vignettes/DqdForCohorts.rmd
DqdForCohorts.rmdRunning 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.