extract_all: Run the full source data extraction pipeline.

In syrona: Stratified Prevalence Comparison Across OMOP CDM Datasets

Run the full source data extraction pipeline.

Description

Derives stratified prevalence tables from the records in an OMOP CDM database for one or more clinical domains. Applies k-anonymity suppression and optionally saves results to CSV.

Usage

extract_all(
  dataset_name,
  db,
  domains = c("conditions", "procedures", "drugs"),
  cohort_id = NULL,
  cohort_schema = NULL,
  save = TRUE
)

Arguments

dataset_name	Short label for the dataset (e.g. "EH30", "EstBB").
db	Either a DuckDB file path (string) or an existing connection list from syrona_connect / syrona_connect_pg.
domains	Character vector of domains to extract. Options: "conditions", "procedures", "drugs".
cohort_id	Integer cohort_definition_id to filter by. If NULL (default), extracts the full dataset.
cohort_schema	Schema containing the cohort table.
save	If TRUE (default), saves CSV to data/sources/<dataset_name>/.

Value

Named list of tibbles matching the Syrona schema (invisible).

syrona documentation built on Sept. 5, 2026, 1:06 a.m.