runCcrAnalyses: Run a list of analyses
In OHDSI/CaseCrossover: Case-Crossover

Run a list of analyses

runCcrAnalyses(
  connectionDetails,
  cdmDatabaseSchema,
  oracleTempSchema = cdmDatabaseSchema,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_era",
  nestingCohortDatabaseSchema = cdmDatabaseSchema,
  nestingCohortTable = "condition_era",
  outputFolder = "./CcrOutput",
  ccrAnalysisList,
  exposureOutcomeNestingCohortList,
  getDbCaseCrossoverDataThreads = 1,
  selectSubjectsToIncludeThreads = 1,
  getExposureStatusThreads = 1,
  fitCaseCrossoverModelThreads = 1
)

`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 specify both the database and the schema, so for example 'cdm_instance.dbo'.
`oracleTempSchema`	A schema where temp tables can be created in Oracle.
`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 but 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 outcomeTable = CONDITION_ERA, outcomeDatabaseSchema is not used. Requires read permissions to this database.
`outcomeTable`	The tablename that contains the outcome cohorts. If outcomeTable is not CONDITION_OCCURRENCE or CONDITION_ERA, then expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
`nestingCohortDatabaseSchema`	The name of the database schema that is the location where the nesting cohort is defined.
`nestingCohortTable`	Name of the table holding the nesting cohort. This table should have the same structure as the cohort table.
`outputFolder`	Name of the folder where all the outputs will written to.
`ccrAnalysisList`	A list of objects of type `ccrAnalysis` as created using the `createCcrAnalysis` function.
`exposureOutcomeNestingCohortList`	A list of objects of type `exposureOutcomeNestingCohort` as created using the `createExposureOutcomeNestingCohort` function.
`getDbCaseCrossoverDataThreads`	The number of parallel threads to use for building the caseControlData objects.
`selectSubjectsToIncludeThreads`	The number of parallel threads to use for selecting subjects
`getExposureStatusThreads`	The number of parallel threads to use for getting exposure status.
`fitCaseCrossoverModelThreads`	The number of parallel threads to use for fitting the models.

Run a list of analyses for the exposure-outcome-nesting cohorts of interest. This function will run all specified analyses against all hypotheses of interest, meaning that the total number of outcome models is 'length(ccrAnalysisList) * length(exposureOutcomeNestingCohortList)'. 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 control windows are specified then this function will extract the data and select the subjects only once, and re-use this in all the analysis.

OHDSI/CaseCrossover documentation built on Nov. 21, 2020, 7:03 a.m.