reformat_icd10_codes: Reformat ICD-10 codes

In rmgpanw/codemapper: Functions for Mapping Between Clinical Coding Systems

Reformat ICD-10 codes

Description

The lookup sheet in UKB resource 592 for ICD-10 ("icd10_lkp") has a column called ALT_CODE, which is an alternative format for ICD-10 codes. This is the format used in the mapping sheets for this resource, as well as in Field ID 41270. Note however that in contrast to the ICD10 lookup and mapping sheets, undivided 3 character codes do not have an 'X' appended in the UK Biobank dataset. This function converts from one format to the other, with the option to strip the final 'X' from undivided 3 character codes if converting to ALT_CODE format.

Usage

reformat_icd10_codes(
  icd10_codes,
  all_lkps_maps = NULL,
  input_icd10_format = "ICD10_CODE",
  output_icd10_format = "ALT_CODE",
  unrecognised_codes = "error",
  strip_x = FALSE
)

Arguments

icd10_codes	character vector of ICD-10 codes
all_lkps_maps	Either a named list of lookup and mapping tables (either data frames or tbl_dbi objects), or the path to a SQLite database containing these tables (see also build_all_lkps_maps() and all_lkps_maps_to_db()). If NULL, will attempt to connect to an SQLite database named 'all_lkps_maps.db' in the current working directory, or to a a SQLite database specified by an environmental variable named 'ALL_LKPS_MAPS_DB' (see here for how to set environment variables using a .Renviron file). The latter method will be used in preference.
input_icd10_format	character. Must be either "ICD10_CODE" or "ALT_CODE".
output_icd10_format	character. Must be either "ICD10_CODE" or "ALT_CODE".
unrecognised_codes	Either 'error' (default) or 'warning'. If any input codes are unrecognised, then either an error or warning will be raised.
strip_x	If TRUE and converting to ALT_CODE format, 'X' is removed from the end of undivided 3 character codes (default is FALSE).

Value

character vector of ICD-10 codes, reformatted as specified by output_icd10_format.

See Also

Other Clinical code lookups and mappings: codes_starting_with(), default_col_filters(), get_mapping_df(), lookup_codes(), map_codes()

Examples

# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# reformat from ICD10_CODE to ALT_CODE
reformat_icd10_codes(
  icd10_codes = c("E10.9"),
  all_lkps_maps = all_lkps_maps_dummy,
  input_icd10_format = "ICD10_CODE",
  output_icd10_format = "ALT_CODE"
)

# reformat from ALT_CODE to ICD10_CODE
reformat_icd10_codes(
  icd10_codes = c("E109"),
  all_lkps_maps = all_lkps_maps_dummy,
  input_icd10_format = "ALT_CODE",
  output_icd10_format = "ICD10_CODE"
)

rmgpanw/codemapper documentation built on Aug. 30, 2023, 4:07 p.m.