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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# WHOicd
<!-- badges: start -->
[](https://CRAN.R-project.org/package=WHOicd)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://app.codecov.io/gh/RodrigoZepeda/WHOicd?branch=main)
[](https://github.com/RodrigoZepeda/WHOicd/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
Access the World Health Organization's (WHO) International Classification of Diseases (ICD) [API](https://icd.who.int/icdapi). This allows you to use ICD-10 and ICD-11 codes, encode text directly into ICD-11, search for diseases in ICD-10, and detect underlying causes of death using the [DORIS system](https://icd.who.int/doris).
## Installation
You can install the development version of WHOicd using the `remotes` package:
``` r
#install.packages("remotes")
remotes::install_github("RodrigoZepeda/WHOicd")
```
## Setup
```{r, echo=FALSE}
CLIENT_ID <- Sys.getenv("CLIENT_ID")
CLIENT_SECRET <- Sys.getenv("CLIENT_SECRET")
```
For the examples we'll assume you already have a `CLIENT_ID` and `CLIENT_SECRET`
for the WHO API as obtained in the [**Generaring your token**](/articles/Generating-your-token.html) article.
To interact with the API you'll need to continuously create a token using the `get_token` function:
```{r}
library(WHOicd)
#Substitute CLIENT_ID and CLIENT_SECRET by your credentials
token <- get_token(CLIENT_ID, CLIENT_SECRET)
```
> **Note** These tokens last for 1 hour and once the hour passes you'll need to generate a new token. The package will try to auto-generate one for you.
There are three main objectives for this package:
1. Use of the DORIS system to obtain underlying cause of death from death certificate information.
2. [Use of ICD-11 to codify causes of death](https://rodrigozepeda.github.io/WHOicd/articles/ICD-11.html).
3. [Use of ICD-10 to search for causes of death](https://rodrigozepeda.github.io/WHOicd/articles/ICD-10.html).
## DORIS (WHO Digital Open Rule Integrated Cause of Death Selection)
The [Digital Open Rule Integrated Cause of Death Selection](https://icd.who.int/doris/en), DORIS,
provides a framework for obtaining the underlying cause of death from a death certificate. DORIS
functionality has been implemented in the `doris()` function.
The following example considers a 60 year old female whose primary cause of death was `2D42`:
`Malignant neoplasms of ill-defined sites` due to `2E03`: `Malignant neoplasm metastasis in bone or bone marrow` due to `CB41.0Z`: `Acute respiratory failure, unspecified`.
```{r}
doris(token, sex = "Female", age = iso_8601(years = 60), cause_of_death_code_a = "2D42",
cause_of_death_code_b = "2E03", cause_of_death_code_c = "CB41.0Z")
```
All of the options are available in the function's help page [`doris()`](https://rodrigozepeda.github.io/WHOicd/reference/doris.html).
## ICD-11 examples
The main functions relating to ICD-11 are `icd11_search()` and `icd11_autocode()`. The first one allows you to search for a specific diagnosis using keywords inside `ICD-11` either in the _Mortality and Morbidity Statistics (MMS)_ or in the _International Classification of Functioning, Disability and Health (ICF)_.
The following example searches for any coding related to Dementia related to HIV stage 4
```{r}
#Look for Dementia and HIV stage 4
search_results <- icd11_search(token, "Dementia HIV stage 4")
#Recover all of the titles matched
search_results |> retrieve("title")
```
Another function of importance is `autocode` which reads plain-text diagnostic text and returns the best matching code either in _MMS_ or _ICF_
```{r}
#Auto code a diagnostic text such as `cerebrovascular accident`
code_results <- icd11_autocode(token, "Patient with cerebrovascular accident")
#Recover the code that matched
code_results |> retrieve("theCode")
```
Additional information on ICD-11 can be found in the [ICD-11 article](https://rodrigozepeda.github.io/WHOicd/articles/ICD-11.html)
## ICD-10 examples
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`:
```{r}
#| results: false
#Search for code, specific code, chapter and block
codes <- c("D60", "IX", "I10-I15")
icd10_search(token, codes)
```
```{r}
#| echo: false
icd10_search(token, codes) |> tibble::as_tibble()
```
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:
```{r}
#| results: false
#Search for code, specific code, chapter and block
codes <- c("D60", "IX", "I10-I15")
icd10_title(token, codes)
```
```{r}
#| echo: false
#Search for code, specific code, chapter and block
icd10_title(token, codes) |> tibble::as_tibble()
```
Additional information on ICD-10 can be found in the [ICD-10 article](https://rodrigozepeda.github.io/WHOicd/articles/ICD-10.html)
## Support
This is not an official product of the WHO. However we are happy to provide support if you [raise an issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue).