extras/CodeToRun.R

In lhjohn/EmcWaltersDementiaModel: A Package Skeleton for Replicating Published Prediction Models

library(EmcWaltersDementiaModel)
# USER INPUTS
#=======================
# The folder where the study intermediate and result files will be written:
outputFolder <- "./EmcWaltersDementiaModelResults"
options(andromedaTempFolder = "S:/temp/tempandromeda")

# Details for connecting to the server:
dbms <- "pdw"
user <- NULL
pw <- NULL
server <- 'JRDUSAPSCTL01'
port <- 17001

connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
                                                                server = server,
                                                                user = user,
                                                                password = pw,
                                                                port = port)

# Add the database containing the OMOP CDM data
cdmDatabaseSchema <- c("CDM_Optum_Panther_v1355.dbo",
                       "CDM_CPRD_v1299.dbo",
                       "CDM_IBM_MDCR_v1352.dbo",
                       "CDM_IQVIA_Germany_DA_v1376.dbo",
                       "CDM_Optum_Extended_SES_v1387.dbo")

cdmDatabaseName <- c('OPPANv1355',
                     "CPRDv1299",
                     "MDCRv1352",
                     "IQGERv1376",
                     "OPSESv1387")

# Add a database with read/write access as this is where the cohorts will be generated
cohortDatabaseSchema <- 'Scratch.dbo'

oracleTempSchema <- NULL

# table name where the cohorts will be generated
cohortTable <- 'EmcWaltersDementiaModelCohort'

# # TAR settings
sampleSize <- 1000000 #1000000
# riskWindowStart <- 1
# startAnchor <- 'cohort start'
# riskWindowEnd <- 365*5
# endAnchor <- 'cohort start'
# firstExposureOnly <- F
# removeSubjectsWithPriorOutcome <- F
# priorOutcomeLookback <- 99999
# requireTimeAtRisk <- T
# minTimeAtRisk <- 365
# includeAllOutcomes <- T

#=======================
for (i in 4:length(cdmDatabaseName)) {
  
  EmcWaltersDementiaModel::execute(connectionDetails = connectionDetails,
                                    cdmDatabaseSchema = cdmDatabaseSchema[i],
                                    cdmDatabaseName = cdmDatabaseName[i],
                                    cohortDatabaseSchema = cohortDatabaseSchema,
                                    cohortTable = cohortTable,
                                    sampleSize = sampleSize,
                                    riskWindowStart = riskWindowStart,
                                    startAnchor = startAnchor,
                                    riskWindowEnd = riskWindowEnd,
                                    endAnchor = endAnchor,
                                    firstExposureOnly = firstExposureOnly,
                                    removeSubjectsWithPriorOutcome = removeSubjectsWithPriorOutcome,
                                    priorOutcomeLookback = priorOutcomeLookback,
                                    requireTimeAtRisk = requireTimeAtRisk,
                                    minTimeAtRisk = minTimeAtRisk,
                                    includeAllOutcomes = includeAllOutcomes,
                                    outputFolder = outputFolder,
                                    createCohorts = T,
                                    runAnalyses = T,
                                    recalibrate = T,
                                    viewShiny = F,
                                    packageResults = F,
                                    minCellCount= 5,
                                    verbosity = "INFO",
                                    cdmVersion = 5)
}