achilles: The main Achilles analysis

In hxia/Achilles4Impala: Creates descriptive statistics summary for an entire OMOP CDM instance.

Description

achilles creates descriptive statistics summary for an entire OMOP CDM instance.

Usage

achilles(connectionDetails, cdmDatabaseSchema,
  oracleTempSchema = cdmDatabaseSchema,
  resultsDatabaseSchema = cdmDatabaseSchema, sourceName = "", analysisIds,
  createTable = TRUE, smallcellcount = 5, cdmVersion = "4",
  runHeel = TRUE, validateSchema = FALSE)

Arguments

connectionDetails	An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
cdmDatabaseSchema	string name of database schema that contains OMOP CDM and vocabulary. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.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.
resultsDatabaseSchema

string name of database schema that we can write results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.

sourceName	string name of the database, as recorded in results
analysisIds

(optional) a vector containing the set of Achilles analysisIds for which results will be generated. If not specified, all analyses will be executed. Use getAnalysisDetails to get a list of all Achilles analyses and their Ids.

createTable	If true, new results tables will be created in the results schema. If not, the tables are assumed to already exists, and analysis results will be added
smallcellcount

To avoid patient identifiability, cells with small counts (<= smallcellcount) are deleted.

cdmVersion

Define the OMOP CDM version used: currently support "4" and "5". Default = "4"

runHeel	Boolean to determine if Achilles Heel data quality reporting will be produced based on the summary statistics. Default = TRUE
validateSchema	Boolean to determine if CDM Schema Validation should be run. This could be very slow. Default = FALSE

Details

achilles creates descriptive statistics summary for an entire OMOP CDM instance.

Value

An object of type achillesResults containing details for connecting to the database containing the results

Examples

## Not run: 
  connectionDetails <- createConnectionDetails(dbms="sql server", server="RNDUSRDHIT07.jnj.com")
  achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="cdm4_sim", resultsDatabaseSchema="scratch", sourceName="TestDB", validateSchema="TRUE")
  fetchAchillesAnalysisResults(connectionDetails, "scratch", 106)

## End(Not run)

hxia/Achilles4Impala documentation built on May 17, 2019, 9:15 p.m.