Last updated: 2022-03-16

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Unstaged changes:
    Modified:   R/clinical_codes.R
    Modified:   R/lookups_and_mappings.R
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    Modified:   analysis/read3_icd10_mapping.Rmd

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File	Version	Author	Date	Message
Rmd	a81c1e7	rmgpanw	2022-03-14	add notes; add `filter_cols` function plus tests (all passing)
html	a81c1e7	rmgpanw	2022-03-14	add notes; add `filter_cols` function plus tests (all passing)
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)

Summary

The ICD10 lookup table includes 2 formats: ICD10_CODE and ALT_CODE.
In UK Biobank data, ICD10 codes are recorded in the ALT_CODE format (details below), 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.
Some ICD10 codes have a one-to-many relationship from ICD10_CODE to ALT_CODE format. These codes have modifier descriptions under the MODIFIER_5 column.

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.

Dagger/asterisk pairs

Some ICD10 codes use the ‘dagger’ and ‘asterisk’ system, where the primary code for the underlying disease is the ‘dagger’ and an optional additional code for the manifestation is marked with an ‘asterisk’. See this [online article] for a fuller discussion

Dagger and asterisk codes are labelled DAGGER and ASTERIS For dagger coAsterisks codes are under QUALIFIER column

Below: USAGE_UK == 1. Here, USAGE is labelled DAGGER and the corresponding asterisk term(s) are shown under QUALIFIERS. Note that other dagger and asterisk code types have different USAGE_UK categories (see https://silo.tips/download/icd-10-4-th-edition-codes-and-titles-and-metadata-file-specification (update this link to direct link to ICD10 metadata file))

# mapping df for ICD10_CODE:ALT_CODE format
icd10_alt_code_map <- all_lkps_maps_raw$icd10_lkp %>% 
  select(ICD10_CODE, ALT_CODE)

# df of dagger/asterisk pairs
icd10_dagger_asterisk_pairs <- all_lkps_maps_raw$icd10_lkp %>%
  filter(!is.na(QUALIFIERS)) 

all_lkps_maps_raw$icd10_lkp %>% 
  filter(USAGE %in% c("DAGGER", "ASTERIS"))

# A tibble: 926 × 12
   ICD10_CODE ALT_CODE USAGE  USAGE_UK DESCRIPTION         MODIFIER_4 MODIFIER_5
   <chr>      <chr>    <chr>  <chr>    <chr>               <chr>      <chr>     
 1 A06.4      A064     DAGGER 1        Amoebic liver absc… <NA>       <NA>      
 2 A06.5      A065     DAGGER 1        Amoebic lung absce… <NA>       <NA>      
 3 A06.6      A066     DAGGER 1        Amoebic brain absc… <NA>       <NA>      
 4 A17        A17      DAGGER 4        Tuberculosis of ne… <NA>       <NA>      
 5 A17.0      A170     DAGGER 1        Tuberculous mening… <NA>       <NA>      
 6 A17.1      A171     DAGGER 1        Meningeal tubercul… <NA>       <NA>      
 7 A17.8      A178     DAGGER 4        Other tuberculosis… <NA>       <NA>      
 8 A17.9      A179     DAGGER 1        Tuberculosis of ne… <NA>       <NA>      
 9 A18.0      A180     DAGGER 4        Tuberculosis of bo… <NA>       <NA>      
10 A18.7      A187     DAGGER 1        Tuberculosis of ad… <NA>       <NA>      
# … with 916 more rows, and 5 more variables: QUALIFIERS <chr>,
#   GENDER_MASK <chr>, MIN_AGE <chr>, MAX_AGE <chr>, TREE_DESCRIPTION <chr>

# get descriptions for these codes
icd10_dagger_asterisk_descriptions <- icd10_dagger_asterisk_pairs %>%
  select(ICD10_CODE,
         QUALIFIERS) %>%
  map(reformat_icd10_codes) %>%
  map( ~ lookup_codes(codes = .x, code_type = "icd10")) %>% 
  bind_rows() %>% 
  left_join(icd10_alt_code_map,
            by = c("code" = "ALT_CODE")) %>% 
  select(description,
         ALT_CODE = code,
         ICD10_CODE)

# append descriptions to df of dagger/asterisk pairs
icd10_dagger_asterisk_pairs %>% 
  left_join(icd10_dagger_asterisk_descriptions %>% 
               select(-ICD10_CODE),
             by = c("ALT_CODE" = "ALT_CODE")) %>% 
  left_join(icd10_dagger_asterisk_descriptions %>% 
               select(-ALT_CODE),
             by = c("QUALIFIERS" = "ICD10_CODE"),   
             suffix = c("_ALT_CODE", "_QUALIFIERS")) %>% 
  select(ICD10_CODE,
         ALT_CODE,
         description_ALT_CODE,
         DESCRIPTION,
         USAGE,
         QUALIFIERS,
         description_QUALIFIERS,
         USAGE_UK) %>% 
  reactable(filterable = TRUE,
            searchable = TRUE,
            showPageSizeOptions = TRUE)

Other details

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. See https://silo.tips/download/icd-10-4-th-edition-codes-and-titles-and-metadata-file-specification (TODO - replace with direct link to ICD10 metadata file)

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("### USAGE_UK ", .y, "\n\n")
    
    flextable::flextable(.x) %>%
      flextable::autofit() %>%
      flextable::flextable_to_rmd()
    
    cat("\n\n")
  })

USAGE_UK 3

USAGE_UK 1

ICD10_CODE	ALT_CODE	USAGE	USAGE_UK	DESCRIPTION	QUALIFIERS
A06.4	A064	DAGGER	1	Amoebic liver abscess	K77.0
A06.5	A065	DAGGER	1	Amoebic lung abscess	J99.8
A06.6	A066	DAGGER	1	Amoebic brain abscess	G07
A17.0	A170	DAGGER	1	Tuberculous meningitis	G01
A17.1	A171	DAGGER	1	Meningeal tuberculoma	G07
A17.9	A179	DAGGER	1	Tuberculosis of nervous system, unspecified	G99.8

USAGE_UK 4

USAGE_UK 2

USAGE_UK 0

GENDER_MASK, MIN_AGE, MAX_AGE, TREE_DESCRIPTION (examples)

all_lkps_maps_raw$icd10_lkp %>% 
  filter(!is.na(GENDER_MASK)) %>% 
  head() %>% 
  flextable::flextable() %>% 
  flextable::flextable_to_rmd()


```{=html}
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  border-color: transparent;
}
.tabwid_left table{
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}
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}
.tabwid td {
    padding: 0;
}
.tabwid a {
  text-decoration: none;
}
.tabwid thead {
    background-color: transparent;
}
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    background-color: transparent;
}
.tabwid table tr {
background-color: transparent;
}
</style><div class="tabwid"><style>.cl-421d8042{}.cl-4217feb0{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-42180d10{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-42184514{width:54pt;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-42184532{width:54pt;background-color:transparent;vertical-align: middle;border-bottom: 2pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-42184546{width:54pt;background-color:transparent;vertical-align: middle;border-bottom: 2pt solid rgba(102, 102, 102, 1.00);border-top: 2pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table class='cl-421d8042'>
```

```{=html}
<thead><tr style="overflow-wrap:break-word;"><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">ICD10_CODE</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">ALT_CODE</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">USAGE</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">USAGE_UK</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">DESCRIPTION</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">MODIFIER_4</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">MODIFIER_5</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">QUALIFIERS</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">GENDER_MASK</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">MIN_AGE</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">MAX_AGE</span></p></td><td class="cl-42184546"><p class="cl-42180d10"><span class="cl-4217feb0">TREE_DESCRIPTION</span></p></td></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">A34</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">A34X</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">DEFAULT</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">3</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Obstetrical tetanus</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">15</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">45</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">B26.0</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">B260</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">DAGGER</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Mumps orchitis</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">N51.1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">2</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">B37.3</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">B373</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">DAGGER</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Candidiasis of vulva and vagina</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">N77.1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">C51.0</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">C510</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">DEFAULT</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">3</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Malignant neoplasm: Labium majus</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Labium majus</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">C51.1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">C511</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">DEFAULT</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">3</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Malignant neoplasm: Labium minus</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184514"><p class="cl-42180d10"><span class="cl-4217feb0">Labium minus</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">C51.2</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">C512</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">DEFAULT</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">3</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">Malignant neoplasm: Clitoris</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">1</span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0"></span></p></td><td class="cl-42184532"><p class="cl-42180d10"><span class="cl-4217feb0">Clitoris</span></p></td></tr></tbody></table></div></template>
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```

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          bit64_4.0.5       lubridate_1.7.10  httr_1.4.2       
 [5] rprojroot_2.0.2   tools_4.1.0       backports_1.2.1   bslib_0.3.1      
 [9] utf8_1.2.2        R6_2.5.1          DBI_1.1.1         colorspace_2.0-2 
[13] withr_2.4.3       tidyselect_1.1.1  processx_3.5.2    bit_4.0.4        
[17] compiler_4.1.0    git2r_0.28.0      cli_3.0.1         rvest_1.0.1      
[21] flextable_0.6.10  xml2_1.3.2        officer_0.4.1     sass_0.4.0       
[25] scales_1.1.1      callr_3.7.0       systemfonts_1.0.4 digest_0.6.28    
[29] rmarkdown_2.11    base64enc_0.1-3   pkgconfig_2.0.3   htmltools_0.5.2  
[33] dbplyr_2.1.1      fastmap_1.1.0     highr_0.9         htmlwidgets_1.5.4
[37] rlang_0.4.11      RSQLite_2.2.9     rstudioapi_0.13   shiny_1.7.0      
[41] jquerylib_0.1.4   generics_0.1.0    jsonlite_1.7.2    zip_2.2.0        
[45] magrittr_2.0.1    Rcpp_1.0.7        munsell_0.5.0     fansi_0.5.0      
[49] gdtools_0.2.4     lifecycle_1.0.1   stringi_1.7.4     whisker_0.4      
[53] yaml_2.2.1        blob_1.2.2        grid_4.1.0        promises_1.2.0.1 
[57] crayon_1.4.1      haven_2.4.3       hms_1.1.1         knitr_1.34       
[61] ps_1.6.0          pillar_1.6.3      uuid_0.1-4        igraph_1.2.6     
[65] codetools_0.2-18  reprex_2.0.1      glue_1.4.2        evaluate_0.14    
[69] data.table_1.14.2 renv_0.13.2       modelr_0.1.8      vctrs_0.3.8      
[73] tzdb_0.1.2        httpuv_1.6.3      cellranger_1.1.0  gtable_0.3.0     
[77] reactR_0.4.4      assertthat_0.2.1  cachem_1.0.6      xfun_0.24        
[81] mime_0.12         xtable_1.8-4      broom_0.7.9       later_1.3.0      
[85] memoise_2.0.0     ellipsis_0.3.2

ICD10_CODE	ALT_CODE	USAGE	USAGE_UK	DESCRIPTION	MODIFIER_4	MODIFIER_5	QUALIFIERS	GENDER_MASK	MIN_AGE	MAX_AGE	TREE_DESCRIPTION
V01	V01	DEFAULT	0	Pedestrian injured in collision with pedal cycle
V01.0	V010	DEFAULT	0	Pedestrian injured in collision with pedal cycle	Nontraffic accident
V01.1	V011	DEFAULT	0	Pedestrian injured in collision with pedal cycle	Traffic accident
V01.9	V019	DEFAULT	0	Pedestrian injured in collision with pedal cycle	Unspecified whether traffic or nontraffic accident
V02	V02	DEFAULT	0	Pedestrian injured in collision with two- or three-wheeled motor vehicle
V02.0	V020	DEFAULT	0	Pedestrian injured in collision with two- or three-wheeled motor vehicle	Nontraffic accident

ICD10 lookup table

A Warwick and CY Ung

16 March, 2022

Summary

ICD10 formats: `ICD10_CODE` and `ALT-CODE`

Dagger/asterisk pairs

Other details

USAGE_UK

USAGE_UK 3

USAGE_UK 1

USAGE_UK 4

USAGE_UK 2

USAGE_UK 0

GENDER_MASK, MIN_AGE, MAX_AGE, TREE_DESCRIPTION (examples)

ICD10_CODE	ALT_CODE	USAGE	USAGE_UK	DESCRIPTION	MODIFIER_4	MODIFIER_5	QUALIFIERS	GENDER_MASK	MIN_AGE	MAX_AGE	TREE_DESCRIPTION
A00	A00	DEFAULT	3	Cholera
A00.0	A000	DEFAULT	3	Cholera due to Vibrio cholerae 01, biovar cholerae
A00.1	A001	DEFAULT	3	Cholera due to Vibrio cholerae 01, biovar eltor
A00.9	A009	DEFAULT	3	Cholera, unspecified
A01	A01	DEFAULT	3	Typhoid and paratyphoid fevers
A01.0	A010	DEFAULT	3	Typhoid fever

ICD10_CODE	ALT_CODE	USAGE	USAGE_UK	DESCRIPTION	MODIFIER_4	MODIFIER_5	QUALIFIERS	GENDER_MASK	MIN_AGE	MAX_AGE	TREE_DESCRIPTION
D63	D63	ASTERIS	2	Anaemia in chronic diseases classified elsewhere
D63.0	D630	ASTERIS	2	Anaemia in neoplastic disease
D63.8	D638	ASTERIS	2	Anaemia in other chronic diseases classified elsewhere
D77	D77X	ASTERIS	2	Other disorders of blood and blood-forming organs in diseases classified elsewhere
E35	E35	ASTERIS	2	Disorders of endocrine glands in diseases classified elsewhere
E35.0	E350	ASTERIS	2	Disorders of thyroid gland in diseases classified elsewhere

ICD10 lookup table

A Warwick and CY Ung

16 March, 2022

Summary

ICD10 formats: ICD10_CODE and ALT-CODE

Dagger/asterisk pairs

Other details

USAGE_UK

USAGE_UK 3

USAGE_UK 1

USAGE_UK 4

USAGE_UK 2

USAGE_UK 0

GENDER_MASK, MIN_AGE, MAX_AGE, TREE_DESCRIPTION (examples)

ICD10 formats: `ICD10_CODE` and `ALT-CODE`