extractDatabaseToCsv: Exports all the results from a database into csv files

In OHDSI/PatientLevelPrediction: Develop Clinical Prediction Models Using the Common Data Model

Exports all the results from a database into csv files

Description

Exports all the results from a database into csv files

Usage

extractDatabaseToCsv(
  conn = NULL,
  connectionDetails,
  databaseSchemaSettings = createDatabaseSchemaSettings(resultSchema = "main"),
  csvFolder,
  minCellCount = 5,
  sensitiveColumns = getPlpSensitiveColumns(),
  fileAppend = NULL
)

Arguments

conn	The connection to the database with the results
connectionDetails	The connectionDetails for the result database
databaseSchemaSettings	The result database schema settings
csvFolder	Location to save the csv files
minCellCount	The min value to show in cells that are sensitive (values less than this value will be replaced with -1)
sensitiveColumns	A named list (name of table columns belong to) with a list of columns to apply the minCellCount to.
fileAppend	If set to a string this will be appended to the start of the csv file names

Details

Extracts the results from a database into a set of csv files

Value

The directory path where the results were saved

Examples

 
# develop a simple model on simulated data
data("simulationProfile")
plpData <- simulatePlpData(simulationProfile, n = 500)
saveLoc <- file.path(tempdir(), "extractDatabaseToCsv")
results <- runPlp(plpData, outcomeId = 3, saveDirectory = saveLoc)
# now upload the results to a sqlite database
databasePath <- insertResultsToSqlite(saveLoc)
# now extract the results to csv
connectionDetails <- 
  DatabaseConnector::createConnectionDetails(dbms = "sqlite", 
                                             server = databasePath)
extractDatabaseToCsv(
  connectionDetails = connectionDetails,
  csvFolder = file.path(saveLoc, "csv")
)
# show csv file
list.files(file.path(saveLoc, "csv"))
# clean up
unlink(saveLoc, recursive = TRUE)

OHDSI/PatientLevelPrediction documentation built on Feb. 14, 2025, 9:44 a.m.