#' @title Execute OHDSI Study (FILL IN NAME)
#'
#' @details
#' This function executes OHDSI Study (FILL IN NAME).
#' This is a study of (GIVE SOME DETAILS).
#' Detailed information and protocol are available on the OHDSI Wiki.
#'
#' @return
#' Study results are placed in CSV format files in specified local folder and returned
#' as an R object class \code{OhdsiStudy} when sufficiently small. The properties of an
#' \code{OhdsiStudy} may differ from study to study.
#' @param dbms The type of DBMS running on the server. Valid values are
#' \itemize{
#' \item{"mysql" for MySQL}
#' \item{"oracle" for Oracle}
#' \item{"postgresql" for PostgreSQL}
#' \item{"redshift" for Amazon Redshift}
#' \item{"sql server" for Microsoft SQL Server}
#' \item{"pdw" for Microsoft Parallel Data Warehouse (PDW)}
#' \item{"netezza" for IBM Netezza}
#' }
#' @param user The user name used to access the server. If the user is not specified for SQL Server,
#' Windows Integrated Security will be used, which requires the SQL Server JDBC drivers
#' to be installed.
#' @param domain (optional) The Windows domain for SQL Server only.
#' @param password The password for that user
#' @param server The name of the server
#' @param port (optional) The port on the server to connect to
#' @param cdmSchema Schema name where your patient-level data in OMOP CDM format resides
#' @param resultsSchema (Optional) Schema where you'd like the results tables to be created (requires user to have create/write access)
#' @param file (Optional) Name of local file to place results; makre sure to use forward slashes (/)
#' @param ... (FILL IN) Additional properties for this specific study.
#'
#' @examples \dontrun{
#' # Run study
#' execute(dbms = "postgresql",
#' user = "joebruin",
#' password = "supersecret",
#' server = "myserver",
#' cdmSchema = "cdm_schema",
#' resultsSchema = "results_schema")
#'
#' # Email result file
#' email(from = "collaborator@@ohdsi.org",
#' dataDescription = "CDM4 Simulated Data")
#' }
#'
#' @importFrom DBI dbDisconnect
#' @export
execute <- function(dbms, user = NULL, domain = NULL, password = NULL, server,
port = NULL,
cdmSchema, resultsSchema,
file = getDefaultStudyFileName(),
...) {
# Open DB connection
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms=dbms,
server=server,
user=user,
domain=domain,
password=password,
schema=cdmSchema,
port = port)
conn <- DatabaseConnector::connect(connectionDetails)
if (is.null(conn)) {
stop("Failed to connect to db server.")
}
# Record start time
start <- Sys.time()
# Place execution code here
result <- 42
# Execution duration
executionTime <- Sys.time() - start
# List of R objects to save
objectsToSave <- c(
"result",
"executionTime"
)
# Save results to disk
saveOhdsiStudy(list = objectsToSave, file = file)
# Clean up
DBI::dbDisconnect(conn)
# Package and return result if return value is used
result <- mget(objectsToSave)
class(result) <- "OhdsiStudy"
invisible(result)
}
# Package must provide a default gmail address to receive result files
#' @keywords internal
getDestinationAddress <- function() { return("nobody@gmail.com") }
# Package must provide a default result file name
#' @keywords internal
getDefaultStudyFileName <- function() { return("OhdsiStudy.rda") }
# Packge must provide default email subject
#' @keywords internal
getDefaultStudyEmailSubject <- function() { return("OHDSI Study Results") }
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