createDatabaseDetails: Create a setting that holds the details about the cdmDatabase...

In OHDSI/PatientLevelPrediction: Developing patient level prediction using data in the OMOP Common Data Model

Create a setting that holds the details about the cdmDatabase connection for data extraction

Description

Create a setting that holds the details about the cdmDatabase connection for data extraction

Usage

createDatabaseDetails(
  connectionDetails,
  cdmDatabaseSchema,
  cdmDatabaseName,
  cdmDatabaseId,
  tempEmulationSchema = cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "cohort",
  targetId = NULL,
  outcomeIds = NULL,
  cdmVersion = 5,
  cohortId = NULL
)

Arguments

connectionDetails	An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cdmDatabaseSchema	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
cdmDatabaseName	A string with the name of the database - this is used in the shiny app and when externally validating models to name the result list and to specify the folder name when saving validation results (defaults to cdmDatabaseSchema if not specified)
cdmDatabaseId	A string with a unique identifier for the database and version - this is stored in the plp object for future reference and used by the shiny app (defaults to cdmDatabaseSchema if not specified)
tempEmulationSchema	For dmbs like Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
cohortDatabaseSchema	The name of the database schema that is the location where the target cohorts are available. Requires read permissions to this database.
cohortTable	The tablename that contains the target cohorts. Expectation is cohortTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
outcomeDatabaseSchema	The name of the database schema that is the location where the data used to define the outcome cohorts is available. Requires read permissions to this database.
outcomeTable	The tablename that contains the outcome cohorts. Expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
targetId	An integer specifying the cohort id for the target cohort
outcomeIds	A single integer or vector of integers specifying the cohort ids for the outcome cohorts
cdmVersion	Define the OMOP CDM version used: currently support "4" and "5".
cohortId	(depreciated: use targetId) old input for the target cohort id

Details

This function simply stores the settings for communicating with the cdmDatabase when extracting the target cohort and outcomes

Value

A list with the the database specific settings (this is used by the runMultiplePlp function and the skeleton packages)

OHDSI/PatientLevelPrediction documentation built on Sept. 15, 2024, 6:38 a.m.