Eunomia (version 2.0.0)

getDatabaseFile: Create a copy of a Eunomia dataset

Description

Creates a copy of a Eunomia database, and returns the path to the new database file. If the dataset does not yet exist on the user's computer it will attempt to download the source data to the the path defined by the EUNOMIA_DATA_FOLDER environment variable.

Usage

getDatabaseFile(
  datasetName,
  cdmVersion = "5.3",
  pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"),
  dbms = "sqlite",
  databaseFile = tempfile(fileext = paste0(".", dbms)),
  inputFormat = "csv",
  verbose = FALSE,
  overwrite = TRUE
)

Value

The file path to the new Eunomia dataset copy

Arguments

datasetName

The data set name as found on https://github.com/OHDSI/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: <datasetName>_<cdmVersion>.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.

dbms

The database system to use. "sqlite" (default) or "duckdb"

databaseFile

The path where the database file will be copied to. By default, the database will be copied to a temporary folder, and will be deleted at the end of the R session.

inputFormat

The format of the files expected in the archive. (csv or parquet)

verbose

Provide additional logging details during execution

overwrite

Remove and replace an existing data set.

Examples

if (FALSE) {
 conn <- DBI::dbConnect(RSQLite::SQLite(), getDatabaseFile("GiBleed"))
 DBI::dbDisconnect(conn)

 conn <- DBI::dbConnect(duckdb::duckdb(), getDatabaseFile("GiBleed", dbms = "duckdb"))
 DBI::dbDisconnect(conn, shutdown = TRUE)

 conn <- DatabaseConnector::connect(dbms = "sqlite", server = getDatabaseFile("GiBleed"))
 DatabaseConnector::disconnect(conn)
}