Export pregnancy results into shareable summary CSVs

Reads the patient-level pregnancy episode results produced by the pipeline (from outputFolder; see runPregnancyIdentifier()), generates a set of de-identified summary tables (counts, age summaries, timing distributions, outcome counts, and date completeness checks), and writes them to exportFolder. runPregnancyIdentifier() runs this step automatically and writes to exportFolder (default file.path(outputFolder, "export")); use exportPregnancies() when you need to re-export or write to a different directory. Does not create a ZIP file; use zipExportFolder() after export (and optionally after writing PET comparison tables to the same folder) to create an archive.

Usage

exportPregnancies(
  cdm,
  outputFolder,
  exportFolder,
  minCellCount = 5,
  res = NULL
)

Arguments

cdm

(`cdm_reference`) CDM reference used to compute exports that require database tables (e.g., `person`, `observation_period`).

outputFolder

(`character(1)`) Directory containing pipeline outputs (e.g., `final_pregnancy_episodes.rds`, logs, `pps_concept_counts.csv`).

exportFolder

(`character(1)`) Directory where shareable CSVs will be written.

minCellCount

(`integer(1)`) Minimum count threshold for suppression of small cells (default 5). Values in (0, minCellCount) are replaced with `NA`.

res

Optional data frame of pregnancy episodes. If provided, used instead of reading final_pregnancy_episodes.rds from outputFolder. Used when exporting a conformed copy (e.g. conformToValidation = "both").

Value

Invisibly returns `NULL`. Writes CSVs to `exportFolder`.

Details

The export is intended for lightweight QA and sharing across sites. Small cell counts can be suppressed via minCellCount.