getCohortCovariateData: Extracts covariates based on cohorts

In OHDSI/PatientLevelPrediction: Develop Clinical Prediction Models Using the Common Data Model

Extracts covariates based on cohorts

Description

Extracts covariates based on cohorts

Usage

getCohortCovariateData(
  connection,
  tempEmulationSchema = NULL,
  oracleTempSchema = NULL,
  cdmDatabaseSchema,
  cdmVersion = "5",
  cohortTable = "#cohort_person",
  rowIdField = "row_id",
  aggregated,
  cohortIds,
  covariateSettings,
  ...
)

Arguments

connection	The database connection
tempEmulationSchema	The schema to use for temp tables
oracleTempSchema	DEPRECATED The temp schema if using oracle
cdmDatabaseSchema	The schema of the OMOP CDM data
cdmVersion	version of the OMOP CDM data
cohortTable	the table name that contains the target population cohort
rowIdField	string representing the unique identifier in the target population cohort
aggregated	whether the covariate should be aggregated
cohortIds	cohort id for the target cohort
covariateSettings	settings for the covariate cohorts and time periods
...	additional arguments from FeatureExtraction

Details

The user specifies a cohort and time period and then a covariate is constructed whether they are in the cohort during the time periods relative to target population cohort index

Value

CovariateData object with covariates, covariateRef, and analysisRef tables

Examples

 
library(DatabaseConnector)
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
# create some cohort of people born in 1969, index date is their date of birth
con <- connect(connectionDetails)
executeSql(con, "INSERT INTO main.cohort 
                 SELECT 1969 as COHORT_DEFINITION_ID, PERSON_ID as SUBJECT_ID,
                 BIRTH_DATETIME as COHORT_START_DATE, BIRTH_DATETIME as COHORT_END_DATE
                 FROM main.person WHERE YEAR_OF_BIRTH = 1969")
covariateData <- getCohortCovariateData(connection = con,
                                        cdmDatabaseSchema = "main",
                                        aggregated = FALSE,
                                        rowIdField = "SUBJECT_ID",
                                       cohortTable = "cohort",
                                        covariateSettings = createCohortCovariateSettings(
                                                               cohortName="summerOfLove",
                                                               cohortId=1969, 
                                                               settingId=1,
                                                               cohortDatabaseSchema="main",
                                                               cohortTable="cohort"))
covariateData$covariateRef
covariateData$covariates

OHDSI/PatientLevelPrediction documentation built on Feb. 14, 2025, 9:44 a.m.