runDiagnostic: Title

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

Title

Description

Title

Usage

runDiagnostic(
  cdm_bbdd,
  cdm_schema,
  results_sc,
  cohortTable,
  cohortDefinitionSet,
  exportFolder = "export"
)

Arguments

cdm_bbdd	A connection for a OMOP database via DatabaseConnector
cdm_schema	A name for OMOP schema
results_sc	A name for result schema
cohortTable	A name of the result cohort
cohortDefinitionSet	Object including SQL and JSON for create Cohort
exportFolder	Directory to save Diagnostic

Value

Character

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)

Blanch-Font/SOPHIA documentation built on May 12, 2023, 1:09 a.m.