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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(codemapper)
library(dplyr)

all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

Two formats: 'ICD10_CODE' and 'ALT_CODE'

ICD10 codes may be recorded as either 'ICD10_CODE' or 'ALT_CODE' format. For example, 'E10.9' (Type 1 diabetes mellitus without complications) is recorded as 'E109' in 'ALT_CODE' format.

Both formats are provided in the ICD10 lookup table:

all_lkps_maps_dummy$icd10_lkp

However only the 'ALT_CODE' format is used in all other mapping tables that include ICD10 codes:

all_lkps_maps_dummy$icd9_icd10 %>% 
  select(ICD9,
         ICD10,
         DESCRIPTION_ICD10)

Searching for ICD10 codes in 'ICD10_FORMAT' will yield no results:

# ICD10_CODE format - no codes found
lookup_codes(codes = "E10.9",
             code_type = "icd10",
             all_lkps_maps = all_lkps_maps_dummy, 
             unrecognised_codes = "warning")

# ALT_CODE format - now recognised
lookup_codes(codes = "E109",
             code_type = "icd10",
             all_lkps_maps = all_lkps_maps_dummy, 
             unrecognised_codes = "warning")

Use reformat_icd10_codes() to convert from one form to the other:

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") %>% 
  lookup_codes(code_type = "icd10",
               all_lkps_maps = all_lkps_maps_dummy)

While for many ICD10 codes simply removing the '.' will correctly convert from 'ICD10_CODE' format to 'ALT_CODE' format, this approach will not work in the following cases:

1. Undivided 3 character ICD10 codes, which have an appended 'X' character in 'ALT_CODE' format. For example, 'I10' for Essential (primary) hypertension is recorded as 'I10X'.

   r reformat_icd10_codes(icd10_codes = c("I10"), all_lkps_maps = all_lkps_maps_dummy, input_icd10_format = "ICD10_CODE", output_icd10_format = "ALT_CODE") %>% lookup_codes(code_type = "icd10", all_lkps_maps = all_lkps_maps_dummy)

2. ICD10 codes with a 5th character modifier. In these cases, a single code in 'ICD10_CODE' format will map to multiple codes in 'ALT_CODE`format and vice versa.

   ```r

   ICD10_CODE to ALT_CODE

   m90_alt_code <- reformat_icd10_codes(icd10_codes = c("M90.0"), all_lkps_maps = all_lkps_maps_dummy, input_icd10_format = "ICD10_CODE", output_icd10_format = "ALT_CODE") %>% lookup_codes(code_type = "icd10", all_lkps_maps = all_lkps_maps_dummy)

   m90_alt_code

   ALT_CODE to ICD10_CODE

   reformat_icd10_codes( icd10_codes = m90_alt_code$code, all_lkps_maps = all_lkps_maps_dummy, input_icd10_format = "ALT_CODE", output_icd10_format = "ICD10_CODE" ) ```

UK Biobank

UK Biobank data also records ICD10 codes in 'ALT_CODE' format, with the exception of undivided 3 character ICD10 codes, where no 'X' is appended. For example, 'I10X' for Essential (primary) hypertension is recorded as 'I10' in UK Biobank.

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