extras/CodeToRun.R

In alondhe/PADManuscript: A Package Skeleton for Comparative Effectiveness Studies

library(PADManuscript)

source("/home/alondhe2/Desktop/setCredentials.R")

# Optional: specify where the temporary files (used by the ff package) will be created:
options(fftempdir = "/ebs3/fftemp")

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

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

outputFolder <- "output_mdcr"
#outputFolder <- "output_ccae"
#outputFolder <- "output_panther"

# Details for connecting to the server:
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "pdw",
                                                                server = Sys.getenv("cdmServer"),
                                                                user = Sys.getenv("cdmUser"),
                                                                password = Sys.getenv("cdmPassword"),
                                                                port = as.integer(Sys.getenv("cdmServerPort")))

# The name of the database schema where the CDM data can be found:
cdmDatabaseSchema <- "cdm_truven_mdcr_v779.dbo"
#cdmDatabaseSchema <- "cdm_optum_extended_dod_v774.dbo"
#cdmDatabaseSchema <- "cdm_truven_ccae_v778.dbo"
#cdmDatabaseSchema <- "cdm"


# The name of the database schema and table where the study-specific cohorts will be instantiated:
#cohortDatabaseSchema <- "ohdsi_results"
cohortDatabaseSchema <- "scratch.alondhe2"
#cohortDatabaseSchema <- "cdm_truven_mdcr_v779.ohdsi_results"
#cohortDatabaseSchema <- "cdm_optum_extended_dod_v774.ohdsi_results"
#cohortDatabaseSchema <- "cdm_truven_ccae_v778.ohdsi_results"

#cohortTable <- "scratch_alondhe2"
#cohortTable <- "padman_cohort_optum"
#cohortTable <- "padman_cohort_ccae"
#cohortTable <- "padman_cohort_panther"
cohortTable <- "padman_cohort_mdcr"

# Some meta-information that will be used by the export function:
databaseId <- "IBMMDCR"
databaseName <- "IBM MarketScan Medicare"
# databaseId <- "OPTUM"
# databaseName <- "Optum Extended DOD"
# databaseId <- "IBMCCAE"
# databaseName <- "IBM MarketScan Commercial"

# databaseId <- "PANTHER"
# databaseName <- "Optum Panther"
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 = FALSE,
        maxCores = maxCores)

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

dataFolder <- file.path(getwd(), outputFolder, "shinyData")

prepareForEvidenceExplorer(resultsZipFile = resultsZipFile, dataFolder = dataFolder)

launchEvidenceExplorer(dataFolder = dataFolder, blind = FALSE, launch.browser = FALSE)