Run the HIP pregnancy identification algorithm

This function runs the HIP outcome based pregnancy identification algorithm. It assumes that the `initPregnancies` function has already been run and the preg_hip_records and preg_hip_concepts tables are in the cdm. The algorithm identifies start and end dates for pregnancies by first prioritizing pregnancy outcomes and then using inference to set a pregnancy start date. Each pregnancy is classified into one of several categories. - "LB": Live birth - "SB": Still birth - "AB": abortion, - "SA": miscarriage, - "DELIV": unspecified delivery - "ECT": ectopic pregnancy - "PREG": unspecified/ongoing pregnancy

Usage

runHip(
  cdm,
  outputFolder = NULL,
  startDate = as.Date("1900-01-01"),
  endDate = Sys.Date(),
  justGestation = TRUE,
  logger
)

Arguments

cdm

(`cdm_reference`) A cdm reference object from CDMConnector.

outputFolder

(`character(1)`) Output directory to write output to.

startDate

(`Date(1)`: `as.Date("1900-01-01"`) Start date of data to use. By default 1900-01-01

endDate

(`Date(1)`: `Sys.Date()`) End date of data to use. By default today.

justGestation

(`logical(1)`: `TRUE`) Should episodes that only have gestational concepts be considered?

logger

(`logger`) A log4r logger object created with `makeLogger()`.

Value

The input cdm object with the `cdm$preg_hip_episodes` table added. This table contains episode-level information about each identified pregnancy per individual. The columns are: - `person_id`: Unique identifier for the person. - `hip_episode`: Sequential episode number for the person (1 = first episode, etc.). - `hip_pregnancy_start`: Estimated start date of the pregnancy episode, based on outcome and available gestational age information. - `hip_pregnancy_end`: Date of the principal pregnancy outcome event (the pregnancy end date). - `hip_outcome_category`: HIP-assigned pregnancy outcome type. One of "LB" (live birth), "SB" (stillbirth), "AB" (abortion), "SA" (miscarriage), "DELIV" (unspecified delivery), "ECT" (ectopic pregnancy), or "PREG" (ongoing/unspecified). - `hip_first_gest_date`: First gestation date in the episode (if available). NA if not identified. - `hip_gest_flag`: Indicates if gestational age concepts were found in the episode ("yes" or "no"). - `hip_episode_length`: Length of the pregnancy episode, in days (from `hip_pregnancy_start` to `hip_pregnancy_end`).

A file named `hip_episodes.rds` is saved in the `outputFolder` directory. This file contains a dataframe with the same columns as listed above for the `cdm$preg_hip_episodes` table.