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()

Basic usage

Use map_codes() to map a vector of codes from one clinical coding system to another:

map_codes(codes = "G20..",
          from = "read2",
          to = "icd10",
          all_lkps_maps = all_lkps_maps_dummy)

Alternatively, use get_mapping_df() to return a mapping data frame:

get_mapping_df(from = "read3",
               to = "icd10",
               all_lkps_maps = all_lkps_maps_dummy)

Filters

Mapping between different clinical coding systems is not perfect and should be manually reviewed. Some mapping tables list multiple possible code mappings, with a separate column indicating the type of mapping.[^1] For example, the Read 2 to Read 3 mapping table includes an 'IS_ASSURED' column, where '1' and '0' indicate that a code mapping is or is not assured respectively:

[^1]: Refer to the accompanying documentation for UKB resource 592 for further details.

all_lkps_maps_dummy$read_v2_read_ctv3 %>% 
  dplyr::select(READV2_CODE,
                READV3_CODE,
                IS_ASSURED)

Similarly, the Read 3 to ICD10 mapping table includes 'mapping_status' and 'refine_flag' columns:

all_lkps_maps_dummy$read_ctv3_icd10 %>% 
  dplyr::select(read_code:refine_flag)

It is important to decide which mappings to include. For example, if no filters are applied then the Read 3 code for sebaceous cyst 'XaIP9' will map to a number of ICD10 codes, some of which are sex-specific ('N508' and 'N948'):

map_codes(codes = "XaIP9",
          from = "read3",
          to = "icd10",
          all_lkps_maps = all_lkps_maps_dummy,
          col_filters = NULL)

Default filters are applied by default_col_filters():

map_codes(codes = "XaIP9",
          from = "read3",
          to = "icd10",
          all_lkps_maps = all_lkps_maps_dummy,
          col_filters = default_col_filters())

See additional notes at https://rmgpanw.gitlab.io/codemapper_notes/.

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