readPatients.csv {TestGenerator}

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())