Achilles (version 1.5)

achilles: The main Achilles analysis

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,
  vocabDatabaseSchema = cdmDatabaseSchema, runCostAnalysis = FALSE,
  sqlOnly = FALSE, conceptHierarchy = TRUE, createIndices = TRUE)

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. 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

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'.

runCostAnalysis

Boolean to determine if cost analysis should be run. Note: only works on CDM v5.0 style cost tables.

sqlOnly

Boolean to determine if the SQL generated by this function call should be executed or simply returned as a string. DEFAULT = FALSE indicating that the SQL code should be executed.

conceptHierarchy

Boolean to determine if the concept_hierarchy result table should be created, for use by Atlas treemaps. Note: only works on CDM v5.0 tables.

createIndices

Boolean to determine if indices should be created on the resulting Achilles and concept_hierarchy table. Default= TRUE

Value

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

Details

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

Examples

# NOT RUN {
  connectionDetails <- DatabaseConnector::createConnectionDetails(dbms="sql server", server="myserver")
  achillesResults <- achilles(connectionDetails, cdmDatabaseSchema="cdm4_sim", resultsDatabaseSchema="scratch", sourceName="TestDB", validateSchema="TRUE", vocabDatabaseSchema="vocabulary")
  fetchAchillesAnalysisResults(connectionDetails, "scratch", 106)
# }