OxfordIHTM · ernestguevarra · Feb 10, 2024 · Feb 10, 2024
diff --git a/R/data.R b/R/data.R
@@ -21,3 +21,64 @@
 #' @source https://icd.who.int/docs/icd-api/SupportedClassifications/
 #'
 "icd_versions"
+
+
+#'
+#' ICD-11 Mortality and Morbidity Linearization Outputs
+#'
+#' @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 |
+#'
+#' @examples
+#' icd11_linearization_mms
+#'
+#' @source https://icd.who.int/dev11/Downloads/Download?fileName=LinearizationMiniOutput-MMS-en.zip
+#'
+"icd11_linearization_mms"
+
+
+#'
+#' ICD-11 Mortality and Morbidity Simple Table Outputs
+#'
+#' @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 |
+#'
+#' @examples
+#' icd11_simple_table_mms
+#'
+#' @source https://icdcdn.who.int/static/releasefiles/2024-01/SimpleTabulation-ICD-11-MMS-en.zip
+#'
+"icd11_simple_table_mms"
diff --git a/data-raw/dataset.R → data-raw/icd_classification_versions.R b/data-raw/dataset.R → data-raw/icd_classification_versions.R
diff --git a/data-raw/icd_linearization_tables.R b/data-raw/icd_linearization_tables.R
@@ -0,0 +1,62 @@
+# Download and process ICD-11 linearizations -----------------------------------
+
+## Load libraries ----
+library(openxlsx2)
+
+
+## Download data ----
+
+### Linearization MMS from ICD-11 download page ----
+### https://icd.who.int/dev11/downloads
+
+download_url <- "https://icd.who.int/dev11/Downloads/Download?fileName=LinearizationMiniOutput-MMS-en.zip"
+
+download.file(
+  url = download_url,
+  destfile = "data-raw/linear-mms.zip"
+)
+
+unzip(
+  zipfile = "data-raw/linear-mms.zip",
+  overwrite = TRUE,
+  exdir = "data-raw/linear-mms"
+)
+
+icd11_linearization_mms <- read_xlsx(
+  file = "data-raw/linear-mms/LinearizationMiniOutput-MMS-en.xlsx",
+  sheet = 1, data_only = TRUE
+)
+
+header_values <- names(icd11_linearization_mms)[ncol(icd11_linearization_mms)] |>
+  stringr::str_split(pattern = ":", simplify = TRUE)
+
+names(icd11_linearization_mms)[ncol(icd11_linearization_mms)] <- header_values |>
+  (\(x) x[1])()
+
+icd11_linearization_mms$Version <- header_values |>
+  (\(x) x[2:3])() |>
+  paste(collapse = ":")
+
+usethis::use_data(icd11_linearization_mms, overwrite = TRUE, compress = "xz")
+
+### Simple Table MMS ----
+
+download_url <- "https://icdcdn.who.int/static/releasefiles/2024-01/SimpleTabulation-ICD-11-MMS-en.zip"
+
+download.file(
+  url = download_url,
+  destfile = "data-raw/simple-tab-icd11-mms.zip"
+)
+
+unzip(
+  zipfile = "data-raw/simple-tab-icd11-mms.zip",
+  overwrite = TRUE,
+  exdir = "data-raw/simple-tab-icd11-mms"
+)
+
+icd11_simple_table_mms <- read_xlsx(
+  file = "data-raw/simple-tab-icd11-mms/SimpleTabulation-ICD-11-MMS-en.xlsx",
+  sheet = 1, data_only = TRUE
+)
+
+usethis::use_data(icd11_simple_table_mms, overwrite = TRUE, compress = "xz")
diff --git a/data-raw/linear-mms.zip b/data-raw/linear-mms.zip
diff --git a/data-raw/linear-mms/LinearizationMiniOutput-MMS-en.txt b/data-raw/linear-mms/LinearizationMiniOutput-MMS-en.txt
diff --git a/data-raw/linear-mms/LinearizationMiniOutput-MMS-en.xlsx b/data-raw/linear-mms/LinearizationMiniOutput-MMS-en.xlsx
diff --git a/data-raw/simple-tab-icd11-mms.zip b/data-raw/simple-tab-icd11-mms.zip
diff --git a/data-raw/simple-tab-icd11-mms/SimpleTabulation-ICD-11-MMS-en.txt b/data-raw/simple-tab-icd11-mms/SimpleTabulation-ICD-11-MMS-en.txt
diff --git a/data-raw/simple-tab-icd11-mms/SimpleTabulation-ICD-11-MMS-en.xlsx b/data-raw/simple-tab-icd11-mms/SimpleTabulation-ICD-11-MMS-en.xlsx
diff --git a/data-raw/simple-tab-icd11-mms/readme.txt b/data-raw/simple-tab-icd11-mms/readme.txt
@@ -0,0 +1,16 @@
+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 idetifier 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 bu 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
diff --git a/data/icd11_linearization_mms.rda b/data/icd11_linearization_mms.rda
diff --git a/data/icd11_simple_table_mms.rda b/data/icd11_simple_table_mms.rda
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-02-10T06:32Z
+last_built: 2024-02-10T07:39Z
 urls:
   reference: https://oxford-ihtm.io/icd/reference
   article: https://oxford-ihtm.io/icd/articles

diff --git a/docs/reference/icd.html b/docs/reference/icd.html
diff --git a/docs/reference/icd11_linearization_mms.html b/docs/reference/icd11_linearization_mms.html
diff --git a/docs/reference/icd11_simple_table_mms.html b/docs/reference/icd11_simple_table_mms.html
diff --git a/docs/reference/icd_authenticate.html b/docs/reference/icd_authenticate.html
diff --git a/docs/reference/icd_versions.html b/docs/reference/icd_versions.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -21,6 +21,12 @@
   <url>
     <loc>https://oxford-ihtm.io/icd/reference/icd.html</loc>
   </url>
+  <url>
+    <loc>https://oxford-ihtm.io/icd/reference/icd11_linearization_mms.html</loc>
+  </url>
+  <url>
+    <loc>https://oxford-ihtm.io/icd/reference/icd11_simple_table_mms.html</loc>
+  </url>
   <url>
     <loc>https://oxford-ihtm.io/icd/reference/icd_authenticate.html</loc>
   </url>

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,18 +1,34 @@
+BlockId
+BrowserLink
 CMD
+ChapterNo
+ClassKind
 CodeFactor
 Codecov
+DepthInKind
+GroupingX
 ICF
+IsLeaf
+IsResidual
 Lifecycle
+LinearizationMiniOutput
 OAuth
 ORCID
+PrimaryLocation
 RC
+SimpleTabulation
 SupportedClassifications
 WIP
 api
-httr
+depthinkind
+fileName
+iCatLink
 icdapi
+icdcdn
 int
-oauth
+isLeaf
+noOfNonResidualChildren
 org
+releasefiles
 rfc
 www
diff --git a/man/icd.Rd b/man/icd.Rd
diff --git a/man/icd11_linearization_mms.Rd b/man/icd11_linearization_mms.Rd
diff --git a/man/icd11_simple_table_mms.Rd b/man/icd11_simple_table_mms.Rd
diff --git a/man/icd_authenticate.Rd b/man/icd_authenticate.Rd
diff --git a/man/icd_versions.Rd b/man/icd_versions.Rd
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -51,3 +51,6 @@ reference:
   - title: Supporting datasets
     contents:
     - icd_versions
+    - icd11_linearization_mms
+    - icd11_simple_table_mms
+