runSccAnalyses: Run a list of analyses

Description Usage Arguments Details

View source: R/RunAnalyses.R

Description

Run a list of analyses

Usage

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runSccAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  oracleTempSchema = cdmDatabaseSchema,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_occurrence",
  cdmVersion = 5,
  outputFolder = "./SelfControlledCohortOutput",
  sccAnalysisList,
  exposureOutcomeList,
  analysisThreads = 1,
  computeThreads = 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.

sccAnalysisList

A list of objects of type sccAnalysis as created using the createSccAnalysis function.

exposureOutcomeList

A list of objects of type exposureOutcome as created using the createExposureOutcome function.

analysisThreads

The number of parallel threads to use to execute the analyses.

computeThreads

Number of parallel threads per analysis thread for computing IRRs with exact confidence intervals.

Details

Run a list of analyses for the drug-comparator-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(cmAnalysisList) * length(drugComparatorOutcomesList)'.


OHDSI/SelfControlledCohort documentation built on Oct. 2, 2021, 2:07 p.m.