Add UK Biobank Resource 592 tables to CodeMiner database

Reads UK Biobank Resource 592 and adds these tables to the active codeminer database. This is a convenience wrapper around read_ukb_resource_592() that automatically calls add_lookup_table(), add_mapping_table(), and add_relationship_table() for each sheet.

The function processes lookup tables, mapping tables, and relationship tables from the specified sheets and adds them to the database with their associated metadata.

Usage

add_ukb_resource_592(
  path = get_ukb_resource_592(),
  sheets = c("bnf_lkp", "dmd_lkp", "icd9_lkp", "icd10_lkp", "icd9_icd10", "read_v2_lkp",
    "read_v2_drugs_lkp", "read_v2_drugs_bnf", "read_v2_icd9", "read_v2_icd10",
    "read_v2_opcs4", "read_v2_read_ctv3", "read_ctv3_lkp", "read_ctv3_icd9",
    "read_ctv3_icd10", "read_ctv3_opcs4", "read_ctv3_read_v2"),
  ukb_version = "UKB v4",
  ukb_source = "https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592"
)

Arguments

path

Path to the UKB Resource 592 Excel file. Default uses get_ukb_resource_592() to download the file if needed.

sheets

Character vector of sheet names to read. See read_ukb_resource_592() for available sheet names. By default, reads all 17 sheets.

ukb_version

Version label for the UKB resource (default: "UKB v4").

ukb_source

Source URL or description for the UKB resource.

Value

Invisibly returns the result from read_ukb_resource_592() (a named list of tables with metadata).

Details

The function performs the following steps:

1. Calls read_ukb_resource_592() to read the specified sheets

2. Iterates through each sheet and table type (lookup/mapping/relationship)

3. Adds each table to the database using the appropriate add_* function

4. Returns the parsed data invisibly

This function requires an active database connection set up via build_database() or similar.

See also

• read_ukb_resource_592() for reading without adding to database

• add_lookup_table(), add_mapping_table(), add_relationship_table()

• get_ukb_resource_592() for downloading the file

Examples

if (FALSE) { # \dontrun{
# Set up database connection
build_database(db_path = "my_codes.db")

# Add all sheets from UKB Resource 592
add_ukb_resource_592()

# Add specific sheets only
add_ukb_resource_592(
  sheets = c("icd10_lkp", "read_v2_icd10")
)

# Use local file
add_ukb_resource_592(
  path = "path/to/all_lkps_maps_v4.xlsx",
  sheets = "icd9_icd10"
)
} # }

# Example with dummy data (for testing/demonstration)
if (FALSE) { # \dontrun{
build_database(db_path = tempfile(fileext = ".db"))
add_ukb_resource_592(
  path = dummy_ukb_resource_592_path(),
  sheets = "icd10_lkp"
)
} # }