Compare runPregnancyIdentifier results with the OMOP Pregnancy Extension Table (PET) — comparePregnancyIdentifierWithPET • PregnancyIdentifier

Compares algorithm output (from final_pregnancy_episodes.rds) to the PET table and writes comparison summaries to exportFolder. Comparisons include: pregnancy episode and person counts; raw and filtered (gestation 0-308, end >= start) person overlap; Venn counts (both, PET only, algorithm only); a 2x2 confusion matrix (TP, FN, FP, TN) with sensitivity and PPV (no gold-standard negatives, so specificity and NPV are not defined); date differences for matched pairs (start, end, duration, overall and stratified by outcome); outcome confusion matrix and accuracy; outcome comparison by year (same-year pairs, cross-tab LB/SB/AB vs PET outcome); and pregnancy duration distributions.

Usage

comparePregnancyIdentifierWithPET(
  cdm,
  outputFolder,
  exportFolder,
  petSchema,
  petTable,
  startDate = NULL,
  endDate = NULL,
  minOverlapDays = 1L,
  removeWithinSourceOverlaps = FALSE,
  minCellCount = 5L,
  outputLogToConsole = TRUE
)

Arguments

cdm: A cdm_reference (from CDMConnector) with a database connection. The PET table is read via petSchema and petTable.
outputFolder: character(1). Directory containing pipeline outputs (final_pregnancy_episodes.rds), i.e. the episode-level input to the comparison.
exportFolder: character(1). Directory where comparison CSVs and log.txt are written. Created if it does not exist. Log file is appended if it already exists.
petSchema: character(1). Schema name of the PET table (e.g. "omop_cmbd").
petTable: character(1). Table name of the pregnancy episode table (e.g. "pregnancy_episode"). Must contain at least person_id, pregnancy_start_date, pregnancy_end_date, and pregnancy_outcome (concept_id). Gestational length in days is computed from start and end dates in the database via CDMConnector::datediff(); the table need not have a gestational_length_in_day column.
startDate: Date(1) or NULL. If provided, the PET table is filtered to episodes that overlap the study period defined by [startDate, endDate]. An episode overlaps if its end date is on or after startDate and its start date is on or before endDate. Must be before endDate. Default NULL (no date filtering).
endDate: Date(1) or NULL. End of the study period. Required when startDate is provided and vice versa. Default NULL.
minOverlapDays: integer(1). Minimum overlap in days to consider an algorithm episode and a PET episode as the same pregnancy (default 1).
removeWithinSourceOverlaps: logical(1). If TRUE, before matching the code removes overlapping episodes within PET and within the algorithm (greedy non-overlapping by start date per person), which can reduce many-to-many candidate pairs. Default FALSE.
minCellCount: integer(1). Minimum count threshold for suppression. Any record count or person count less than minCellCount is replaced with NA in the exported summarised result. Default 5.
outputLogToConsole: logical(1). Whether to log to the console as well as to file.path(exportFolder, "log.txt").

Value

Nothing. The summarised result is written to file.path(exportFolder, "pet_comparison_summarised_result.csv"). Use omopgenerics::importSummarisedResult() to read it and visOmopResults::visTable() to display it.