cdmInspection: The main CdmInspection analyses (for v5.x)

In EHDEN/CdmInspection: R Package to support quality control inspection of an OMOP-CDM instance

The main CdmInspection analyses (for v5.x)

Description

CdmInspection runs a list of checks as part of the CDM inspection procedure

Usage

cdmInspection(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  oracleTempSchema = resultsDatabaseSchema,
  databaseName = "",
  databaseId = "",
  databaseDescription = "",
  analysisIds = "",
  smallCellCount = 5,
  runVocabularyChecks = TRUE,
  runDataTablesChecks = TRUE,
  runPerformanceChecks = TRUE,
  runWebAPIChecks = TRUE,
  baseUrl,
  sqlOnly = FALSE,
  outputFolder = "output",
  verboseMode = TRUE
)

Arguments

connectionDetails	An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cdmDatabaseSchema	Fully qualified name of database schema that contains OMOP CDM schema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_instance.dbo'.
resultsDatabaseSchema	Fully qualified name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_results.dbo'.
scratchDatabaseSchema	Fully qualified name of database schema that we can write temporary tables to. Default is resultsDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example, on SQL Server, 'cdm_scratch.dbo'.
vocabDatabaseSchema	String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
oracleTempSchema	For Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
databaseName	String name of the database name. If blank, CDM_SOURCE table will be queried to try to obtain this.
databaseId	ID of your database, this will be used as subfolder for the results.
databaseDescription	Provide a short description of the database.
analysisIds	Analyses to run
smallCellCount	To avoid patient identifiability, cells with small counts (<= smallCellCount) are deleted. Set to NULL if you don't want any deletions.
runVocabularyChecks	Boolean to determine if vocabulary checks need to be run. Default = TRUE
runDataTablesChecks	Boolean to determine if table checks need to be run. Default = TRUE
runPerformanceChecks	Boolean to determine if performance checks need to be run. Default = TRUE
runWebAPIChecks	Boolean to determine if WebAPI checks need to be run. Default = TRUE
baseUrl	WebAPI url, example: http://server.org:80/WebAPI
sqlOnly	Boolean to determine if Achilles should be fully executed. TRUE = just generate SQL files, don't actually run, FALSE = run Achilles
outputFolder	Path to store logs and SQL files
verboseMode	Boolean to determine if the console will show all execution steps. Default = TRUE

Details

CdmInspection runs a list of checks as part of the CDM inspection procedure

Value

                            An object of type \code{achillesResults} containing details for connecting to the database containing the results

EHDEN/CdmInspection documentation built on April 25, 2024, 12:36 p.m.