Last updated: 2022-03-10

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Knit directory: codemapper/

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File Version Author Date Message
Rmd e5c5381 rmgpanw 2022-03-10 update mainly icd10-related codes.
Rmd a64a35e rmgpanw 2022-03-10 change arg quiet = TRUE to unrecognised_codes = “error”. Also updated tests (passing) 
library(tidyverse)
library(reactable)
library(readxl)
library(crosstalk)
library(targets)
library(codemapper)

tar_load(all_lkps_maps_raw)

Overview

codemapper tldr

  • In UK Biobank data, ICD10 codes are recorded in the ALT_CODE format, however an ‘X’ filler is not appended for codes where the 3 character category is undivided. For example, the ICD10 code for Scarlet fever, A38, is recorded as A38X under ALT_CODE in the ICD10 lookup table, but recorded as A38 in UK Biobank data.

ICD10 formats: ICD10_CODE and ALT-CODE

ICD10 codes are recorded in 2 formats in UK Biobank resource 592 ICD10_CODE and ALT_CODE. The documentation states:

- ICD10_CODE = ICD10 code
- ALT_CODE = This form strips the decimal point from the code and appends the filler X where the 3 character category is undivided.

In UK Biobank data, ICD10 codes are recorded in the ALT_CODE format, however an ‘X’ filler is not appended for codes where the 3 character category is undivided. For example, the ICD10 code for Scarlet fever, A38, is recorded as A38X under ALT_CODE in the ICD10 lookup table, but recorded as A38 in UK Biobank data:

all_lkps_maps_raw$icd10_lkp %>% 
  filter(ICD10_CODE == "A38") %>% 
  select(ICD10_CODE:DESCRIPTION) %>% 
  knitr::kable()
ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION
A38 A38X DEFAULT 3 Scarlet fever

A full list of undivided 3 character ICD10 codes is listed below:

alt_code_ends_x <- all_lkps_maps_raw$icd10_lkp %>% 
  filter(str_detect(ALT_CODE,
             ".X$"))

alt_code_ends_x %>% 
  reactable(filterable = TRUE,
            resizable = TRUE,
            searchable = TRUE,
            showPageSizeOptions = TRUE,
            pageSizeOptions = c(5, 10, 25, 50, 100, 200),
            paginationType = "jump",
            defaultPageSize = 5)

While some ICD10 codes end with ‘X’ (e.g. M45.X), only undivided 3 character codes end with ‘X’ in ALT_CODE format:

alt_code_ends_x %>% 
  mutate(ICD10_CODE_length = str_length(ICD10_CODE)) %>% 
  count(ICD10_CODE_length, 
        name = "n_ALT_CODEs_ending_with_X") %>% 
  knitr::kable()
ICD10_CODE_length n_ALT_CODEs_ending_with_X
3 254

There are also some other differences between the ICD10_CODE and ALT_CODE formats. In some cases, the same ICD10_CODE can have multiple descriptions that are differentiated by MODIFIER_5. For example, S27.9 describes ‘Injury unspecified intrathoracic organ’, which can be further modified as follows:

all_lkps_maps_raw$icd10_lkp %>% 
  filter(ICD10_CODE == "S27.9") %>% 
  select(ICD10_CODE:MODIFIER_5) %>% 
  knitr::kable()
ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
S27.9 S279 DEFAULT 3 Injury of unspecified intrathoracic organ NA NA
S27.9 S2790 DEFAULT 3 Injury of unspecified intrathoracic organ NA without open wound into thoracic cavity
S27.9 S2791 DEFAULT 3 Injury of unspecified intrathoracic organ NA with open wound into thoracic cavity

Simply removing the ‘.’ from ICD10-CODE will not capture all codes in these cases. Note also that in some cases, removing the ‘.’ will not capture any codes used inn UK Biobank:

all_lkps_maps_raw$icd10_lkp %>% 
  filter(ICD10_CODE == "M45.X") %>% 
  select(ICD10_CODE:MODIFIER_5) %>% 
  knitr::kable()
ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
M45.X M45X0 DEFAULT 3 Ankylosing spondylitis NA Multiple sites in spine
M45.X M45X1 DEFAULT 3 Ankylosing spondylitis NA Occipito-atlanto-axial region
M45.X M45X2 DEFAULT 3 Ankylosing spondylitis NA Cervical region
M45.X M45X3 DEFAULT 3 Ankylosing spondylitis NA Cervicothoracic region
M45.X M45X4 DEFAULT 3 Ankylosing spondylitis NA Thoracic region
M45.X M45X5 DEFAULT 3 Ankylosing spondylitis NA Thoracolumbar region
M45.X M45X6 DEFAULT 3 Ankylosing spondylitis NA Lumbar region
M45.X M45X7 DEFAULT 3 Ankylosing spondylitis NA Lumbosacral region
M45.X M45X8 DEFAULT 3 Ankylosing spondylitis NA Sacral and sacrococcygeal region
M45.X M45X9 DEFAULT 3 Ankylosing spondylitis NA Site unspecified

The number of ICD10 codes with multiple descriptions is summarised by the following table. Note that these all have a MODIFIER_5 description.

n_non_unique_icd10_code_df <- all_lkps_maps_raw$icd10_lkp %>% 
  group_by(ICD10_CODE) %>% 
  summarise(n = n(),
         n_MODIFIER_5_not_na = sum(!is.na(MODIFIER_5)),
         n_MODIFIER_4_not_na = sum(!is.na(MODIFIER_4))) %>% 
  filter(n > 1) %>% 
  # select(ICD10_CODE:MODIFIER_5,
  #        contains("not_na")) %>% 
  arrange(n_MODIFIER_5_not_na)

list(
  n_non_unique_icd10_code = nrow(n_non_unique_icd10_code_df),
  n_with_modifier_5 = sum(n_non_unique_icd10_code_df$n_MODIFIER_5_not_na > 0),
  n_with_modifier_4 = sum(n_non_unique_icd10_code_df$n_MODIFIER_4_not_na > 0)
) %>% 
  as_tibble() %>% 
  knitr::kable()
n_non_unique_icd10_code n_with_modifier_5 n_with_modifier_4
498 498 0

ICD10 codes with MODIFIER_4 descriptions are differentiated by their 4th digit. For example:

all_lkps_maps_raw$icd10_lkp %>% 
  filter(str_detect(ICD10_CODE,
                    "^E10")) %>% 
  select(ICD10_CODE:MODIFIER_5) %>% 
  knitr::kable()
ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
E10 E10 DEFAULT 3 Type 1 diabetes mellitus NA NA
E10.0 E100 DEFAULT 3 Type 1 diabetes mellitus With coma NA
E10.1 E101 DEFAULT 3 Type 1 diabetes mellitus With ketoacidosis NA
E10.2 E102 DAGGER 4 Type 1 diabetes mellitus With renal complications NA
E10.3 E103 DAGGER 4 Type 1 diabetes mellitus With ophthalmic complications NA
E10.4 E104 DAGGER 4 Type 1 diabetes mellitus With neurological complications NA
E10.5 E105 DEFAULT 3 Type 1 diabetes mellitus With peripheral circulatory complications NA
E10.6 E106 DEFAULT 3 Type 1 diabetes mellitus With other specified complications NA
E10.7 E107 DEFAULT 3 Type 1 diabetes mellitus With multiple complications NA
E10.8 E108 DEFAULT 3 Type 1 diabetes mellitus With unspecified complications NA
E10.9 E109 DEFAULT 3 Type 1 diabetes mellitus Without complications NA

Note, there are no ICD10 codes with values for both MODIFIER_4 AND MODIFIER_5.

Miscellaneous

More documentation from UK Biobank resource 592:

- USAGE = Dagger / Asterisk indication
- USAGE_UK = Dagger / Asterisk indication
- DESCRIPTION = Longest preferred rubric
- MODIFIER_4 = 4th character modifier suffix
- MODIFIER_5 = 5th character modifier suffix
- QUALIFIERS = Dual classification (asterisk codes)
- GENDER_MASK = Gender mask: Identifies single sex conditions
- MIN_AGE = Minimum age that applies to this code
- MAX_AGE = Max age that applies to this code
- TREE_DESCRIPTION = This data field also contains descriptions that are functional in the context of the 3 character descriptions of their parent category, and are thus suitable for presentation where that context is available. For example:
C00 Malignant neoplasm of lip
C00.0 External upper lip
C00.1 External lower lip
C00.2 External lip, unspecified

USAGE_UK

Describes different combinations of USAGE, MODIFIER_4, MODIFIER_5 and QUALIFIERS.

all_lkps_maps_raw$icd10_lkp %>%
  filter(!is.na(USAGE_UK)) %>%
  pull(USAGE_UK) %>%
  unique() %>%
  set_names() %>%
  map( ~ all_lkps_maps_raw$icd10_lkp %>%
         filter(USAGE_UK == .x) %>%
         head()) %>%
  iwalk( ~ {
    cat("### ", .y, "\n\n")
    
    flextable::flextable(.x) %>%
      flextable::autofit() %>%
      flextable::flextable_to_rmd()
    
    cat("\n\n")
  })

3

1

4

2

0

all_lkps_maps_raw$icd10_lkp %>% 
  filter(!is.na(QUALIFIERS) | !is.na(USAGE) | !is.na(USAGE_UK)) %>% 
  reactable(filterable = TRUE,
            searchable = TRUE,
            sortable = TRUE,
            showPageSizeOptions = TRUE)

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] codemapper_0.0.0.9000 ukbwranglr_0.0.0.9000 targets_0.8.0        
 [4] crosstalk_1.1.1       readxl_1.3.1          reactable_0.2.3      
 [7] forcats_0.5.1         stringr_1.4.0         dplyr_1.0.7          
[10] purrr_0.3.4           readr_2.0.2           tidyr_1.1.4          
[13] tibble_3.1.4          ggplot2_3.3.5         tidyverse_1.3.1      
[16] workflowr_1.6.2      

loaded via a namespace (and not attached):
 [1] fs_1.5.0          lubridate_1.7.10  httr_1.4.2        rprojroot_2.0.2  
 [5] tools_4.1.0       backports_1.2.1   bslib_0.3.1       utf8_1.2.2       
 [9] R6_2.5.1          DBI_1.1.1         colorspace_2.0-2  withr_2.4.3      
[13] tidyselect_1.1.1  processx_3.5.2    compiler_4.1.0    git2r_0.28.0     
[17] cli_3.0.1         rvest_1.0.1       flextable_0.6.10  xml2_1.3.2       
[21] officer_0.4.1     sass_0.4.0        scales_1.1.1      callr_3.7.0      
[25] systemfonts_1.0.4 digest_0.6.28     rmarkdown_2.11    base64enc_0.1-3  
[29] pkgconfig_2.0.3   htmltools_0.5.2   dbplyr_2.1.1      fastmap_1.1.0    
[33] highr_0.9         htmlwidgets_1.5.4 rlang_0.4.11      rstudioapi_0.13  
[37] shiny_1.7.0       jquerylib_0.1.4   generics_0.1.0    jsonlite_1.7.2   
[41] zip_2.2.0         magrittr_2.0.1    Rcpp_1.0.7        munsell_0.5.0    
[45] fansi_0.5.0       gdtools_0.2.4     lifecycle_1.0.1   stringi_1.7.4    
[49] whisker_0.4       yaml_2.2.1        grid_4.1.0        promises_1.2.0.1 
[53] crayon_1.4.1      haven_2.4.3       hms_1.1.1         knitr_1.34       
[57] ps_1.6.0          pillar_1.6.3      uuid_0.1-4        igraph_1.2.6     
[61] codetools_0.2-18  reprex_2.0.1      glue_1.4.2        evaluate_0.14    
[65] data.table_1.14.2 renv_0.13.2       modelr_0.1.8      vctrs_0.3.8      
[69] tzdb_0.1.2        httpuv_1.6.3      cellranger_1.1.0  gtable_0.3.0     
[73] reactR_0.4.4      assertthat_0.2.1  xfun_0.24         mime_0.12        
[77] xtable_1.8-4      broom_0.7.9       later_1.3.0       ellipsis_0.3.2