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createPregnancyCohort

createPregnancyCohort.Rd

Creates the pregnancy cohort from a specified pregnancy extension table (PET) in a specified schema

Usage

createPregnancyCohort(
  cdm,
  petTable,
  petSchema,
  keepExtensionTable = TRUE,
  samePregDiffDates = "None",
  cohortDefinitionID = 101,
  minGestationalDuration = 0,
  maxGestationalDuration = 308,
  minAge = 12,
  maxAge = 55,
  startDate = NULL,
  endDate = NULL,
  sex = "Female",
  outputDir,
  .softValidation = FALSE
)

Arguments

cdm

(cdm_reference) Created with i.e. CDMConnector::cdmFromCon.

petTable

(character(1)) Name of the Pregnancy Extension Table.

petSchema

(character(1)) Name of the schema where the Pregnancy Extension Table resides

keepExtensionTable

(logical(1): TRUE) Keep the reference to the pregnancy extension table? default = TRUE

samePregDiffDates

(character(1): "none") In the case of same subject_id and pregnancy_id, but differing start/end dates, which record to keep? "None" will drop all records, "Earliest" will keep the record with the earliest pregnancy start date, and "latest" will keep the record with the latest start date. For selection of "Earliest" or "Latest", if there is more than one record with that start date, then the record with the greatest gestational duration for that start date will be kept.

cohortDefinitionID

(numeric(1): 101) Cohort definition id to assign to newly created cohort

minGestationalDuration

(numeric(1): NULL) Minimum gestational duration to include.

maxGestationalDuration

(numeric(1): 308) Maximum gestational duration to include.

minAge

(numeric(1): 12) Minimum age to include.

maxAge

(numeric(1): 55) Maximum age to include.

startDate

(Date(1): NULL) Earliest pregnancy start date to include, e.g. as.Date("2001-09-20", "%Y-%m-%d")

endDate

(Date(1): NULL) Latest pregnancy end date to include, e.g as.Date("10/20/21", "%m/%d/%y")

sex

(character(2): "Female") Sexes to include. One of or both c("Female", "Male").

outputDir

(path) Path to output pregnancy_duplicate_map.csv to

.softValidation

(logical(1): FALSE) Should a softValidation be done? default = FALSE

Value

(cdm_reference) Returns the CDM with the added cohort table.

Note

A pregnancy of multiples will be recorded with one pregnancy record

  • Multiple pregnancies of the same pregnancy_id these will be collapsed to one record.

  • If a multiples pregnancy with different pregnancy_ids for a birthing parent is recognized, then this will be collapsed to one pregnancy record with the smallest pregnancy_id kept to represent it

A pregnancy which appears as multiple records with differing dates (same pregnancy_id, different dates) will be dropped