Running the DQD on a Cohort

Running the Data Quality Dashboard for a cohort is fairly straightforward. There are two options in the executeDqChecks function, cohortDefinitionId and cohortDatabaseSchema. These options will point the DQD to the schema where the cohort table is located and provide the id of the cohort on which the DQD will be run. By default, the tool assumes that the table being referenced is the standard OHDSI cohort table named COHORT with at least the columns cohort_definition_id and subject_id. For example, if I have a cohort number 123 and the cohort is in the results schema of the IBM_CCAE database, the executeDqChecks function would look like this:


DataQualityDashboard::executeDqChecks(connectionDetails = connectionDetails, 
                                    cdmDatabaseSchema = cdmDatabaseSchema, 
                                    resultsDatabaseSchema = resultsDatabaseSchema,
                                    cdmSourceName = "IBM_CCAE_cohort_123",
                                    cohortDefinitionId = 123,
                                    cohortDatabaseSchema = "IBM_CCAE.results",
                                    cohortTableName = "cohort",
                                    numThreads = numThreads,
                                    sqlOnly = sqlOnly, 
                                    outputFolder = outputFolder, 
                                    verboseMode = verboseMode,
                                    writeToTable = writeToTable,
                                    writeTableName = "dqdashboard_results_123",
                                    checkLevels = checkLevels,
                                    tablesToExclude = tablesToExclude,
                                    checkNames = checkNames)

As a note, it is good practice to have the cdmSourceName option and the writeTableName option reflect the name of the cohort so that the results don’t get confused with those of the entire database.

Clair Blacketer

2024-12-22