The International Classification of Diseases (ICD) serves a broad range of uses globally and provides critical knowledge on the extent, causes and consequences of human disease and death worldwide via data that is reported and coded with the ICD. ICD API allows programmatic access to the ICD. It is an HTTP based REST API. This package provides functions that interface with the ICD API.
What does codigo do?
Please note that codigo is still experimental but is nearing a stable release. It is possible that some functionalities described below and in the rest of the package documentation may change interface or approach but these changes will likely be minor.
Currently, the package provides functions for:
- Authenticating with the ICD API (stable);
- Performing a search of ICD-11 foundation and linearization components (stable);
- Performing autocoding of causes of death using the ICD-11 foundation and linearization components (stable);
- Getting information on various ICD-11 foundation and linearization entities (experimental);
- Converting ICD-10 codes to ICD-11 codes and vice versa (stable); and,
- Determining the underlying cause of death based on reported information on a death certificate (experimental).
Installation
codigo is not yet on CRAN but can be installed from the Oxford iHealth R Universe as follows:
install.packages(
"codigo",
repos = c('https://oxfordihtm.r-universe.dev', 'https://cloud.r-project.org')
)and then can be loaded into an R session
Usage
Authenticating with the ICD API
The ICD API uses OAuth2 for authentication. The package has a set of utility functions that support the ICD API authentication specifications leading to the generation of an OAuth2 token. The icd_oauth_client() function is the downstream and user-facing function that creates an ICD OAuth2 client that can be used for token retrieval by future functions that wrap ICD API for entity and linearization information retrieval.
An ICD OAuth2 client can be generated as follows:
This function uses a built in OAuth2 client created for light use and for purposes of package development and testing.
It is recommended that those intending to use this package for programmatically performing high volume of calls to the ICD API to create their own access keys (client id and client secret) using these instructions.
Then, with your access keys, perform the following commands:
## Create your own OAuth client ----
my_oauth_client <- icd_oauth_client(
id = "YOUR_CLIENT_ID",
token_url = "https://icdaccessmanagement.who.int/connect/token",
secret = "YOUR_CLIENT_SECRET",
name = "NAME_OF_YOUR_APP"
)This OAuth2 client can now be used to the various functions in the package that require an OAuth2 client for authentication for making requests to the ICD API.
Performing a basic search
The main feature of the ICD API is the ability to search ICD 11 Foundation and ICD 11 Linearization for information regarding an illness/disease. This feature is captured by the icd_search functions. For example, if colorectal cancer is the disease of interest and information available from ICD 11 is needed, the following call can be made:
icd_search("colorectal cancer", client = my_oauth_client)which gives the following output:
#> Release `2024-01` matches a known release for ICD-11.
#> Language `en` is available for the release specified.
#> # A tibble: 18 × 19
#> id title stemId isLeaf postcoordinationAvai…¹ hasCodingNote
#> * <chr> <chr> <chr> <lgl> <int> <lgl>
#> 1 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 2 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 3 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 4 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 5 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 6 http://id.who.in… Mali… http:… TRUE 1 FALSE
#> 7 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 8 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 9 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 10 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 11 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 12 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 13 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 14 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 15 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 16 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 17 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> 18 http://id.who.in… Othe… http:… TRUE 1 FALSE
#> # ℹ abbreviated name: ¹postcoordinationAvailability
#> # ℹ 13 more variables: hasMaternalChapterLink <lgl>,
#> # hasPerinatalChapterLink <lgl>, matchingPVs <named list>,
#> # propertiesTruncated <lgl>, isResidualOther <lgl>,
#> # isResidualUnspecified <lgl>, chapter <chr>, theCode <chr>, score <dbl>,
#> # titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>,
#> # important <lgl>The output is a tibble created from parsed JSON body text of the HTTP response from the ICD API.
Citation
If you find the codigo package useful please cite using the suggested citation provided by a call to the citation() function as follows:
citation("codigo")
#> To cite codigo in publications use:
#>
#> Anita Makori, Ernest Guevarra (2024). _codigo: Interface to the
#> International Classification of Diseases (ICD) API_. R package
#> version 0.0.9000, <https://oxford-ihtm.io/codigo/>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {codigo: Interface to the International Classification of Diseases (ICD) API},
#> author = {{Anita Makori} and {Ernest Guevarra}},
#> year = {2024},
#> note = {R package version 0.0.9000},
#> url = {https://oxford-ihtm.io/codigo/},
#> }Community guidelines
Feedback, bug reports and feature requests are welcome; file issues or seek support here. If you would like to contribute to the package, please see our contributing guidelines.
This project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.