Extracts covariates that occur during a cohort

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,
  ...
)

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

Value

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

Details

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

See also

Other CovariateSetting: createDuringCovariateSettings()

Examples

conDet <- exampleOmopConnectionDetails()
connection <- DatabaseConnector::connect(conDet)
#> Connecting using SQLite driver

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

duringData <- getDbDuringCovariateData(
  connection <- connection,
  cdmDatabaseSchema = 'main',
  cohortIds = 1,
  covariateSettings = settings,
  cohortTable = 'cohort'
)
#> Constructing during cohort covariates
#> Executing SQL took 0.00329 secs
#> Executing SQL took 0.00298 secs
#> Executing during sql code for ConditionOccurrenceDuring
#> Executing SQL took 0.0181 secs
#> Execution took 0.02 secs
#> Extracting covariates
#> Downloading covariates
#> Extracting covariates took 0.19 secs
#> Removing temp covariate tables

DatabaseConnector::disconnect(connection)