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Add UK Biobank codings tables to CodeMiner database

Source: R/add_ukb_codings.R
add_ukb_codings.Rd

Reads the UK Biobank Codings.tsv file and adds lookup tables for OPCS-4 and UKB self-reported code types to the active CodeMiner database. This is a convenience wrapper around read_ukb_codings() that automatically calls add_lookup_table() for each table.

Usage

add_ukb_codings(
  path = get_ukb_codings(),
  tables = c("opcs4_lkp", "data_coding_3", "data_coding_4", "data_coding_5",
    "data_coding_6"),
  version = "v0",
  source = "https://biobank.ctsu.ox.ac.uk/crystal/exinfo.cgi?src=accessing_data_guide"
)

Arguments

path

Path to the Codings.tsv file. Default uses get_ukb_codings() to download the file.

tables

Character vector of table names to add. See read_ukb_codings() for available table names. By default, adds all five tables.

version

Character string for the version label (default: "v0").

source

Character string for the data source URL or description.

Value

Invisibly returns the result from read_ukb_codings() (a named list of tables with metadata).

See also

read_ukb_codings(), get_ukb_codings()

Examples

if (FALSE) { # \dontrun{
build_database(db_path = "my_codes.db")
add_ukb_codings()
add_ukb_codings(tables = c("opcs4_lkp", "data_coding_4"))
} # }

# Example with dummy data
if (FALSE) { # \dontrun{
build_database(db_path = tempfile(fileext = ".db"))
add_ukb_codings(
  path = dummy_ukb_codings_path(),
  tables = "opcs4_lkp"
)
} # }