Execution of data quality rules (for v5 and above)

achillesHeel executes data quality rules (or checks) on pre-computed analyses (or measures).

achillesHeel(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  oracleTempSchema = scratchDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  cdmVersion = "5",
  numThreads = 1,
  tempHeelPrefix = "tmpheel",
  dropScratchTables = FALSE,
  ThresholdAgeWarning = 125,
  ThresholdOutpatientVisitPerc = 0.43,
  ThresholdMinimalPtMeasDxRx = 20.5,
  outputFolder,
  sqlOnly = FALSE,
  verboseMode = TRUE
)

Arguments

connectionDetails	An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cdmDatabaseSchema	string name of database schema that contains OMOP CDM. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
resultsDatabaseSchema	string 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 'results.dbo'.
scratchDatabaseSchema	(OPTIONAL, multi-threaded mode) Name of a fully qualified schema that is accessible to/from the resultsDatabaseSchema, that can store all of the scratch tables. Default is resultsDatabaseSchema.
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.
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'.
cdmVersion	Define the OMOP CDM version used: currently supports v5 and above. Default = "5".
numThreads	(OPTIONAL, multi-threaded mode) The number of threads to use to run Achilles in parallel. Default is 1 thread.
tempHeelPrefix	(OPTIONAL, multi-threaded mode) The prefix to use for the "temporary" (but actually permanent) Heel tables. Default is "tmpheel"
dropScratchTables	(OPTIONAL, multi-threaded mode) TRUE = drop the scratch tables (may take time depending on dbms), FALSE = leave them in place
ThresholdAgeWarning	The maximum age to allow in Heel
ThresholdOutpatientVisitPerc	The maximum percentage of outpatient visits among all visits
ThresholdMinimalPtMeasDxRx	The minimum percentage of patients with at least 1 Measurement, 1 Dx, and 1 Rx
outputFolder	Path to store logs and SQL files
sqlOnly	Boolean to determine if Heel should be fully executed. TRUE = just generate SQL files, don't actually run, FALSE = run Achilles Heel
verboseMode	Boolean to determine if the console will show all execution steps. Default = TRUE

Value

The full Heel SQL code

Details

achillesHeel contains number of rules (authored in SQL) that are executed against achilles results tables.

Examples

if (FALSE) {
  connectionDetails <- createConnectionDetails(dbms="sql server", server="some_server")
  achillesHeel <- achillesHeel(connectionDetails = connectionDetails, 
                               cdmDatabaseSchema = "cdm", 
                               resultsDatabaseSchema = "results", 
                               scratchDatabaseSchema = "scratch",
                               vocabDatabaseSchema = "vocab",
                               cdmVersion = "5.3.0",
                               numThreads = 10,
                               outputFolder = "output")
}