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runEsd

Source: R/ESD.R
runEsd.Rd

Runs the Episode Start Date (ESD) algorithm to infer pregnancy episode start dates for merged HIP/PPS episodes.

Usage

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

Arguments

cdm

A CDM reference, must include all necessary OMOP tables and concept sets for pregnancy inference algorithms.

outputFolder

Character. Path to directory where input and output RDS files reside.

startDate

Earliest episode date to include (as.Date). Default: as.Date("1900-01-01").

endDate

Latest episode date to include (as.Date). Default: Sys.Date().

logger

A log4r logger object for info/debug messages.

debugMode

(`logical(1)`) Should the ESD algorithm write intermediate datasets to the outputFolder? `TRUE` or `FALSE` (default)

conformToValidation

(`logical(1)`: `FALSE`) If `TRUE`, modify episodes to conform (remove overlaps and length > 308 days). Validation and logging always run.

Value

Invisibly returns NULL. Main result is written as an RDS file (final_pregnancy_episodes.rds) to outputFolder. The output contains one row per inferred pregnancy episode. Columns include: final_episode_start_date, final_episode_end_date, final_outcome_category (no prefix), and ESD-derived columns with esd_ prefix: esd_precision_days, esd_precision_category, esd_gestational_age_days_calculated, esd_gw_flag, esd_gr3m_flag, esd_outcome_match, esd_term_duration_flag, esd_outcome_concordance_score, esd_preterm_status_from_calculation, plus merge/HIPPS metadata (e.g. merge_episode_start, hip_end_date, pps_end_date).

Details

This function performs the following major steps:

  1. Loads previously merged HIPPS episode table from outputFolder.

  2. Extracts gestational timing concept evidence (e.g. gestational week, trimester concepts) for each episode within the specified date range.

  3. Infers episode start and start precision using all available gestational timing evidence, with logging.

  4. Merges inferred start dates, timing evidence, and metadata back onto the merged episodes table and computes final start/end/outcome fields.

  5. Filters episodes to retain only those with start on/after startDate and end on/before endDate; episodes with missing inferred dates are retained.

  6. Writes the resulting cohort of identified pregnancy episodes to an RDS file (final_pregnancy_episodes.rds) in outputFolder.