,
  site_col = "site",
  target_table = NULL,
  group_by = NULL
)

Arguments

con: Active DuckDB DBI connection.
stays: Input data frame, CSV/parquet path, or table name.
id_type: Identifier type ('person_source_value' or 'person_id').
person_source_col: Patient identifier column in input stays (default 'person_source_value').
visit_source_col: Optional encounter identifier column (default 'visit_source_value').
index_date_col: Index/admission date column in input stays (default 'index_date').
end_date_col: Optional discharge/end date column in input stays (default 'end_date').
cohort_definition_id: OMOP cohort definition identifier (default 1).
site_col: Site column name if present (default 'site').
target_table: Optional table name to persist the cohort in DuckDB.
group_by: Optional column name (e.g. 'SITE') to stratify match diagnostics by.

Value

A list with cohort (data frame) and audit (list of match metrics).