Package 'Eunomia'

Construct cohorts

Description

Creates a set of predefined cohorts in a cohort table. WARNING: this will delete all existing cohorts in the table!

Usage

createCohorts(
  connectionDetails,
  cdmDatabaseSchema = "main",
  cohortDatabaseSchema = "main",
  cohortTable = "cohort"
)

Arguments

connectionDetails	The connection details to connect to the (Eunomia) database.
cdmDatabaseSchema	Deprecated. The cdm must be created in the main schema.
cohortDatabaseSchema	Deprecated. The cohort table will be created in the main schema.
cohortTable	Deprecated. Cohort table will be named "cohort".

Value

A data frame listing all created cohorts.

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Download Eunomia data files

Description

Download the Eunomia data files from https://github.com/OHDSI/EunomiaDatasets

Usage

downloadEunomiaData(
  datasetName,
  cdmVersion = "5.3",
  pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"),
  overwrite = FALSE,
  verbose = FALSE
)

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.
overwrite	Control whether the existing archive file will be overwritten should it already exist.
verbose	Provide additional logging details during execution.

Value

Invisibly returns the destination if the download was successful.

Examples

## Not run: 
downloadEunomiaData("GiBleed")

## End(Not run)

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Export data files from a database(sqlite or duckdb)

Description

Helper function to export data to csv or parquet files from a database file (sqlite or duckdb).

Usage

exportDataFiles(
  dbPath,
  outputFolder,
  outputFormat = "csv",
  dbms = "sqlite",
  verbose = FALSE
)

Arguments

dbPath	The path to the source .sqlite or .duckdb file
outputFolder	The path to the export destination directory
outputFormat	The output format for the files. Supported formats include csv, parquet.
dbms	The file-based database system to use: 'sqlite' (default) or 'duckdb'
verbose	Boolean argument controlling verbose debugging output

Value

No return value, called to export to outputFolder.

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Extract the Eunomia data files and load into a database Extract files from a .ZIP file and creates a OMOP CDM database that is then stored in the same directory as the .ZIP file.

Description

Extract the Eunomia data files and load into a database Extract files from a .ZIP file and creates a OMOP CDM database that is then stored in the same directory as the .ZIP file.

Usage

extractLoadData(
  from,
  to,
  dbms = "sqlite",
  cdmVersion = "5.3",
  inputFormat = "csv",
  verbose = FALSE
)

Arguments

from	The path to the .ZIP file that contains the csv CDM source files
to	The path to the .sqlite or .duckdb file that will be created
dbms	The file based database system to use: 'sqlite' (default) or 'duckdb'
cdmVersion	The version of the OMOP CDM that are represented in the archive files.
inputFormat	The format of the files expected in the archive. (csv or parquet)
verbose	Provide additional logging details during execution.

Value

No return value, called to load archive into a database file.

See Also

downloadEunomiaData

Examples

## Not run: 
extractLoadData("c:/strategusData/GiBleed_5.3.zip")

## End(Not run)

---

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
)

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.

Value

The file path to the new Eunomia dataset copy

Examples

## Not run: 
 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)

## End(Not run)

---

Get Default Eunomia Connection Details

Description

Creates a copy of the default (GiBleed) Eunomia database, and provides details for connecting to that copy. Function provides backwards compatibility to prior releases of Eunomia default (GiBleed) dataset

Usage

getEunomiaConnectionDetails(
  databaseFile = tempfile(fileext = ".sqlite"),
  dbms = "sqlite"
)

Arguments

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.
dbms	The target dialect, by default "sqlite".

Value

A ConnectionDetails object, to be used with the DatabaseConnector package.

---

Load data files into a database(sqlite or duckdb)

Description

Load data from csv or parquet files into a database file (sqlite or duckdb).

Usage

loadDataFiles(
  dataPath,
  dbPath,
  inputFormat = "csv",
  cdmVersion = "5.3",
  cdmDatabaseSchema = "main",
  dbms = "sqlite",
  verbose = FALSE,
  overwrite = FALSE
)

Arguments

dataPath	The path to the directory containing CDM source files (csv or parquet)
dbPath	The path to the .sqlite or .duckdb file that will be created
inputFormat	The input format of the files to load. Supported formats include csv, parquet.
cdmVersion	The CDM version to create in the resulting database. Supported versions are 5.3 and 5.4
cdmDatabaseSchema	The schema in which to create the CDM tables. Default is main.
dbms	The file-based database system to use: 'sqlite' (default) or 'duckdb'
verbose	Provide additional logging details during execution.
overwrite	Remove and replace an existing data set.

Value

No return value, loads data into database file.

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