extras/codeToRun.R

In OHDSI/SkeletonPredictionValidationStudy: Add the title of the package here

library(SkeletonPredictionValidationStudy)

# the location to save the models validation results to:
outputFolder <- './Validation'

# add the database connection details
dbms = 'your database management system'
server = 'your server'
user = 'your username'
password = 'top secret'
port = 'your port'
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
                                                                server = server,
                                                                user = user,
                                                                password = pw,
                                                                port = port)

# add cdm database details:
cdmDatabaseSchema <- 'your cdm database schema'

# add a schema you have read/write access to
# this is where the cohorts will be created (or are already created)
cohortDatabaseSchema <- 'your cohort database schema'

# if using oracle specify the temp schema
oracleTempSchema <- NULL

# Add a sharebale name for the database containing the OMOP CDM data
databaseName <- 'your database name'

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

#===== execution choices =====

# how much details do you want for in progress report?
verbosity <- "INFO"

# create the cohorts using the sql in the package?
createCohorts = T

# apply the models in the package to your data?
runValidation = F
# if you only want to apply models to a sample of
# patients put the number as the sampleSize
sampleSize = NULL
# do you want to recalibrate results?
# NULL means none (see ?SkeletonPredictionValidationStudy::execute for options)
recalibrate <- NULL

# extract the results to share as a zip file?
packageResults = T
# when extracting results - what is the min cell count?
minCellCount = 5

#=============================
# configure the settings
databaseDetails <- PatientLevelPrediction::createDatabaseDetails(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = cdmDatabaseSchema,
  cdmDatabaseName = databaseName,
  tempEmulationSchema = tempEmulationSchema,
  cohortDatabaseSchema = cohortDatabaseSchema,
  cohortTable = cohortTable,
  outcomeDatabaseSchema = cohortDatabaseSchema,
  outcomeTable = cohortTable,
  cdmVersion = 5
)

restrictPlpDataSettings <- PatientLevelPrediction::createRestrictPlpDataSettings(
  sampleSize = sampleSize
)

validationSettings <- PatientLevelPrediction::createValidationSettings(
  recalibrate = recalibrate
)

logSettings <- PatientLevelPrediction::createLogSettings(
  verbosity = verbosity
)

#=============================
# Now run the study
SkeletonPredictionValidationStudy::execute(
  databaseDetails = databaseDetails,
  restrictPlpDataSettings = restrictPlpDataSettings,
  validationSettings = validationSettings,
  logSettings = logSettings,
  outputFolder = outputFolder,
  createCohorts = createCohorts,
  runValidation = runValidation,
  packageResults = packageResults,
  minCellCount = minCellCount
)