Extract Harmonized Inpatient Lab Panels with Outlier Sanitization

Usage

extract_standard_labs(
  con,
  cohort_table = "cohort",
  cohort_id = NULL,
  panel = "core_14",
  aggregation = "last_before_discharge",
  window = "stay",
  winsorize = TRUE,
  format = "df"
)

Arguments

con: Active DuckDB connection (DBI::dbConnect).
cohort_table: Name of cohort table (default "cohort").
cohort_id: Optional cohort definition ID filter.
panel: Standard lab panel to extract (default "core_14").
aggregation: Aggregation strategy ("last_before_discharge", "first_on_admission", "mean", "median", "min", "max").
window: Windowing scope ("stay", "lookback", "all").
winsorize: Logical TRUE to clamp to physiologic bounds, numeric vector c(low_q, high_q) for percentile winsorization, or FALSE for raw values.
format: Output format ("df", "arrow").

Value

A data.frame or arrow::Table of harmonized laboratory values.