execute: Execute the Study

In ohdsi-studies/MethodsLibraryPleEvaluation: Evaluation of Population-Level Estimation Methods

Description

Execute the Study

Usage

execute(connectionDetails, cdmDatabaseSchema, oracleTempSchema = NULL,
  outcomeDatabaseSchema, outcomeTable,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era", nestingCohortDatabaseSchema,
  nestingCohortTable, outputFolder, databaseName, maxCores = 1,
  cdmVersion = "5", createNegativeControlCohorts = TRUE,
  imputeExposureLengthForPanther = TRUE,
  synthesizePositiveControls = TRUE, runCohortMethod = TRUE,
  runSelfControlledCaseSeries = TRUE, runSelfControlledCohort = TRUE,
  runCaseControl = TRUE, runCaseCrossover = TRUE,
  packageResults = 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'.
oracleTempSchema	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
outcomeDatabaseSchema	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'.
outcomeTable	The name of the table that will be created in the outcomeDatabaseSchema. This table will hold the outcome cohorts used in this study.
exposureDatabaseSchema	For PanTher only: Schema name where exposure 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'.
exposureTable	For PanTher only: The name of the table that will be created in the exposureDatabaseSchema This table will hold the exposure cohorts used in this study.
nestingCohortDatabaseSchema	Schema name where nesting cohort 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'.
nestingCohortTable	The name of the table that will be created in the nestingCohortDatabaseSchema This table will hold the nesting 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.
databaseName	A short string for identifying the database (e.g. 'Synpuf').
maxCores	How many parallel cores should be used? If more cores are made available this can speed up the analyses.
cdmVersion	Version of the Common Data Model used. Currently only version 5 is supported.
createNegativeControlCohorts	Create the negative control outcome and nesting cohorts?
imputeExposureLengthForPanther	For PanTher only: impute exposure length?
synthesizePositiveControls	Should positive controls be synthesized?
runCohortMethod	Perform the cohort method analyses?
runSelfControlledCaseSeries	Perform the SCCS analyses?
runSelfControlledCohort	Perform the SCC analyses?
runCaseControl	Perform the case-control analyses?
runCaseCrossover	Perform the case-crossover analyses?
packageResults	Should results be packaged for later sharing and viewing?

Details

This function executes the Study.

The createCohorts, synthesizePositiveControls, runAnalyses, and runDiagnostics arguments are intended to be used to run parts of the full study at a time, but none of the parts are considerd to be optional.

ohdsi-studies/MethodsLibraryPleEvaluation documentation built on Feb. 5, 2020, 2:16 p.m.