R/runDiagnostic.R

In Blanch-Font/SOPHIA: What the Package Does (One Line, Title Case)

#' Title
#'
#' @param cdm_bbdd A connection for a OMOP database via DatabaseConnector
#' @param cdm_schema A name for OMOP schema
#' @param results_sc A name for result schema
#' @param cohortTable A name of the result cohort
#' @param cohortDefinitionSet Object including SQL and JSON for create Cohort
#' @param exportFolder Directory to save Diagnostic
#'
#' @return Character
#' @export
#'
#' @examples
#' # Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = "~idiap/projects/SOPHIA_codi/data/jdbcDrivers/")
#' # dbms = Sys.getenv("DBMS")
#' # user <- if (Sys.getenv("DB_USER") == "") NULL else Sys.getenv("DB_USER")
#' # password <- if (Sys.getenv("DB_PASSWORD") == "") NULL else Sys.getenv("DB_PASSWORD")
#' # server = Sys.getenv("DB_SERVER")
#' # port = Sys.getenv("DB_PORT")
#' # connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
#' #                                                                  server = server,
#' #                                                                  user = user,
#' #                                                                  password = password,
#' #                                                                  port = port)
#' # cdm_bbdd <- DatabaseConnector::connect(connectionDetails = connectionDetails)
#' # cdm_schema <- 'omop21t2_test'
#' # results_sc <- 'sophia_test'
#' # cohortTable <- 'prova_Capr'
#' # cohortInfo <- CreateSQL_T2DM(cdm_bbdd, cdm_schema, results_sc, cohortTable)
#' # outcomeInfo <- CreateSQL_T2DM_outcome(cdm_bbdd, cdm_schema, results_sc, cohortTable)
#' # cohortDefinitionSet <- data.frame(atlasId = rep(NA, 2),
#' #                                    cohortId = 1:2,
#' #                                    cohortName = c("SIDIAP T2DM-WP5: Entrada",
#' #                                                   "SIDIAP T2DM-WP5: Outcome"),
#' #                                    sql = c(cohortInfo$ohdiSQL,
#' #                                            outcomeInfo$ohdiSQL),
#' #                                    json = c(cohortInfo$circeJson,
#' #                                             outcomeInfo$circeJson),
#' #                                    logicDescription = rep(as.character(NA), 2),
#' #                                    generateStats = rep(TRUE, 2))
#' # cohortCounts <- createCohort(cdm_bbdd, cdm_schema, results_sc, cohortTable,
#' #                              cohortDefinitionSet)
#' # fet_diag <- runDiagnostic(cdm_bbdd, cdm_schema, results_sc, cohortTable,
#' #                           cohortDefinitionSet)
runDiagnostic <- function(cdm_bbdd,
                          cdm_schema,
                          results_sc,
                          cohortTable,
                          cohortDefinitionSet,
                          exportFolder = 'export'){
  CohortDiagnostics::executeDiagnostics(
    cohortDefinitionSet = cohortDefinitionSet,
    exportFolder = exportFolder,
    databaseId = "SIDIAP",
    cohortDatabaseSchema = results_sc,
    connection = cdm_bbdd,
    cdmDatabaseSchema = cdm_schema,
    cohortTable = cohortTable,
    temporalCovariateSettings = FeatureExtraction::createTemporalCovariateSettings(
      useDemographicsGender = TRUE,
      useDemographicsAge = TRUE,
      useDemographicsAgeGroup = TRUE,
      useDemographicsRace = TRUE,
      useDemographicsEthnicity = TRUE,
      useDemographicsIndexYear = TRUE,
      useDemographicsIndexMonth = TRUE,
      useDemographicsIndexYearMonth = TRUE,
      useDemographicsPriorObservationTime = TRUE,
      useDemographicsPostObservationTime = TRUE,
      useDemographicsTimeInCohort = TRUE,
      useConditionOccurrence = TRUE,
      useProcedureOccurrence = TRUE,
      useDrugEraStart = TRUE,
      useMeasurement = TRUE,
      useConditionEraStart = TRUE,
      useConditionEraOverlap = TRUE,
      useConditionEraGroupStart = FALSE,
      useConditionEraGroupOverlap = TRUE,
      useDrugExposure = FALSE,
      useDrugEraOverlap = FALSE,
      useDrugEraGroupStart = FALSE,
      useDrugEraGroupOverlap = TRUE,
      useObservation = TRUE,
      useDeviceExposure = TRUE,
      useCharlsonIndex = TRUE,
      useDcsi = FALSE,
      useChads2 = FALSE,
      useChads2Vasc = FALSE,
      useHfrs = FALSE,
      temporalStartDays = c(-9999, -365, -180, -30, -365, -30, 0, 1, 31, -9999),
      temporalEndDays = c(0,          0, 0, 0, -31, -1, 0, 30, 365, 9999)),
    minCellCount = 0)
  cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable)
  CohortGenerator::dropCohortStatsTables(connection = cdm_bbdd,
                                         cohortDatabaseSchema = results_sc,
                                         cohortTableNames = cohortTableNames)
  CohortDiagnostics::createMergedResultsFile(exportFolder,
                                             overwrite = TRUE)
  return("Fet")
}