getDbDuringCovariateData: Extracts covariates that occur during a cohort

Description

Extracts covariates that occur during a cohort

Usage

getDbDuringCovariateData(
  connection,
  oracleTempSchema = NULL,
  cdmDatabaseSchema,
  cdmVersion = "5",
  cohortTable = "#cohort_person",
  rowIdField = "subject_id",
  aggregated = TRUE,
  cohortIds = c(-1),
  covariateSettings,
  minCharacterizationMean = 0,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  targetDatabaseSchema = NULL,
  targetCovariateTable = NULL,
  targetCovariateContinuousTable = NULL,
  targetCovariateRefTable = NULL,
  targetAnalysisRefTable = NULL,
  targetTimeRefTable = NULL,
  ...
)

Value

A 'FeatureExtraction' covariateData object containing the during covariates based on user settings

Arguments

connection: The database connection
oracleTempSchema: 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
minCharacterizationMean: The minimum mean value for binary characterization output. Values below this will be cut off from output. This will help reduce the file size of the characterization output, but will remove information on covariates that have very low values. The default is 0.
tempEmulationSchema: Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created
targetDatabaseSchema: (Optional) The schema to save the tables targetCovariateTable/targetCovariateContinuousTable/targetCovariateRefTable/targetCovariateRefTable/targetAnalysisRefTable when they are not temp tables and the output is being exported to database tables.
targetCovariateTable: (Optional) The name of the table where the resulting binary covariates will be stored. If not provided, results will be fetched to R. The table can be a permanent table in the targetDatabaseSchema or a temp table. If it is a temp table, do not specify targetDatabaseSchema.
targetCovariateContinuousTable: (Optional) The name of the table where the resulting continuous covariates will be stored. If not provided, results will be fetched to R. The table can be a permanent table in the targetDatabaseSchema or a temp table. If it is a temp table, do not specify targetDatabaseSchema.
targetCovariateRefTable: (Optional) The name of the table where the covariate reference will be stored.
targetAnalysisRefTable: (Optional) The name of the table where the analysis reference will be stored.
targetTimeRefTable: (Optional) The name of the table for the time reference
...: additional arguments from FeatureExtraction

Details

The user specifies a what during covariates they want and this executes them using FE

Examples

Run this code


conDet <- exampleOmopConnectionDetails()
connection <- DatabaseConnector::connect(conDet)

settings <- createDuringCovariateSettings(
  useConditionOccurrenceDuring = TRUE,
  useConditionOccurrencePrimaryInpatientDuring = FALSE,
  useConditionEraDuring = FALSE,
  useConditionGroupEraDuring = FALSE
)

duringData <- getDbDuringCovariateData(
  connection <- connection,
  cdmDatabaseSchema = 'main',
  cohortIds = 1,
  covariateSettings = settings,
  cohortTable = 'cohort'
)

DatabaseConnector::disconnect(connection)