Package 'DataQualityDashboard'

Title: Execute and View Data Quality Checks on OMOP CDM Database
Description: Assesses data quality in Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) databases. Executes data quality checks and provides an R 'shiny' application to view the results.
Authors: Katy Sadowski [aut, cre], Clair Blacketer [aut], Maxim Moinat [aut], Ajit Londhe [aut], Anthony Sena [aut], Anthony Molinaro [aut], Frank DeFalco [aut], Pavel Grafkin [aut]
Maintainer: Katy Sadowski <[email protected]>
License: Apache License 2.0
Version: 2.8.9
Built: 2026-05-18 02:45:08 UTC
Source: https://github.com/ohdsi/dataqualitydashboard

Help Index

Convert JSON results file case

Description

Convert a DQD JSON results file between camelcase and (all-caps) snakecase. Enables viewing of pre-v.2.1.0 results files in later DQD versions, and vice versa

Usage

convertJsonResultsFileCase(
  jsonFilePath,
  writeToFile,
  outputFolder = NA,
  outputFile = "",
  targetCase
)

Arguments

jsonFilePath

Path to the JSON results file to be converted
writeToFile

Whether or not to write the converted results back to a file (must be either TRUE or FALSE)
outputFolder

The folder to output the converted JSON results file to
outputFile

(OPTIONAL) File to write converted results JSON object to. Default is name of input file with a "_camel" or "_snake" postfix
targetCase

Case into which the results file parameters should be converted (must be either "camel" or "snake")

Value

DQD results object (a named list)

Execute DQ checks

Description

This function will connect to the database, generate the sql scripts, and run the data quality checks against the database. By default, results will be written to a json file as well as a database table.

Usage

executeDqChecks(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  vocabDatabaseSchema = cdmDatabaseSchema,
  cdmSourceName,
  numThreads = 1,
  sqlOnly = FALSE,
  sqlOnlyUnionCount = 1,
  sqlOnlyIncrementalInsert = FALSE,
  outputFolder,
  outputFile = "",
  verboseMode = FALSE,
  writeToTable = TRUE,
  writeTableName = "dqdashboard_results",
  writeToCsv = FALSE,
  csvFile = "",
  checkLevels = c("TABLE", "FIELD", "CONCEPT"),
  checkNames = c(),
  checkSeverity = c("fatal", "convention", "characterization"),
  cohortDefinitionId = c(),
  cohortDatabaseSchema = resultsDatabaseSchema,
  cohortTableName = "cohort",
  tablesToExclude = c("CONCEPT", "VOCABULARY", "CONCEPT_ANCESTOR",
    "CONCEPT_RELATIONSHIP", "CONCEPT_CLASS", "CONCEPT_SYNONYM", "RELATIONSHIP", "DOMAIN"),
  cdmVersion = "5.3",
  tableCheckThresholdLoc = "default",
  fieldCheckThresholdLoc = "default",
  conceptCheckThresholdLoc = "default"
)

Arguments

connectionDetails

A connectionDetails object for connecting to the CDM database
cdmDatabaseSchema

The fully qualified database name of the CDM schema
resultsDatabaseSchema

The fully qualified database name of the results schema
vocabDatabaseSchema

The fully qualified database name of the vocabulary schema (default is to set it as the cdmDatabaseSchema)
cdmSourceName

The name of the CDM data source
numThreads

The number of concurrent threads to use to execute the queries
sqlOnly

Should the SQLs be executed (FALSE) or just returned (TRUE)?
sqlOnlyUnionCount

(OPTIONAL) In sqlOnlyIncrementalInsert mode, how many SQL commands to union in each query to insert check results into results table (can speed processing when queries done in parallel). Default is 1.
sqlOnlyIncrementalInsert

(OPTIONAL) In sqlOnly mode, boolean to determine whether to generate SQL queries that insert check results and associated metadata into results table. Default is FALSE (for backwards compatibility to <= v2.2.0)
outputFolder

The folder to output logs, SQL files, and JSON results file to
outputFile

(OPTIONAL) File to write results JSON object
verboseMode

Boolean to determine if the console will show all execution steps. Default is FALSE
writeToTable

Boolean to indicate if the check results will be written to the dqdashboard_results table in the resultsDatabaseSchema. Default is TRUE
writeTableName

The name of the results table. Defaults to 'dqdashboard_results'. Used when sqlOnly or writeToTable is True.
writeToCsv

Boolean to indicate if the check results will be written to a csv file. Default is FALSE
csvFile

(OPTIONAL) CSV file to write results
checkLevels

Choose which DQ check levels to execute. Default is all 3 (TABLE, FIELD, CONCEPT)
checkNames

(OPTIONAL) Choose which check names to execute. Names can be found in inst/csv/OMOP_CDM_v[cdmVersion]_Check_Descriptions.csv. Note that "cdmTable", "cdmField" and "measureValueCompleteness" are always executed.
checkSeverity

Choose which DQ check severity levels to execute. Default is all 3 (fatal, convention, characterization)
cohortDefinitionId

The cohort definition id for the cohort you wish to run the DQD on. The package assumes a standard OHDSI cohort table with the fields cohort_definition_id and subject_id.
cohortDatabaseSchema

The schema where the cohort table is located.
cohortTableName

The name of the cohort table. Defaults to 'cohort'.
tablesToExclude

(OPTIONAL) Choose which CDM tables to exclude from the execution.
cdmVersion

The CDM version to target for the data source. Options are "5.2", "5.3", or "5.4". By default, "5.3" is used.
tableCheckThresholdLoc

The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
fieldCheckThresholdLoc

The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
conceptCheckThresholdLoc

The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.

Value

A list object of results

List DQ checks

Description

Details on all checks defined by the DataQualityDashboard Package.

Usage

listDqChecks(
  cdmVersion = "5.3",
  tableCheckThresholdLoc = "default",
  fieldCheckThresholdLoc = "default",
  conceptCheckThresholdLoc = "default"
)

Arguments

cdmVersion

The CDM version to target for the data source. By default, 5.3 is used.
tableCheckThresholdLoc

The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
fieldCheckThresholdLoc

The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
conceptCheckThresholdLoc

The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.

Value

A list containing check descriptions, table checks, field checks, and concept checks

Re-evaluate Thresholds

Description

Re-evaluate an existing DQD result against an updated thresholds file.

Usage

reEvaluateThresholds(
  jsonFilePath,
  outputFolder,
  outputFile,
  tableCheckThresholdLoc = "default",
  fieldCheckThresholdLoc = "default",
  conceptCheckThresholdLoc = "default",
  cdmVersion = "5.3"
)

Arguments

jsonFilePath

Path to the JSON results file generated using the execute function
outputFolder

The folder to output new JSON result file to
outputFile

File to write results JSON object to
tableCheckThresholdLoc

The location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied.
fieldCheckThresholdLoc

The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
conceptCheckThresholdLoc

The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
cdmVersion

The CDM version to target for the data source. By default, 5.3 is used.

Value

A list containing the re-evaluated DQD results

View DQ Dashboard

Description

View DQ Dashboard

Usage

viewDqDashboard(jsonPath, launch.browser = NULL, display.mode = NULL, ...)

Arguments

jsonPath

The fully-qualified path to the JSON file produced by executeDqChecks
launch.browser

Passed on to shiny::runApp
display.mode

Passed on to shiny::runApp
...

Extra parameters for shiny::runApp() like "port" or "host"

Value

NULL (launches Shiny application)

Write DQD results database table to json

Description

Write DQD results database table to json

Usage

writeDBResultsToJson(
  connection,
  resultsDatabaseSchema,
  cdmDatabaseSchema,
  writeTableName,
  outputFolder,
  outputFile
)

Arguments

connection

A connection object
resultsDatabaseSchema

The fully qualified database name of the results schema
cdmDatabaseSchema

The fully qualified database name of the CDM schema
writeTableName

Name of DQD results table in the database to read from
outputFolder

The folder to output the json results file to
outputFile

The output filename of the json results file

Value

NULL (writes results to JSON file)

Write JSON Results to CSV file

Description

Write JSON Results to CSV file

Usage

writeJsonResultsToCsv(
  jsonPath,
  csvPath,
  columns = c("checkId", "failed", "passed", "isError", "notApplicable", "checkName",
    "checkDescription", "thresholdValue", "notesValue", "checkLevel", "category",
    "subcategory", "context", "checkLevel", "cdmTableName", "cdmFieldName", "conceptId",
    "unitConceptId", "numViolatedRows", "pctViolatedRows", "numDenominatorRows",
    "executionTime", "notApplicableReason", "error", "queryText"),
  delimiter = ","
)

Arguments

jsonPath

Path to the JSON results file generated using the execute function
csvPath

Path to the CSV output file
columns

(OPTIONAL) List of desired columns
delimiter

(OPTIONAL) CSV delimiter

Value

NULL (writes results to CSV file)

Write JSON Results to SQL Table

Description

Write JSON Results to SQL Table

Usage

writeJsonResultsToTable(
  connectionDetails,
  resultsDatabaseSchema,
  jsonFilePath,
  writeTableName = "dqdashboard_results",
  cohortDefinitionId = c(),
  singleTable = FALSE
)

Arguments

connectionDetails

A connectionDetails object for connecting to the CDM database
resultsDatabaseSchema

The fully qualified database name of the results schema
jsonFilePath

Path to the JSON results file generated using the execute function
writeTableName

Name of table in the database to write results to
cohortDefinitionId

If writing results for a single cohort this is the ID that will be appended to the table name
singleTable

If TRUE, writes all results to a single table. If FALSE (default), writes to 3 separate tables by check level (table, field, concept) (NOTE this default behavior will be deprecated in the future)

Value

NULL (writes results to database table)