extras/CodeToRun.R

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

library(WaltersDementiaModelJson)
# USER INPUTS
#=======================
# The folder where the study intermediate and result files will be written:
outputFolder <- "./WaltersDementiaModelJsonResults"
# 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 <- 'WaltersDementiaModelJsonCohort'

# # 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 1:length(cdmDatabaseName)) {
  
  WaltersDementiaModelJson::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 = T,
                                      packageResults = F,
                                      minCellCount= 5,
                                      verbosity = "INFO",
                                      cdmVersion = 5)
}