R/createCohort.R

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

#' create a Cohort
#'
#' @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
#'
#' @return Count of the cohorts
#' @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)
createCohort <- function(cdm_bbdd,
                         cdm_schema,
                         results_sc,
                         cohortTable,
                         cohortDefinitionSet){
  # 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(T, 2))

    cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable)
    CohortGenerator::createCohortTables(connection = cdm_bbdd,
                                        cohortTableNames = cohortTableNames,
                                        cohortDatabaseSchema = results_sc,
                                        incremental = FALSE)
    CohortGenerator::generateCohortSet(connection = cdm_bbdd,
                                       cdmDatabaseSchema = cdm_schema,
                                       cohortDatabaseSchema = results_sc,
                                       cohortTableNames = cohortTableNames,
                                       cohortDefinitionSet = cohortDefinitionSet,
                                       incremental = FALSE)
    cohortCounts <- CohortGenerator::getCohortCounts(connection = cdm_bbdd,
                                                     cohortDatabaseSchema = results_sc,
                                                     cohortTable = cohortTableNames$cohortTable)
    return(list(cohortDefinitionSet = cohortDefinitionSet,
                cohortCounts = cohortCounts))
}