Run the PPS Algorithm to Identify Pregnancy Episodes

This function executes the Pregnancy Progression Signature (PPS) algorithm against a Common Data Model (CDM) instance. It inserts the required PPS concept lookup table, extracts gestational timing evidence (e.g., gestational weeks, trimesters) across OMOP clinical domains, assembles person-level gestational timing records, and writes intermediate episode and summary files to the specified output directory.

Usage

runPps(
  cdm,
  outputFolder,
  startDate = as.Date("1900-01-01"),
  endDate = Sys.Date(),
  logger,
  debugMode = FALSE
)

Arguments

cdm

A `cdm_reference` object; must include all OMOP tables and structure needed for pregnancy concept search.

outputFolder

Character. Directory path where intermediate and output RDS files will be saved.

startDate

Date (`Date(1)`). Earliest clinical date to be considered for gestational timing evidence (default: `"1900-01-01"`).

endDate

Date (`Date(1)`). Latest clinical date to be considered for gestational timing evidence (default: `Sys.Date()`).

logger

`log4r` logger object (required) for emitting information and debug messages.

debugMode

(`Logical`) Should intermediate datasets be written to the output folder for debugging? TRUE or FALSE (default)

Value

Returns the input `cdm_reference` invisibly, possibly modified with intermediate tables in its environment. Main results are side effects: RDS files with person-level gestational timing episodes and summary statistics are written to `outputFolder`.