runIctpdAnalyses: Run a list of analyses

In OHDSI/IcTemporalPatternDiscovery: IC Temporal Pattern Discovery

Run a list of analyses

Description

Run a list of analyses

Usage

runIctpdAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  oracleTempSchema = cdmDatabaseSchema,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_era",
  cdmVersion = 4,
  outputFolder = "./IctpdOutput",
  ictpdAnalysisList,
  exposureOutcomeList,
  getDbIctpdDataThreads = 1,
  calculateStatisticsIcThreads = 1
)

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'.
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.
exposureDatabaseSchema	The name of the database schema that is the location where the exposure data used to define the exposure cohorts is available. If exposureTable = DRUG_ERA, exposureDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
exposureTable	The tablename that contains the exposure cohorts. If exposureTable <> DRUG_ERA, then expectation is exposureTable 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. If exposureTable = CONDITION_ERA, exposureDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
outcomeTable	The tablename that contains the outcome cohorts. If outcomeTable <> CONDITION_OCCURRENCE, then expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
cdmVersion	Define the OMOP CDM version used: currently support "4" and "5".
outputFolder	Name of the folder where all the outputs will written to.
ictpdAnalysisList	A list of objects of type ictpdAnalysis as created using the createIctpdAnalysis function.
exposureOutcomeList	A list of objects of type exposureOutcome as created using the createExposureOutcome function.
getDbIctpdDataThreads	The number of parallel threads to use to load the data from the database.
calculateStatisticsIcThreads	The number of threads used to perform the IC statistics computations.

Details

Run a list of analyses for the exposure-outcomes of interest. This function will run all specified analyses against all hypotheses of interest, meaning that the total number of outcome models is 'length(ictpdAnalysisList) * length(exposureOutcomeList)'. When you provide several analyses it will determine whether any of the analyses have anything in common, and will take advantage of this fact. For example, if we specify several analyses that only differ in the way the outcome model is fitted, then this function will extract the data and fit the propensity model only once, and re-use this in all the analysis.

OHDSI/IcTemporalPatternDiscovery documentation built on Sept. 16, 2022, 1:11 p.m.