insertCsvToDatabase: Function to insert results into a database from csvs

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

Function to insert results into a database from csvs

Description

This function converts a folder with csv results into plp objects and loads them into a plp result database

Usage

insertCsvToDatabase(
  csvFolder,
  connectionDetails,
  databaseSchemaSettings,
  modelSaveLocation,
  csvTableAppend = ""
)

Arguments

csvFolder	The location to the csv folder with the plp results
connectionDetails	A connection details for the plp results database that the csv results will be inserted into
databaseSchemaSettings	A object created by createDatabaseSchemaSettings with all the settings specifying the result tables to insert the csv results into
modelSaveLocation	The location to save any models from the csv folder - this should be the same location you picked when inserting other models into the database
csvTableAppend	A string that appends the csv file names

Details

The user needs to have plp csv results in a single folder and an existing plp result database

Value

Returns a data.frame indicating whether the results were inported into the database

Examples

 
# develop a simple model on simulated data
data("simulationProfile")
plpData <- simulatePlpData(simulationProfile, n=1000)
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"))
# now insert the csv results into a database
newDatabasePath <- file.path(tempdir(), "newDatabase.sqlite")
connectionDetails <- 
 DatabaseConnector::createConnectionDetails(dbms = "sqlite", 
                                            server = newDatabasePath)
insertCsvToDatabase(csvFolder = file.path(saveLoc, "csv"),
                     connectionDetails = connectionDetails,
                     databaseSchemaSettings = createDatabaseSchemaSettings(),
                     modelSaveLocation = file.path(saveLoc, "models"))
# clean up
unlink(saveLoc, recursive = TRUE)

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