execute: Execute the Study

In OHDSI/SkeletonComparativeEffectStudy: A Package Skeleton for Comparative Effectiveness Studies

Execute the Study

Description

Execute the Study

Usage

execute(
  connectionDetails,
  cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  cohortInclusionTable = paste0(cohortTable, "_inclusion"),
  cohortInclusionResultTable = paste0(cohortTable, "_inclusion_result"),
  cohortInclusionStatsTable = paste0(cohortTable, "_inclusion_stats"),
  cohortSummaryStatsTable = paste0(cohortTable, "_summary_stats"),
  cohortCensorStatsTable = paste0(cohortTable, "_censor_stats"),
  oracleTempSchema = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  verifyDependencies = TRUE,
  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	Name of the cohort table.
cohortInclusionTable	Name of the inclusion table, one of the tables for storing inclusion rule statistics.
cohortInclusionResultTable	Name of the inclusion result table, one of the tables for storing inclusion rule statistics.
cohortInclusionStatsTable	Name of the inclusion stats table, one of the tables for storing inclusion rule statistics.
cohortSummaryStatsTable	Name of the summary stats table, one of the tables for storing inclusion rule statistics.
cohortCensorStatsTable	Name of the censor stats table, one of the tables for storing inclusion rule statistics.
oracleTempSchema	DEPRECATED: use 'tempEmulationSchema' instead.
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.
verifyDependencies	Check whether correct package versions are installed?
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 SkeletonComparativeEffectStudy 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 considered 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)

OHDSI/SkeletonComparativeEffectStudy documentation built on May 13, 2023, 12:48 p.m.