Type: Package
Title: Integration Unit Tests for Pharmacoepidemiological Studies
Version: 0.5.0
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Description: An R interface to load testing data in the 'OMOP' Common Data Model ('CDM'). An input file, csv or xlsx, can be converted to a 'CDMConnector' object. This object can be used to execute and test studies that use the 'CDM' https://www.ohdsi.org/data-standardization/.
License: Apache License (≥ 2)
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: R (≥ 4.1.0)
Imports: jsonlite, readxl, readr, CDMConnector (≥ 2.3.0), DBI, dplyr, checkmate, glue, duckdb, cli, rlang, withr, ggplot2, tibble, testthat, arrow, openxlsx, omopgenerics
Suggests: knitr, rmarkdown, curl, httr
Config/testthat/edition: 3
URL: https://github.com/darwin-eu/TestGenerator, https://darwin-eu.github.io/TestGenerator/
BugReports: https://github.com/darwin-eu/TestGenerator/issues
NeedsCompilation: no
Packaged: 2026-01-14 08:19:59 UTC; ginberg
Author: Cesar Barboza ORCID iD [aut], Ioanna Nika [aut], Ger Inberg ORCID iD [aut, cre], Adam Black ORCID iD [aut]
Repository: CRAN
Date/Publication: 2026-01-14 09:00:02 UTC

Check if a given remote file is available for download

Description

Check if a given remote file is available for download

Usage

checkRemoteFileAvailable(remoteFile)

Arguments

remoteFile

a remote resource

Value

NULL if the remote resource is not available, other "success"

Check if the given tables and columns are valid and return the loaded data.

Description

Check if the given tables and columns are valid and return the loaded data.

Usage

checkTablesColumns(cdmVersion, filePath, extraTable = FALSE)

Arguments

cdmVersion

cdm version

filePath

Path to the test patient data in xlsx format

extraTable

if extra tables are provided or not, default FALSE

Value

a named list containing the loaded data

Download Test Data Files

Description

Download Test Data Files

Usage

downloadTestData(
  datasetName = "mimicIV",
  cdmVersion = "5.3",
  pathToData = Sys.getenv("STUDY_DATASETS"),
  overwrite = FALSE
)

Arguments

datasetName

The data set name as found on https://github.com/darwin-eu/EunomiaDatasets. The data set name corresponds to the folder with the data set ZIP files

cdmVersion

The OMOP CDM version. This version will appear in the suffix of the data file, for example: synpuf_5.3.zip. Default: '5.3'

pathToData

The path where the Eunomia data is stored on the file system., By default the value of the environment variable "EUNOMIA_DATA_FOLDER" is used.

overwrite

Control whether the existing archive file will be overwritten should it already exist.

Value

Invisibly returns the destination if the download was successful.

Examples


downloadTestData(pathToData = tempdir())

Generates an Excel file with sheets that correspond to an OMOP-CDM tables.

Description

Generates an Excel file with sheets that correspond to an OMOP-CDM tables.

Usage

generateTestTables(
  tableNames,
  cdmVersion,
  outputFolder,
  filename = paste0("test_cdm_", cdmVersion)
)

Arguments

tableNames

A list specifying the table names to include in the Excel file.

cdmVersion

The CDM version to use for creating the requested tables (either 5.3 or 5.4).

outputFolder

The folder where the Excel file will be saved.

filename

The name of the Excel file. It does not include the extension .xlsx.

Value

An Excel file with the tables requested.

'graphCohort()' aids in the visualisation of cohorts timelines, useful to get a grip on intersections.

Description

'graphCohort()' aids in the visualisation of cohorts timelines, useful to get a grip on intersections.

Usage

graphCohort(subject_id, cohorts = list())

Arguments

subject_id

Only one subject id per visualisation

cohorts

List of cohorts

Value

A ggplot graph

Examples

hosptalised <- tibble::tibble(cohort_definition_id = 2,
                              subject_id = 1,
                              cohort_start_date = "2018-01-01",
                              cohort_end_date = "2018-01-10")

icu_patients <- tibble::tibble(cohort_definition_id = 5,
                              subject_id = 1,
                              cohort_start_date = "2018-01-02",
                              cohort_end_date = "2018-01-04")

drugs_treatment <- tibble::tibble(cohort_definition_id = 5,
                                  subject_id = 1,
                              cohort_start_date = "2018-01-07",
                              cohort_end_date = "2018-01-09")

TestGenerator::graphCohort(subject_id = 1, cohorts = list("hosptalised" = hosptalised,
                                                      "icu_patients" = icu_patients,
                                                      "drugs_treatment" = drugs_treatment))

Pushes test population into a blank CDM.

Description

Pushes test population into a blank CDM.

Usage

patientsCDM(
  pathJson = NULL,
  testName = NULL,
  cdmVersion = "5.3",
  cdmName = NULL
)

Arguments

pathJson

Directory where the sample populations in json are located. If NULL, gets the default inst/testCases directory.

testName

Name of the sample population JSON file. If NULL it will push the first sample population in the testCases directory.

cdmVersion

cdm version, default "5.3".

cdmName

Name of the cdm, default NULL.

Value

A CDM reference object with a sample population.

Examples


filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
TestGenerator::readPatients(filePath = filePath, outputPath = tempdir())
cdm <- TestGenerator::patientsCDM(pathJson = tempdir(), testName = "test")
duckdb::duckdb_shutdown(duckdb::duckdb())

Converts a sample of patients into Unit Testing Definition JSON file.

Description

Converts a sample of patients into Unit Testing Definition JSON file.

Usage

readPatients(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.3",
  extraTable = FALSE
)

Arguments

filePath

Path to the test patient data in Excel format. The Excel has sheets that represent tables from the OMOP-CDM, e.g. person, drug_exposure, condition_ocurrence, etc.

testName

A name of the test population in character.

outputPath

Path of the output file, if NULL, a folder will be created in the project folder inst/testCases.

cdmVersion

cdm version, default "5.3".

extraTable

Name of non-standard tables to be included in the test CDM.

Value

A JSON file with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
readPatients(filePath = filePath, outputPath = tempdir())

Converts a sample of patients in CSV format into a Unit Testing Definition JSON file.

Description

Converts a sample of patients in CSV format into a Unit Testing Definition JSON file.

Usage

readPatients.csv(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.3",
  reduceLargeIds = FALSE
)

Arguments

filePath

Path to the test patient data in CSV format. Multiple CSV files representing tables tables from the OMOP-CDM must be provided, e.g. person.csv, drug_exposure.csv, condition_ocurrence.csv, etc.

testName

Name for the test population file in character.

outputPath

Path of the output file, if NULL, a folder will be created in the project folder inst/testCases.

cdmVersion

cdm version, default "5.3".

reduceLargeIds

Reduces the length of very long ids generally in int64 format, such as those found in the MIMIC-IV database.

Value

A JSON file with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "mimic_sample", package = "TestGenerator")
readPatients.csv(filePath = filePath, outputPath = tempdir())

Converts a sample of patients in XLSX format into Unit Testing Definition JSON file.

Description

Converts a sample of patients in XLSX format into Unit Testing Definition JSON file.

Usage

readPatients.xl(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.3",
  extraTable = FALSE
)

Arguments

filePath

Path to the test patient data in Excel format. The Excel has sheets that represent tables from the OMOP-CDM, e.g. person, drug_exposure, condition_ocurrence, etc.

testName

A name of the test population in character.

outputPath

Path to write the test JSON files. If NULL, the files will be written at the project's testthat folder, i.e. tests/testthat/testCases.

cdmVersion

cdm version, default "5.3".

extraTable

TRUE or FALSE. If TRUE, non-standard tables will be included in the test CDM.

Value

A directory with the test JSON files with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
readPatients.xl(filePath = filePath, outputPath = tempdir())