Package 'codigo'

ICD 11 code or categories mapped to one ICD 10 category

Description

ICD 11 code or categories mapped to one ICD 10 category

Usage

eleven_map_to_one_ten

Format

A data.frame with 17908 rows and 7 columns:

Variable	Description
icd11_linearization_uri	ICD 11 linearization URI
icd11_code	ICD 11 code
icd11_chapter	ICD 11 chapter
icd11_title	ICD 11 title
icd10_code	ICD 10 code (for class chapter) or block of codes (for class block)
icd10_chapter	ICD 10 chapter
icd10_title	ICD 10 class or kind: either category or code

Source

https://icdcdn.who.int/static/releasefiles/2024-01/mapping.zip

Examples

eleven_map_to_one_ten

---

Get available ICD-10 releases

Description

Get available ICD-10 releases

Usage

icd_10_get_releases(
  api_version = c("v2", "v1"),
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_10_get_chapters(
  release = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_10_get_release_by_category(
  category,
  api_version = c("v2", "v1"),
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_10_get_info(
  category,
  release = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

Arguments

api_version	Version of the API. Possible values are v1 or v2. For example, if you provide value v2, the API will respond in the format of the version 2 of the API. Default is v2.
base_url	The base URL of the API. Default uses the WHO API server at https://id.who.int. If you are using a locally deployed server or hosting your own ICD API server, you should specify the URL of your instance here.
client	The OAuth2 client produced through a call to icd_oauth_client().
scope	Scopes to be requested from the resource owner. Default is "icdapi_access" as specified in the ICD API documentation.
release	A string specifying the release version of ICD-10 to search from. If not specified, defaults to the latest release version. See the available versions with icd_versions.
language	ICD-API is multi-lingual. By changing this header, you may make the API respond in different languages. Languages will be available as the translations of ICD-11 completes. The values are language codes such as en, es, zh, etc. Depending on the release_id specified, the available languages will vary. Default is English ("en"). Note that language support for ICD-10 is limited to English (en).
verbose	Logical. Should non-warning and non-error messages be printed? Default is TRUE.
category	ICD-10 category code or for blocks, the code range.

Value

A list with information on specified ICD 10 parameters

Examples

icd_10_get_releases()
icd_10_get_chapters()
icd_10_get_release_by_category(category = "A00")
icd_10_get_release_by_category(category = "A00-A09")
icd_10_get_info(category = "A00")
icd_10_get_info(category = "A00-A09")

---

Autocode against the foundation component or linearizations of the ICD-11

Description

Autocode against the foundation component or linearizations of the ICD-11

Usage

icd_autocode_foundation(
  q,
  subtree = NULL,
  release = NULL,
  threshold = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  tabular = TRUE,
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_autocode(
  q,
  linearization = c("mms", "icf"),
  subtree = NULL,
  release = NULL,
  threshold = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  tabular = TRUE,
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

Arguments

q	String. Text to be searched. Having the character ⁠%⁠ at the end will be regarded as a wild card for that word.
subtree	A string or vector of strings of URIs. If provided, the search will be performed on the entities provided and their descendants.
release	A string specifying the release version of the Foundation to search from. If not specified, defaults to the latest release version. See the available versions with icd_versions.
threshold	A numeric value between 0 and 1 that indicates the similarity between the input text and the matched term. threshold is the minimum score to be included in the output. Default is NULL to use default value specified by API.
api_version	Version of the API. Possible values are v1 or v2. For example, if you provide value v2, the API will respond in the format of the version 2 of the API. Default is v2.
language	ICD-API is multi-lingual. By changing this header, you may make the API respond in different languages. Languages will be available as the translations of ICD-11 completes. The values are language codes such as en, es, zh, etc. Depending on the release_id specified, the available languages will vary. Default is English ("en").
tabular	Logical. Should output be structured into a tibble? Default to TRUE.
verbose	Logical. Should non-warning and non-error messages be printed? Default is TRUE.
base_url	The base URL of the API. Default uses the WHO API server at https://id.who.int. If you are using a locally deployed server or hosting your own ICD API server, you should specify the URL of your instance here.
client	The OAuth2 client produced through a call to icd_oauth_client().
scope	Scopes to be requested from the resource owner. Default is "icdapi_access" as specified in the ICD API documentation.
linearization	A character value for which linearization to search. Currently, the possible values for this are "mms" and "icf".

Value

A tibble of autocode results showing the search text, the matching text, the code, URIs for the foundation and linearization entities, the matching level, the matching score, and the matching type.

Examples

icd_autocode_foundation("cholera")
icd_autocode(q = "cholera")
icd_autocode(q = "impairment", linearization = "icf")

---

Checks for specified parameters supplied to search, autocode, and get functions

Description

Checks for specified parameters supplied to search, autocode, and get functions

Usage

icd_check_release(release, icd = c("icd11", "icd10"), verbose = TRUE)

icd_check_language(
  release = NULL,
  language,
  icd = c("icd11", "icd10"),
  verbose = TRUE
)

Arguments

release	A string specifying the release version of the ICD-11.
icd	A character string of available ICD classifications. Currently, this can be either "icd10" or "icd11". Default is "icd11".
verbose	Logical. Should non-warning and non-error messages be printed? Default is TRUE.
language	language codes such as en, es, zh, etc.

Value

A message or an error if release provided is recognised or not. A message or a warning if language requested is available or not for release provided. For icd_check_language(), returns a character value or a character vector of acceptable language codes.

Examples

icd_check_release("2024-01")
try(icd_check_release("2025-01"))
icd_check_language("2024-01", "ar")
icd_check_language("2024-01", "rr")
try(icd_check_language("2025-01", "ar"))

---

Get information on various ICD-11 foundation and linearization entities

Description

Get information on various ICD-11 foundation and linearization entities

Usage

icd_get_foundation(
  release = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  tabular = TRUE,
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_get_entity(
  id,
  release = NULL,
  include = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_get_info(
  linearization = c("mms", "icf"),
  api_version = c("v2", "v1"),
  language = "en",
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_get_chapter(
  linearization = c("mms", "icf"),
  release = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

Arguments

release	A string specifying the release version of the Foundation to search from. If not specified, defaults to the latest release version. See the available versions with icd_versions.
api_version	Version of the API. Possible values are v1 or v2. For example, if you provide value v2, the API will respond in the format of the version 2 of the API. Default is v2.
language	ICD-API is multi-lingual. By changing this header, you may make the API respond in different languages. Languages will be available as the translations of ICD-11 completes. The values are language codes such as en, es, zh, etc. Depending on the release_id specified, the available languages will vary. Default is English ("en").
tabular	Logical. Should output be structured into a tibble? Default to TRUE.
verbose	Logical. Should non-warning and non-error messages be printed? Default is TRUE.
base_url	The base URL of the API. Default uses the WHO API server at https://id.who.int. If you are using a locally deployed server or hosting your own ICD API server, you should specify the URL of your instance here.
client	The OAuth2 client produced through a call to icd_oauth_client().
scope	Scopes to be requested from the resource owner. Default is "icdapi_access" as specified in the ICD API documentation.
id	Unique numerical identifier for an entity.
include	A string or a vector of strings for optional property values to be included in the response. The property values that can be included are "ancestor", "descendant", or "diagnosticCriteria". If not specified, these properties are not included in the response.
linearization	A character value for which linearization to search. Currently, the possible values for this are "mms" and "icf". Default is "mms".

Value

A list with information on specified ICD 11 Foundation and top level entities.

Examples

icd_get_foundation()
icd_get_entity(id = "1435254666")     ## chapter
icd_get_entity(id = "588616678")      ## block; depth 1
icd_get_entity(id = "1465325727")     ## category; depth 1
icd_get_info()
icd_get_info("icf")
icd_get_chapter()
icd_get_chapter("icf")

---

Utility functions for retrieving ICD parameters and definitions

Description

Utility functions for retrieving ICD parameters and definitions

Usage

icd_get_releases(icd = c("icd11", "icd10"), latest = FALSE)

icd_get_languages(icd = c("icd11", "icd10"), latest = FALSE)

icd_get_entities(class = NULL)

Arguments

icd	A character string of available ICD classifications. Currently, this can be either "icd10" or "icd11". Default is "icd11". If NULL, all ICD classifications are used (currently both "icd10" and "icd11").
latest	Logical. If TRUE, identifier for latest release is returned. Default is FALSE.
class	A character string of code classes to retrieve. This can be either "chapter", "block", or "category". If NULL (default), all classes are retrieved.

Value

A tibble for ICD classification values and their corresponding release identifiers (for icd_get_releases()). A names list of corresponding languages (for icd_get_languages()). A tibble of entities with their definitions/titles and classes (for icd_get_entitties()).

Examples

icd_get_releases()
icd_get_languages()
icd_get_entities()

---

Map ICD codes between versions

Description

Map ICD codes between versions

Usage

icd_map(from = c("icd10", "icd11"), to = c("one", "multiple"), code)

Arguments

from	The ICD version to map from. Either icd10 or icd11. Default to icd10.
to	A character value of either multiple or one to map ICD-10 to ICD-11 accordingly. Only relevant if from is icd10. Ignored when from is icd11. Default to one.
code	Corresponding ICD code in version specified in from to map to the other version.

Value

A tibble of information for specified code mapped based on from

Examples

icd_map(code = "A00")

---

OAuth2 authentication to ICD API

Description

OAuth2 authentication to ICD API

Usage

icd_oauth_client(
  id = Sys.getenv("ICD_CLIENT_ID"),
  token_url = "https://icdaccessmanagement.who.int/connect/token",
  secret = Sys.getenv("ICD_CLIENT_SECRET"),
  name = "icd_client",
  ...
)

icd_authenticate(
  req,
  client = icd_oauth_client(),
  scope = "icdapi_access",
  ...
)

Arguments

id	Consumer key, also sometimes called the client ID.
token_url	url used to exchange unauthenticated for authenticated token.
secret	Consumer secret, also sometimes called the client secret. Despite its name, this does not necessarily need to be protected like a password, i.e. the user still has to authenticate themselves and grant the app permission to access resources on their behalf.
name	Name of the application. This is not used for OAuth, but is used to make it easier to identify different applications.
...	Other parameters/arguments to be passed onto httr2::oauth_client() or to httr2::req_oauth_client_credentials()
req	A request
client	An OAuth2 client. Default is a call to icd_oauth_client().
scope	Scopes to be requested from the resource owner. Default is "icdapi_access" as specified in the ICD API documentation.

Value

An httr2_oauth_client class object.

Examples

icd_oauth_client()

---

Search the foundation component or linearizations of the ICD-11

Description

Search the foundation component or linearizations of the ICD-11

Usage

icd_search_foundation(
  q,
  subtree = NULL,
  chapter = NULL,
  flexisearch = FALSE,
  flat = TRUE,
  properties = NULL,
  release = NULL,
  highlight = FALSE,
  api_version = c("v2", "v1"),
  language = "en",
  tabular = TRUE,
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

icd_search(
  q,
  linearization = c("mms", "icf"),
  subtree = NULL,
  use_foundation = FALSE,
  keyword = FALSE,
  chapter = NULL,
  flexisearch = FALSE,
  flat = TRUE,
  release = NULL,
  highlight = FALSE,
  medical_mode = TRUE,
  properties = NULL,
  api_version = c("v2", "v1"),
  language = "en",
  tabular = TRUE,
  verbose = TRUE,
  base_url = "https://id.who.int",
  client = icd_oauth_client(),
  scope = "icdapi_access"
)

Arguments

q	String. Text to be searched. Having the character ⁠%⁠ at the end will be regarded as a wild card for that word.
subtree	A string or vector of strings of URIs. If provided, the search will be performed on the entities provided and their descendants.
chapter	A string or vector of strings of chapter codes eg: c("01", "02") When provided, the search will be performed only on these chapters.
flexisearch	Logical. Default is FALSE. Changes the search mode to flexible search (for more details, see section on flexisearch).
flat	Logical. Default is FALSE. If set to true the search result entities are provided in a nested data structure representing the ICD-11 hierarchy. Otherwise they are listed as flat list of matches.
properties	A string or a vector of strings for the properties to be searched. When set to NULL (default), search is performed on a default set of properties depending on whether foundation or linearization (see section on properties for more details). Should be set/specified if medical_mode = FALSE.
release	A string specifying the release version of the Foundation to search from. If not specified, defaults to the latest release version. See the available versions with icd_versions.
highlight	Logical. Default is FALSE. If set to FALSE the search result highlighting is turned off and the results don't contain special tags for highlighting where the results are found within the text.
api_version	Version of the API. Possible values are v1 or v2. For example, if you provide value v2, the API will respond in the format of the version 2 of the API. Default is v2.
language	Language code for language in which search results are to be shown. Default is English ("en"). See section on language for more details.
tabular	Logical. Should output be structured into a tibble? Default to TRUE.
verbose	Logical. Should non-warning and non-error messages be printed? Default is TRUE.
base_url	The base URL of the API. Default uses the WHO API server at https://id.who.int. If you are using a locally deployed server or hosting your own ICD API server, you should specify the URL of your instance here.
client	The OAuth2 client produced through a call to icd_oauth_client().
scope	Scopes to be requested from the resource owner. Default is "icdapi_access" as specified in the ICD API documentation.
linearization	A character value for which linearization to search. Currently, the possible values for this are "mms" and "icf".
use_foundation	Logical. Default is FALSE. Should subtree filter use foundation descendants (TRUE) or linearization descendants (FALSE)?
keyword	Logical. Default is FALSE. Should search results show keyword list? See section on keyword for more details.
medical_mode	Logical. Default is FALSE. Should medical coding mode be turned on?

Value

A tibble of search results.

On flexisearch

In the regular search mode (flexisearch = FALSE), the function will only give you results that contain all of the words that you've used in your search. It accepts different variants or synonyms of the words but essentially it searches for a result that contains all components of your search. Whereas in flexible search mode, the results do not have to contain all of the words that are typed. It would still try to find the best matching phrase but there may be words in your search that are not matched at all. It is recommended to use flexible search only when regular search does not provide a result.

On keyword

If set to true, the search result will also include keyword list. If the last word provided is incomplete, keyword list includes all words that start with the incomplete word (word completion mode). If the last word is complete, the keyword list will provide suggested additional words that could be added to the search query (word suggestion mode).

On medical_mode

When searching the classification for medical coding purposes, this should be set to TRUE (default). In this mode, the search gives results only from the entities that have a code. The system will search all index terms of an entity. i.e. titles, synonyms, fully specified term, all terms of other entities that are in the foundation are aggregated into this entity. By default, chapters 26, V, and X are not included in the search results. If medical_mode is set to FALSE, then the properties argument will need to be specified (see next section).

On properties

In the Foundation search, by default the function searches "Title", "Synonyms", and "FullySpecifiedName". The valid values that could be used for properties are: "Title", "Synonym", "NarrowerTerm", "FullySpecifiedName", "Definition", and "Exclusion". In the MMS search, this argument is only used when medical_mode = FALSE. The valid values that could be used are: "Title", "FullySpecifiedName", "Definition", "Exclusion", and "IndexTerm". If "IndexTerm" is used, the search will be performed on all "Titles", "Synonyms", and "FullySpecifiedNames" including the ones that are under shoreline (i.e Entities in the foundation but not in MMS). In such cases the results will be shown based on where the match is aggregated into in MMS.

On language

ICD-API is multi-lingual. By setting the language, you may make the API respond in different languages. Languages will be available as the translations of ICD-11 completes. The values are language codes such as en, es, zh, etc. Depending on the release specified, the available languages will vary.

Examples

icd_search_foundation("colorectal cancer")
icd_search("colorectal cancer")
icd_search("impairment", linearization = "icf")

---

Structure ICD list and ICD search outputs

Description

Structure ICD list and ICD search outputs

Usage

icd_structure_foundation(icd_list)

icd_structure_search(icd_search)

icd_structure_autocode(icd_autocode)

Arguments

icd_list	An object produced by a call to any of the icd_get functions
icd_search	An object produced by a call to any of the icd_search functions
icd_autocode	An object produced by a call to any of the icd_autocode functions

Details

These functions are meant to be helper functions and are used within the icd_get, icd_search, and icd_autocode functions to structure the output responses.

Value

A tibble of structured ICD outputs.

Examples

icd_list <- icd_get_foundation(tabular = FALSE)
icd_tbl_foundation <- icd_structure_foundation(icd_list)
icd_structure_search(icd_search_foundation("cholera", tabular = FALSE))
icd_structure_autocode(icd_autocode_foundation("cholera"))

---

Table of supported classifications and versions by the ICD API

Description

Table of supported classifications and versions by the ICD API

Usage

icd_versions

Format

A data frame with 6 columns and 11 rows:

Variable	Description
Classification	Version of classification. Either ICD-11 or ICD-10
Release ID	Release identifier for specific classification version
Foundation	Logical. Does this version include the Foundation?
MMS	Logical. Does this version include the MMS information?
ICF	Logical. Does this version include the ICF?
Languages	Languages in which version and release is available for

For logical fields that specify NA, this indicates that for that particular version and release, the particular field was not applicable or relevant.

Source

https://icd.who.int/docs/icd-api/SupportedClassifications/

Examples

icd_versions

---

ICD-11 Mortality and Morbidity Linearization Outputs

Description

ICD-11 Mortality and Morbidity Linearization Outputs

Usage

icd11_linearization_mms

Format

A data frame with 21 columns and 36753 rows:

Variable	Description
Foundation URI	Foundation URI
Linearization (release) URI	Linearization release URI
Code	ICD-11 Code
BlockId	Block identifier
Title	Title
ClassKind	Class
DepthInKind	Depth
IsResidual	Is residual?
PrimaryLocation	Primary location
ChapterNo	Chapter number
BrowserLink	Browser link
iCatLink	Category link
isLeaf	Is leaf?
noOfNonResidualChildren	Number of non-residual children
Primary tabulation	Primary tabulation
Version	Date and time linearization was produced

Source

https://icd.who.int/dev11/Downloads/Download?fileName=LinearizationMiniOutput-MMS-en.zip

Examples

icd11_linearization_mms

---

ICD-11 Mortality and Morbidity Simple Table Outputs

Description

ICD-11 Mortality and Morbidity Simple Table Outputs

Usage

icd11_simple_table_mms

Format

A data frame with 18 columns and 36044 rows:

Variable	Description
Foundation URI	Unique identifier for the entity that will not change
Linearization (release) URI	Unique identifier for this version of the classification. It includes the linearization name such as MMS and minor version identifier such as 2018 in it
Code	ICD-11 code for the entity. Note that the groupings do not have a code.
BlockId	Identifier for high level groupings that do not bear a code
Title	Title of the entity
ClassKind	One of the three (chapter, block, category); Chapter is top level classification entities; Blocks are high level groupings that do not bear a code; Categories are entities that has a code
DepthInKind	Depth of within the Class Kind. For example, a category with depthinkind=2 means it is category whose parent is also a category but grand parent is not
IsResidual	true if the entity is a residual category (i.e. other specified or unspecified categories)
ChapterNo	The chapter that the entity is in
BrowserLink	Direct link to this entity in ICD-11 browser
IsLeaf	true if this entity does not have any children
Primary Tabulation
GroupingX	Groupings that the entity is included in
Version	Date and time linearization was produced

Source

https://icdcdn.who.int/static/releasefiles/2024-01/SimpleTabulation-ICD-11-MMS-en.zip

Examples

icd11_simple_table_mms

---

ICD 10 code or categories mapped to multiple ICD 11 categories

Description

ICD 10 code or categories mapped to multiple ICD 11 categories

Usage

ten_map_to_multiple_eleven

Format

A data.frame with 15658 rows and 12 columns:

Variable	Description
icd10_class_kind	ICD 10 class or kind: either chapter, block, category, or modifiedcategory
icd10_depth	ICD 10 depth level
icd10_code	ICD 10 code (for class chapter) or block of codes (for class block)
icd10_chapter	ICD 10 chapter
icd10_title	ICD 10 class or kind: either category or code
icd11_class_kind	ICD 11 class or kind: either block, category, or chapter
icd11_depth	ICD 11 depth level
icd11_foundation_uri	ICD 11 foundation URI
icd11_linearization_uri	ICD 11 linearization URI
icd11_code	ICD 11 code
icd11_chapter	ICD 11 chapter
icd11_title	ICD 11 title

Source

https://icdcdn.who.int/static/releasefiles/2024-01/mapping.zip

Examples

ten_map_to_multiple_eleven

---

ICD 10 code or categories mapped to one ICD 11 category

Description

ICD 10 code or categories mapped to one ICD 11 category

Usage

ten_map_to_one_eleven

Format

A data.frame with 12597 rows and 12 columns:

Variable	Description
icd10_class_kind	ICD 10 class or kind: either chapter, block, category, or modifiedcategory
icd10_depth	ICD 10 depth level
icd10_code	ICD 10 code (for class chapter) or block of codes (for class block)
icd10_chapter	ICD 10 chapter
icd10_title	ICD 10 class or kind: either category or code
icd11_class_kind	ICD 11 class or kind: either block, category, or chapter
icd11_depth	ICD 11 depth level
icd11_foundation_uri	ICD 11 foundation URI
icd11_linearization_uri	ICD 11 linearization URI
icd11_code	ICD 11 code
icd11_chapter	ICD 11 chapter
icd11_title	ICD 11 title

Source

https://icdcdn.who.int/static/releasefiles/2024-01/mapping.zip

Examples

ten_map_to_one_eleven

---