Merge pull request #59 from OxfordIHTM/dev

create list of icd10 unlikely causes of death

NAMESPACE

@@ -21,9 +21,12 @@ export(list_ill_defined_icd11)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,mutate)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(stringr,str_count)
 importFrom(stringr,str_detect)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_trim)
 importFrom(tibble,tibble)

R/codeditr-package.R

@@ -15,8 +15,8 @@
 #' @name codeditr
 #' @importFrom methods is
 #' @importFrom tibble tibble
-#' @importFrom dplyr mutate select case_when bind_rows
+#' @importFrom dplyr mutate select case_when bind_rows rename_with
 #' @importFrom rlang .data
-#' @importFrom stringr str_detect str_count
+#' @importFrom stringr str_detect str_count str_replace_all str_trim
 #'
 "_PACKAGE"

R/data.R

@@ -43,6 +43,23 @@
 "icd11_example"
 
 
+#'
+#' Unlikely causes of death for ICD 10
+#'
+#' @format A data frame with 2 columns and 424 rows:
+#'
+#' | **Variable** | **Description** |
+#' | :--- | :--- |
+#' | *code* | ICD 10 Cause of Death code |
+#' | *title* | Cause of death title |
+#'
+#' @examples
+#' icd10_unlikely_cod
+#'
+#' @source https://icd.who.int/browse10/Content/statichtml/ICD10Volume2_en_2019.pdf
+#'
+"icd10_unlikely_cod"
+
 
 #'
 #' Unlikely causes of death for ICD 11

data-raw/process_unlikely_cod.R

@@ -19,3 +19,118 @@ icd11_unlikely_cod <- rvest::read_html(x = "data-raw/value_sets.html") |>
 
 usethis::use_data(icd11_unlikely_cod, compress = "xz")
 
+## ICD 10 unlikely causes of death ----
+
+icd_10_guide <- pdftools::pdf_text("data-raw/ICD10Volume2_en_2019.pdf")
+
+
+icd10_unlikely_cod <- icd_10_guide |>
+  (\(x) x[238:255])() |>
+  stringr::str_split(pattern = "\n") |>
+  lapply(
+    FUN = function(x) ifelse(
+      stringr::str_detect(
+        string = x,
+        pattern = "List of conditions unlikely to cause death|INTERNATIONAL CLASSIFICATION OF DISEASES|[0-9]{3}|Code|HIV|SP3"
+      ),
+      "", x
+    ) |>
+      (\(x) x[x != ""])() |>
+      stringr::str_trim(side = "left") |>
+      stringr::str_replace_all(pattern = "–", replacement = "-") |>
+      stringr::str_replace_all(pattern = ", ", replacement = ",")
+  )
+
+
+icd10_unlikely_cod[[2]] <- icd10_unlikely_cod[[2]] |>
+  (\(x) c(x[1:23], paste(x[24], x[25]), x[26:27]))() |>
+  (\(x) c(x[1:24], paste(x[25], x[26])))()
+
+icd10_unlikely_cod[[3]] <- icd10_unlikely_cod[[3]] |>
+  (\(x)
+    c(x[1:2], paste(x[3], x[4]), x[5:7], paste(x[8], x[9]),
+      x[10:11], paste(x[12], x[13]), paste(x[14], x[15]), x[16:27])
+  )()
+
+icd10_unlikely_cod[[4]] <- icd10_unlikely_cod[[4]] |>
+  (\(x) c(x[1], paste(x[2], x[3]), x[4:9], paste(x[10], x[11]), x[12:27]))()
+
+icd10_unlikely_cod[[5]] <- icd10_unlikely_cod[[5]] |>
+  (\(x) c(x[1:17], paste(x[18], x[19]), x[20:25]))()
+
+icd10_unlikely_cod[[7]] <- icd10_unlikely_cod[[7]] |>
+  (\(x) c(x[1:14], paste(x[15], x[16]), x[17:25]))()
+
+icd10_unlikely_cod[[9]] <- icd10_unlikely_cod[[9]] |>
+  (\(x) c(x[1:17], paste(x[18], x[19]), x[20], paste(x[21], x[22]), x[23:26]))()
+
+icd10_unlikely_cod[[10]] <- icd10_unlikely_cod[[10]] |>
+  (\(x) c(x[1:21], paste(x[22], x[23]), x[24:27]))()
+
+icd10_unlikely_cod[[13]] <- icd10_unlikely_cod[[13]] |>
+  (\(x) c(x[1:6], paste(x[7], x[8]), x[9:25]))()
+
+icd10_unlikely_cod[[14]] <- icd10_unlikely_cod[[14]] |>
+  (\(x)
+    c(paste(x[1], x[2]), x[3:6], paste(x[7], x[8]), x[9:11],
+      paste(x[12], x[13]), x[14:20], paste(x[21], x[22]), paste(x[23], x[24]),
+      paste(x[25], x[26]), paste(x[27], x[28]),
+      paste(x[29], icd10_unlikely_cod[[15]][1]))
+  )()
+
+icd10_unlikely_cod[[15]] <- icd10_unlikely_cod[[15]] |>
+  (\(x)
+    c(paste(x[2], x[3]), paste(x[4], x[5]), paste(x[6], x[7]), x[8],
+      paste(x[9], x[10]), x[11:15], paste(x[16], x[17]), x[18:22],
+      paste(x[23], x[24]), x[25:28])
+  )()
+
+icd10_unlikely_cod[[16]] <- icd10_unlikely_cod[[16]] |>
+  (\(x) c(x[1:19], paste(x[20], x[21]), x[22:25], paste(x[26], x[27])))()
+
+icd10_unlikely_cod[[17]] <- icd10_unlikely_cod[[17]] |>
+  (\(x)
+    c(x[1:11], paste(x[12], x[13]), x[14:16], paste(x[17], x[18]),
+      paste(x[19], x[20]), x[21:27])
+  )()
+
+icd10_unlikely_cod[[18]] <- icd10_unlikely_cod[[18]] |>
+  (\(x) c(x[1:11], paste(x[12], x[13]), x[14], paste(x[15], x[16]), x[17]))()
+
+icd10_unlikely_cod <- lapply(
+  X = icd10_unlikely_cod,
+  FUN = stringr::str_split,
+  pattern = " ",
+  n = 2,
+  simplify = TRUE
+) |>
+  (\(x) do.call(rbind, x))() |>
+  data.frame() |>
+  dplyr::rename_with(.fn = function(x) c("code", "title"))
+
+icd10_unlikely_cod$code[45] <- paste0(
+  icd10_unlikely_cod$code[45], icd10_unlikely_cod$code[46]
+)
+
+icd10_unlikely_cod$code[75] <- paste0(
+  icd10_unlikely_cod$code[75], icd10_unlikely_cod$code[76]
+)
+
+icd10_unlikely_cod$code[212] <- paste0(
+  icd10_unlikely_cod$code[212], icd10_unlikely_cod$code[213]
+)
+
+icd10_unlikely_cod$code[399] <- paste0(
+  icd10_unlikely_cod$code[399], icd10_unlikely_cod$code[400]
+)
+
+icd10_unlikely_cod$code[409] <- paste0(
+  icd10_unlikely_cod$code[409], icd10_unlikely_cod$code[410]
+)
+
+icd10_unlikely_cod <- icd10_unlikely_cod |>
+  dplyr::filter(title != "") |>
+  dplyr::mutate(title = stringr::str_trim(title)) |>
+  tibble::tibble()
+
+usethis::use_data(icd10_unlikely_cod, overwrite = TRUE, compress = "xz")

inst/WORDLIST

@@ -16,9 +16,9 @@ YYYY
 codedit
 icd
 icdcdn
-illdefined
 int
 referenceguide
+statichtml
 tibble
 valuesets
 www

pkgdown/_pkgdown.yml

@@ -73,6 +73,7 @@ reference:
     contents:
     - icd10_example
     - icd11_example
+    - icd10_unlikely_cod
     - icd11_unlikely_cod
     - icd11_cod_by_sex