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
)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) { # \dontrun{
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)
} # }