aou_connect {allofus}

Create a connection to the database in All of Us

Description

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 is Sys.getenv('WORKSPACE_CDR') if not specified otherwise (i.e., the "mainline" CDR). On the controlled tier, specify the "base" CDR with CDR = paste0(Sys.getenv('WORKSPACE_CDR'), "_base").

...

Further arguments passed along to DBI::dbConnect().

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).

Value

A BigQueryConnection object. This object is also saved as an option (getOption("aou.default.con")).

Examples

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)