extras/CodeToRun.R

In jamieweaver/BcnStudyAThon: A Package Skeleton for Comparative Effectiveness Studies

library(BcnStudyAThon)

options(fftempdir = "S:/FFTemp")
maxCores <- parallel::detectCores()
studyFolder <- "G:/StudyResults/BcnStudyAThon"

source("S:/MiscCode/SetEnvironmentVariables.R")
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "pdw",
                                                                server = Sys.getenv("server"),
                                                                user = NULL,
                                                                password = NULL,
                                                                port = Sys.getenv("port"))

mailSettings <- list(from = Sys.getenv("emailAddress"),
                     to = c(Sys.getenv("emailAddress")),
                     smtp = list(host.name = Sys.getenv("emailHost"), port = 25,
                                 user.name = Sys.getenv("emailAddress"),
                                 passwd = Sys.getenv("emailPassword"), ssl = FALSE),
                     authenticate = FALSE,
                     send = TRUE)

# CCAE settings ---------------------------------------------------------------- 
databaseId <- "CCAE"
databaseName <- "CCAE"
databaseDescription <- "CCAE"
cdmDatabaseSchema <- "CDM_IBM_CCAE_V1022.dbo"
outputFolder <- file.path(studyFolder, databaseId)
cohortDatabaseSchema = "scratch.dbo"
cohortTable = "bcn_ccae"

# Optum DOD settings -----------------------------------------------------------
databaseId <- "Optum"
databaseName <- "Optum"
databaseDescription <- "Optum DOD"
cdmDatabaseSchema = "CDM_OPTUM_EXTENDED_DOD_V1027.dbo"
outputFolder <- file.path(studyFolder, databaseId)
cohortDatabaseSchema <- "scratch.dbo"
cohortTable <- "bcn_optum"

# CPRD settings -----------------------------------------------------------
databaseId <- "CPRD"
databaseName <- "CPRD"
databaseDescription <- "CPRD"
cdmDatabaseSchema = "CDM_CPRD_V1017.dbo"
outputFolder <- file.path(studyFolder, databaseId)
cohortDatabaseSchema <- "scratch.dbo"
cohortTable <- "bcn_cprd"

# MDCD settings ---------------------------------------------------------------- DONE
databaseId <- "MDCD"
databaseName <- "MDCD"
databaseDescription <- "MDCD"
cdmDatabaseSchema = "CDM_IBM_MDCD_V1023.dbo"
outputFolder <- file.path(studyFolder, databaseId)
cohortDatabaseSchema <- "scratch.dbo"
cohortTable <- "bcn_mdcd"

# MDCR settings ---------------------------------------------------------------- DONE
databaseId <- "MDCR"
databaseName <- "MDCR"
databaseDescription <- "MDCR"
cdmDatabaseSchema = "CDM_IBM_MDCR_V1024.dbo"
outputFolder <- file.path(studyFolder, databaseName)
cohortDatabaseSchema <- "scratch.dbo"
cohortTable <- "bcn_mdcr"

# Run --------------------------------------------------------------------------
OhdsiRTools::runAndNotify(expression = {
        execute(connectionDetails = connectionDetails,
                cdmDatabaseSchema = cdmDatabaseSchema,
                cohortDatabaseSchema = cohortDatabaseSchema,
                cohortTable = cohortTable,
                oracleTempSchema = NULL,
                outputFolder = outputFolder,
                databaseId = databaseId,
                databaseName = databaseName,
                databaseDescription = databaseDescription,
                createCohorts = TRUE,
                synthesizePositiveControls = FALSE,
                runAnalyses = FALSE,
                runDiagnostics = FALSE,
                packageResults = FALSE,
                maxCores = maxCores)
}, mailSettings = mailSettings, label = paste0("BcnStudyAThon ", databaseId), stopOnWarning = FALSE)

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


#launchEvidenceExplorer(dataFolder = "G:/StudyResults/BcnStudyAThon/shinyDataFull", blind = FALSE, launch.browser = FALSE)