extras/CodeToRun.R

In ohdsi-studies/EhdenRaDmardsEstimation: A Package Skeleton for Comparative Effectiveness Studies

# install dependencies
install.packages("devtools")
library(devtools)
install_github("ohdsi/SqlRender")
install_github("ohdsi/DatabaseConnector")
install_github("ohdsi/OhdsiSharing")
install_github("ohdsi/FeatureExtraction")
install_github("ohdsi/CohortMethod")
install_github("ohdsi/EmpiricalCalibration")
install_github("ohdsi/MethodEvaluation")

library(EhdenRaDmardsEstimation)

# Optional: specify where the temporary files (used by the ff package) will be created:
options(fftempdir = "S:/FFtemp")

# Maximum number of cores to be used:
maxCores <- parallel::detectCores()

# Minimum cell count when exporting data:
minCellCount <- 5

# The folder where the study intermediate and result files will be written:
outputFolder <- "S:/EhdenRaDmardsEstimation"

# Details for connecting to the server:
# See ?DatabaseConnector::createConnectionDetails for help
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "",
                                                                server = "",
                                                                user = "",
                                                                password = "")

# The name of the database schema where the CDM data can be found:
cdmDatabaseSchema <- ""

# The name of the database schema and table where the study-specific cohorts will be instantiated:
cohortDatabaseSchema <- ""
cohortTable <- ""

# Some meta-information that will be used by the export function:
databaseId <- "" # required
databaseName <- "" # required
databaseDescription <- ""

# For Oracle: define a schema that can be used to emulate temp tables:
oracleTempSchema <- NULL

execute(connectionDetails = connectionDetails,
        cdmDatabaseSchema = cdmDatabaseSchema,
        cohortDatabaseSchema = cohortDatabaseSchema,
        cohortTable = cohortTable,
        oracleTempSchema = oracleTempSchema,
        outputFolder = outputFolder,
        databaseId = databaseId,
        databaseName = databaseName,
        databaseDescription = databaseDescription,
        createCohorts = TRUE,
        synthesizePositiveControls = FALSE,
        runAnalyses = TRUE,
        runDiagnostics = TRUE,
        packageResults = TRUE,
        maxCores = maxCores,
        minCellCount = minCellCount)

resultsZipFile <- file.path(outputFolder, "export", paste0("Results", databaseId, ".zip"))
dataFolder <- file.path(outputFolder, "shinyData")
prepareForEvidenceExplorer(resultsZipFile = resultsZipFile, dataFolder = dataFolder)