execute: Execute the Study
In alondhe/PADManuscript: A Package Skeleton for Comparative Effectiveness Studies

Description Usage Arguments Details Examples

View source: R/Main.R

Execute the Study

execute(connectionDetails, cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema, cohortTable = "cohort",
  oracleTempSchema = cohortDatabaseSchema, outputFolder,
  databaseId = "Unknown", databaseName = "Unknown",
  databaseDescription = "Unknown", createCohorts = TRUE,
  synthesizePositiveControls = TRUE, runAnalyses = TRUE,
  runDiagnostics = TRUE, packageResults = TRUE, maxCores = 4,
  minCellCount = 5)

`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 intermediate 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 work database schema. This table will hold the exposure and outcome cohorts used in this study.
`oracleTempSchema`	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
`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 (e.g. 'Medicare Claims Synthetic Public Use Files (SynPUFs)').
`databaseDescription`	A short description (several sentences) of the database.
`createCohorts`	Create the cohortTable table with the exposure and outcome cohorts?
`synthesizePositiveControls`	Should positive controls be synthesized?
`runAnalyses`	Perform the cohort method analyses?
`runDiagnostics`	Compute study diagnostics?
`packageResults`	Should results be packaged for later sharing?
`maxCores`	How many parallel cores should be used? If more cores are made available this can speed up the analyses.
`minCellCount`	The minimum number of subjects contributing to a count before it can be included in packaged results.

This function executes the PADManuscript 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.

## Not run: 
connectionDetails <- createConnectionDetails(dbms = "postgresql",
                                             user = "joe",
                                             password = "secret",
                                             server = "myserver")

execute(connectionDetails,
        cdmDatabaseSchema = "cdm_data",
        cohortDatabaseSchema = "study_results",
        cohortTable = "cohort",
        oracleTempSchema = NULL,
        outputFolder = "c:/temp/study_results",
        maxCores = 4)

## End(Not run)