Build a Duckdb database of clinical code look up and mapping tables

Write the output from build_all_lkps_maps to a Duckdb database.

Usage

all_lkps_maps_to_db(
  all_lkps_maps = build_all_lkps_maps(),
  db_path = "all_lkps_maps.db",
  overwrite = FALSE
)

Arguments

all_lkps_maps

A named list of look up and mapping tables, created by build_all_lkps_maps.

db_path

Where the database will be created. If an Duckdb database file already exists here, then the lookup and mapping tables will be added to this. If NULL (default), then no database will be created/modified.

overwrite

If TRUE, overwrite tables in the database if they already exist. Default value is FALSE.

Value

Returns db_path invisibly

See also

build_all_lkps_maps()

Examples

# build dummy all_lkps_maps resource (supressing warning messages)
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# write to Duckdb database file
db_path <- suppressMessages(
  all_lkps_maps_to_db(
    all_lkps_maps = all_lkps_maps_dummy,
    db_path = tempfile()
  )
)

# connect to Duckdb database
con <- DBI::dbConnect(duckdb::duckdb(), db_path, read_only = TRUE)
on.exit(DBI::dbDisconnect(con, shutdown = TRUE))

# create named list of tbl_dbi objects
all_lkps_maps_dummy_db <- ukbwranglr::db_tables_to_list(con)
#> Error in dbSendQuery(conn, statement, ...): Invalid connection
#> ℹ Context: rapi_prepare

head(all_lkps_maps_dummy_db$icd10_lkp)
#> Error: object 'all_lkps_maps_dummy_db' not found

# import to R with dplyr::collect()
dplyr::collect(all_lkps_maps_dummy_db$icd10_lkp)
#> Error: object 'all_lkps_maps_dummy_db' not found