Add Phecode 1.2 tables to CodeMiner database

Reads Phecode 1.2 definitions and/or ICD mapping files and adds them to the active CodeMiner database. This is a convenience wrapper around read_phecode() that automatically calls add_lookup_table() and add_mapping_table() for each table.

Usage

add_phecode(
  lkp_path = NULL,
  icd10_map_path = NULL,
  icd9_map_path = NULL,
  version = "v1.2",
  source = "https://phewascatalog.org/phecodes"
)

Arguments

lkp_path

Path to the Phecode 1.2 definitions CSV. If NULL, skipped.

icd10_map_path

Path to the Phecode 1.2 to ICD-10 mapping CSV. If NULL, skipped.

icd9_map_path

Path to the Phecode 1.2 to ICD-9 mapping .rda file. If NULL, skipped.

version

Character string for the version label (default: "v1.2").

source

Character string for the data source URL or description.

Value

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

See also

read_phecode(), get_phecode()

Examples

if (FALSE) { # \dontrun{
build_database(db_path = "my_codes.db")

# Download and add all phecode tables
paths <- get_phecode()
add_phecode(
  lkp_path = paths$lkp,
  icd10_map_path = paths$icd10_map,
  icd9_map_path = paths$icd9_map
)
} # }

# Example with dummy data
if (FALSE) { # \dontrun{
build_database(db_path = tempfile(fileext = ".db"))
add_phecode(
  lkp_path = dummy_phecode_lkp_path(),
  icd10_map_path = dummy_icd10_phecode_map_path()
)
} # }