| Type: | Package |
| Title: | Integration Unit Tests for Pharmacoepidemiological Studies |
| Version: | 0.4.0 |
| 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: | 7.3.2 |
| Depends: | R (≥ 4.1.0) |
| Imports: | jsonlite, readxl, readr, CDMConnector, 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: | 2025-05-11 19:32:46 UTC; ginberg |
| Author: | Cesar Barboza 
[aut],
Ioanna Nika [aut],
Ger Inberg [aut,
cre],
Adam Black [aut] |
| Repository: | CRAN |
| Date/Publication: | 2025-05-27 07:30:02 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"
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())