execute: Execute the Study

In ohdsi-studies/Eumaeus: Evaluating Use of Methods for Adverse Event Under Surveillance

Execute the Study

Description

Execute the Study

Usage

execute(
  connectionDetails,
  cdmDatabaseSchema,
  cohortDatabaseSchema,
  cohortTable,
  outputFolder,
  databaseId,
  databaseName = databaseId,
  databaseDescription = databaseId,
  minCellCount = 5,
  maxCores = 1,
  exposureIds = getExposuresOfInterest()$exposureId,
  verifyDependencies = TRUE,
  createCohorts = TRUE,
  synthesizePositiveControls = TRUE,
  runCohortMethod = TRUE,
  runSccs = TRUE,
  runCaseControl = TRUE,
  runHistoricalComparator = TRUE,
  generateDiagnostics = TRUE,
  computeCriticalValues = TRUE,
  createDbCharacterization = TRUE,
  exportResults = TRUE
)

Arguments

connectionDetails	An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
cdmDatabaseSchema	Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortDatabaseSchema	Schema name where outcome data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortTable	The name of the table that will be created in the cohortDatabaseSchema. This table will hold the exposure and outcome cohorts used in this study.
outputFolder	Name of local folder to place results; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.
databaseId	A short string for identifying the database (e.g. 'Synpuf').
databaseName	The full name of the database.
databaseDescription	A short description (several sentences) of the database.
minCellCount	The minimum cell count for fields contains person counts or fractions.
maxCores	How many parallel cores should be used? If more cores are made available this can speed up the analyses.
exposureIds	The IDs of the exposure cohorts to include. See getExposuresOfInterest for the available exposure cohorts and their IDs.
verifyDependencies	Check whether correct package versions are installed?
createCohorts	Create the exposure and outcome cohorts?
synthesizePositiveControls	Should positive controls be synthesized?
runCohortMethod	Perform the cohort method analyses?
runSccs	Perform the SCCS and SCRI analyses?
runCaseControl	Perform the case-control analyses?
runHistoricalComparator	Perform the historical comparator analyses?
generateDiagnostics	Generate additional study diagnostics?
computeCriticalValues	Compute critical values for all methods?
createDbCharacterization	Create a high-level characterization of the database?
exportResults	Export the results to a single zip file (containing several CSV files) for sharing?

Details

This function executes the Study.

ohdsi-studies/Eumaeus documentation built on Feb. 12, 2024, 9:45 p.m.