Connects to the All of Us database and returns a BigQueryConnection object. You can reference this object to query the database using R and or SQL code. A message is printed with the connection status (successful or not).
Usage
aou_connect(CDR = getOption("aou.default.cdr"), ...)
Arguments
- CDR
The name of the "curated data repository" to connect to. Defaults to
getOption("aou.default.cdr")
, which isSys.getenv('WORKSPACE_CDR')
if not specified otherwise (i.e., the "mainline" CDR). On the controlled tier, specify the "base" CDR withCDR = paste0(Sys.getenv('WORKSPACE_CDR'), "_base")
.- ...
Further arguments passed along to
DBI::dbConnect()
.
Value
A BigQueryConnection
object. This object is also saved as an option
(getOption("aou.default.con")
).
Details
You can reference this object to connect to the All of Us database
and run SQL code using, e.g., dbplyr
or DBI
. A message is printed with
the connection status (successful or not).
Examples
if (FALSE) { # on_workbench()
con <- aou_connect()
# reference the observation table in the database
dplyr::tbl(con, "observation")
# print a list of the tables in the database
DBI::dbListTables(con)
}