runMissingAnalyses

runMissingAnalyses Automatically find and compute analyses that haven't been executed.

runMissingAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema,
  scratchDatabaseSchema = resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = resultsDatabaseSchema,
  outputFolder = "output",
  defaultAnalysesOnly = 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 the database schema that will store all of the intermediate scratch tables, so for example, on SQL Server, 'cdm_scratch.dbo'. Must be accessible to/from the cdmDatabaseSchema and the resultsDatabaseSchema. Default is resultsDatabaseSchema. Making this "#" will run Achilles in single-threaded mode and use temporary tables instead of permanent tables.

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'.

tempEmulationSchema

Formerly tempEmulationSchema. For databases like Oracle where you must specify the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.

outputFolder

Path to store logs and SQL files

defaultAnalysesOnly

Boolean to determine if only default analyses should be run. Including non-default analyses is substantially more resource intensive. Default = TRUE

Value

No return value. Run to execute analyses currently missing from results.

Examples

if (FALSE) {
Achilles::runMissingAnalyses(connectionDetails = connectionDetails,
                             cdmDatabaseSchema = "cdm",
                             resultsDatabaseSchema = "results",

  outputFolder = "/tmp")
}