execute: Execute the Study

In ABMI/RanitidineCancerRisk: A Package to compare the risks of cancer between H2 blockers

Description

Execute the Study

Usage

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

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 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?
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.

Details

This function executes the RanitidineCancerRisk 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.

Examples

## 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)

ABMI/RanitidineCancerRisk documentation built on March 11, 2021, 9:02 p.m.