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ICD-10

Source: vignettes/articles/ICD-10.Rmd
ICD-10.Rmd

To interact with ICD-10 you should first get your token:

library(WHOicd)

#Substitute CLIENT_ID and CLIENT_SECRET by your credentials
token <- get_token(CLIENT_ID, CLIENT_SECRET)

Searching given a code

The main function relating to ICD-10 is icd10_search() which searches for the titles and parents of codes, blocks of chapters. As an example, we can search for the following vector and obtain a data.frame:

#Search for code, specific code, chapter and block 
codes <- c("D60", "IX", "I10-I15")
icd10_search(token, codes)
#>   searched code                                          code_title   block
#> 1      D60  D60 Acquired pure red cell aplasia [erythroblastopenia] D60-D64
#> 2       IX <NA>                                                <NA>    <NA>
#> 3  I10-I15 <NA>                                                <NA> I10-I15
#>                   block_title chapter
#> 1 Aplastic and other anaemias     III
#> 2                        <NA>      IX
#> 3       Hypertensive diseases      IX
#>                                                                                         chapter_title
#> 1 Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
#> 2                                                                  Diseases of the circulatory system
#> 3                                                                  Diseases of the circulatory system

If you only want to get the title of the current code/chapter/block you can use icd10_title which is faster as it requires less requests to the API:

#Search for code, specific code, chapter and block 
codes <- c("D60", "IX", "I10-I15")
icd10_title(token, codes)
#>   searched                                               title
#> 1      D60 Acquired pure red cell aplasia [erythroblastopenia]
#> 2       IX                  Diseases of the circulatory system
#> 3  I10-I15                               Hypertensive diseases

Given a chapter you can also list all the blocks in a chapter

icd10_blocks(token, chapter = "III")
#>     codes                                                          title
#> 1 D50-D53                                           Nutritional anaemias
#> 2 D55-D59                                            Haemolytic anaemias
#> 3 D60-D64                                    Aplastic and other anaemias
#> 4 D65-D69 Coagulation defects, purpura and other haemorrhagic conditions
#> 5 D70-D77               Other diseases of blood and blood-forming organs
#> 6 D80-D89               Certain disorders involving the immune mechanism

As well as all of the chapters in a block:

icd10_codes(token, block = "D55-D59")
#>   codes                                title
#> 1   D55      Anaemia due to enzyme disorders
#> 2   D56                         Thalassaemia
#> 3   D57                Sickle-cell disorders
#> 4   D58 Other hereditary haemolytic anaemias
#> 5   D59          Acquired haemolytic anaemia

The same command allows you to search inside a code:

icd10_codes(token, block = "D55")
#>   codes                                                              title
#> 1 D55.0 Anaemia due to glucose-6-phosphate dehydrogenase [G6PD] deficiency
#> 2 D55.1           Anaemia due to other disorders of glutathione metabolism
#> 3 D55.2                     Anaemia due to disorders of glycolytic enzymes
#> 4 D55.3                  Anaemia due to disorders of nucleotide metabolism
#> 5 D55.8                             Other anaemias due to enzyme disorders
#> 6 D55.9                        Anaemia due to enzyme disorder, unspecified

Search for code in releases

Not all codes are available across releases. For example, the C80.0 code was not in the 2008 release of the ICD-10. Hence if you are using that release you will not find it:

icd10_search(token, "C80.0", release = 2008)
#> Warning in value[[3L]](cond): Request not found. Possibly any of release,
#> chapter/block/code or language is not available or incorrectly specified.
#> Warning in value[[3L]](cond): Request not found. Possibly any of release,
#> chapter/block/code or language is not available or incorrectly specified.
#>   searched chapter chapter_title
#> 1    C80.0    <NA>          <NA>

However you can use the icd10_code_search_release to search for a release containing that code:

icd10_code_search_release(token, code = "C80.0")
#> [1] "2019" "2016" "2010"

and use one of those releases instead:

icd10_search(token, "C80.0", release = 2016)
#>   searched level_0                                             title_0 level_1
#> 1    C80.0   C80.0 Malignant neoplasm, primary site unknown, so stated     C80
#>                                             title_1 level_2
#> 1 Malignant neoplasm, without specification of site C76-C80
#>                                                               title_2 level_3
#> 1 Malignant neoplasms of ill-defined, secondary and unspecified sites C00-C97
#>               title_3 level_4   title_4
#> 1 Malignant neoplasms      II Neoplasms

Additional information on releases

The icd10_releases function lists all available ICD-10 releases

icd10_releases(token)
#> [1] "2019" "2016" "2010" "2008"

The default is 2019. You can change it with the release parameter across all functions.

To obtain the complete information on a certain release you can use the icd10_release_info function:

icd10_release_info(token, release = 2016)
#> $`@context`
#> [1] "http://id.who.int/icd/contexts/contextForTopLevel.json"
#> 
#> $`@id`
#> [1] "http://id.who.int/icd/release/10/2016"
#> 
#> $title
#> $title$`@language`
#> [1] "en"
#> 
#> $title$`@value`
#> [1] "International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10) Version for 2016"
#> 
#> 
#> $releaseDate
#> [1] "2016-11-01"
#> 
#> $child
#> $child[[1]]
#> [1] "http://id.who.int/icd/release/10/2016/I"
#> 
#> $child[[2]]
#> [1] "http://id.who.int/icd/release/10/2016/II"
#> 
#> $child[[3]]
#> [1] "http://id.who.int/icd/release/10/2016/III"
#> 
#> $child[[4]]
#> [1] "http://id.who.int/icd/release/10/2016/IV"
#> 
#> $child[[5]]
#> [1] "http://id.who.int/icd/release/10/2016/V"
#> 
#> $child[[6]]
#> [1] "http://id.who.int/icd/release/10/2016/VI"
#> 
#> $child[[7]]
#> [1] "http://id.who.int/icd/release/10/2016/VII"
#> 
#> $child[[8]]
#> [1] "http://id.who.int/icd/release/10/2016/VIII"
#> 
#> $child[[9]]
#> [1] "http://id.who.int/icd/release/10/2016/IX"
#> 
#> $child[[10]]
#> [1] "http://id.who.int/icd/release/10/2016/X"
#> 
#> $child[[11]]
#> [1] "http://id.who.int/icd/release/10/2016/XI"
#> 
#> $child[[12]]
#> [1] "http://id.who.int/icd/release/10/2016/XII"
#> 
#> $child[[13]]
#> [1] "http://id.who.int/icd/release/10/2016/XIII"
#> 
#> $child[[14]]
#> [1] "http://id.who.int/icd/release/10/2016/XIV"
#> 
#> $child[[15]]
#> [1] "http://id.who.int/icd/release/10/2016/XV"
#> 
#> $child[[16]]
#> [1] "http://id.who.int/icd/release/10/2016/XVI"
#> 
#> $child[[17]]
#> [1] "http://id.who.int/icd/release/10/2016/XVII"
#> 
#> $child[[18]]
#> [1] "http://id.who.int/icd/release/10/2016/XVIII"
#> 
#> $child[[19]]
#> [1] "http://id.who.int/icd/release/10/2016/XIX"
#> 
#> $child[[20]]
#> [1] "http://id.who.int/icd/release/10/2016/XX"
#> 
#> $child[[21]]
#> [1] "http://id.who.int/icd/release/10/2016/XXI"
#> 
#> $child[[22]]
#> [1] "http://id.who.int/icd/release/10/2016/XXII"
#> 
#> 
#> $browserUrl
#> [1] "http://apps.who.int/classifications/icd10/browse/2016/en"