added appendices G and H1 (#2)

NAMESPACE

@@ -5,6 +5,8 @@ export(appendix_A)
 export(appendix_B)
 export(appendix_C)
 export(appendix_D)
+export(appendix_G)
+export(appendix_H)
 export(apply_age_edits)
 export(case_chapter_icd10)
 export(ex_data)

R/appendices.R

@@ -113,7 +113,7 @@ appendix_C <- function(icd = NULL,
 
 
 #' Appendix D MS-DRG Surgical Hierarchy by MDC and MS-DRG
-
+#'
 #' Since patients can have multiple procedures related to their principal
 #' diagnosis during a particular hospital stay, and a patient can be assigned to
 #' only one surgical class, the surgical classes in each MDC are defined in a
@@ -160,3 +160,42 @@ appendix_C <- function(icd = NULL,
 appendix_D <- function() {
   pins::pin_read(mount_board(), "msdrg_drg_groups_41.1")
 }
+
+#' Appendix G Diagnoses Defined as Complications or Comorbidities
+#'
+#' Diagnoses in Appendix G are considered complications or comorbidities (CC)
+#' except when used in conjunction with the principal diagnosis in the
+#' corresponding CC Exclusion List in Appendix C.
+#'
+#' @template returns
+#'
+#' @examples
+#' head(appendix_G())
+#'
+#' @autoglobal
+#'
+#' @export
+appendix_G <- function() {
+  pins::pin_read(mount_board(), "msdrg_icd_ccs_41.1")
+}
+
+#' Appendix H Diagnoses Defined as Major Complications or Comorbidities
+#'
+#' Diagnoses in Appendix H Part I are considered major complications or
+#' comorbidities (MCC) except when used in conjunction with the principal
+#' diagnosis in the corresponding CC Exclusion List in Appendix C. In addition to
+#' the CC exclusion list, the diagnoses in Part II are assigned as a major CC
+#' only for patients discharged alive, otherwise they will be assigned as a non
+#' CC.
+#'
+#' @template returns
+#'
+#' @examples
+#' head(appendix_H())
+#'
+#' @autoglobal
+#'
+#' @export
+appendix_H <- function() {
+  pins::pin_read(mount_board(), "msdrg_icd_mccs_41.1")
+}

R/icd_10_cm.R

@@ -17,8 +17,7 @@
 #' @autoglobal
 #'
 #' @export
-icd10cm <- function(icd = NULL,
-                    ...) {
+icd10cm <- function(icd = NULL, ...) {
 
   icd10 <- pins::pin_read(mount_board(), "icd10cm")
 

data-raw/appendix_G.R

@@ -0,0 +1,34 @@
+# Appendix G Diagnoses Defined as Complications or Comorbidities
+#
+# Diagnoses in Appendix G are considered complications or comorbidities (CC)
+# except when used in conjunction with the principal diagnosis in the
+# corresponding CC Exclusion List in Appendix C.
+
+
+library(tidyverse)
+
+path_G <- "C:/Users/Andrew/Desktop/payer_guidelines/data/MSDRG/MSDRGv41.1ICD10_R0_DefinitionsManual_TEXT_0/appendix_G.txt"
+
+g_file <- readr::read_table(
+  path_G,
+  skip = 0,
+  col_names = FALSE) |>
+  dplyr::mutate(dx_type = "CC",
+                X1 = pathologie::add_dot(X1)) |>
+  tidyr::unite("icd_description", X2:X9, na.rm = TRUE, sep = " ") |>
+  dplyr::rename(icd_code = X1)
+
+# Update Pin
+board <- pins::board_folder(here::here("inst/extdata/pins"))
+
+board |> pins::pin_write(
+  g_file,
+  name = "msdrg_icd_ccs_41.1",
+  title = "Appendix G Diagnoses Defined as Complications or Comorbidities 41.1",
+  description = c(
+    "Diagnoses in Appendix G are considered complications or comorbidities (CC) except when used in conjunction with the principal diagnosis in the corresponding CC Exclusion List in Appendix C."
+  ),
+  type = "qs"
+)
+
+board |> pins::write_board_manifest()

data-raw/appendix_H_1.R

@@ -0,0 +1,37 @@
+# Appendix H Diagnoses Defined as Major Complications or Comorbidities
+#
+# Diagnoses in Appendix H Part I are considered major complications or
+# comorbidities (MCC) except when used in conjunction with the principal
+# diagnosis in the corresponding CC Exclusion List in Appendix C. In addition to
+# the CC exclusion list, the diagnoses in Part II are assigned as a major CC
+# only for patients discharged alive, otherwise they will be assigned as a non
+# CC.
+
+
+library(tidyverse)
+
+path_h1 <- "C:/Users/Andrew/Desktop/payer_guidelines/data/MSDRG/MSDRGv41.1ICD10_R0_DefinitionsManual_TEXT_0/appendix_H_1.txt"
+
+h1_file <- readr::read_table(
+  path_h1,
+  skip = 0,
+  col_names = FALSE) |>
+  dplyr::mutate(dx_type = "MCC",
+                X1 = pathologie::add_dot(X1)) |>
+  tidyr::unite("icd_description", X2:X3, na.rm = TRUE, sep = " ") |>
+  dplyr::rename(icd_code = X1)
+
+# Update Pin
+board <- pins::board_folder(here::here("inst/extdata/pins"))
+
+board |> pins::pin_write(
+  h1_file,
+  name = "msdrg_icd_mccs_41.1",
+  title = "Appendix H Diagnoses Defined as Major Complications or Comorbidities 41.1",
+  description = c(
+    "Diagnoses in Appendix H Part I are considered major complications or comorbidities (MCC) except when used in conjunction with the principal diagnosis in the corresponding CC Exclusion List in Appendix C. In addition to the CC exclusion list, the diagnoses in Part II are assigned as a major CC only for patients discharged alive, otherwise they will be assigned as a non CC."
+  ),
+  type = "qs"
+)
+
+board |> pins::write_board_manifest()

inst/extdata/pins/_pins.yaml

@@ -12,5 +12,9 @@ msdrg_ccmcc_41.1:
 - msdrg_ccmcc_41.1/20240415T024824Z-61fa0/
 msdrg_drg_groups_41.1:
 - msdrg_drg_groups_41.1/20240417T055023Z-5ae76/
+msdrg_icd_ccs_41.1:
+- msdrg_icd_ccs_41.1/20240417T083635Z-0c4a4/
+msdrg_icd_mccs_41.1:
+- msdrg_icd_mccs_41.1/20240417T082757Z-dc7a7/
 msdrg_index_41.1:
 - msdrg_index_41.1/20240405T103150Z-3ca9d/

inst/extdata/pins/msdrg_icd_ccs_41.1/20240417T083635Z-0c4a4/data.txt

@@ -0,0 +1,12 @@
+file: msdrg_icd_ccs_41.qs
+file_size: 102992
+pin_hash: 0c4a423d52bd6b86
+type: qs
+title: Appendix G Diagnoses Defined as Complications or Comorbidities 41.1
+description: Diagnoses in Appendix G are considered complications or comorbidities
+  (CC) except when used in conjunction with the principal diagnosis in the corresponding
+  CC Exclusion List in Appendix C.
+tags: ~
+urls: ~
+created: 20240417T083635Z
+api_version: 1

inst/extdata/pins/msdrg_icd_mccs_41.1/20240417T082757Z-dc7a7/data.txt

@@ -0,0 +1,14 @@
+file: msdrg_icd_mccs_41.qs
+file_size: 13433
+pin_hash: dc7a76ff31084a35
+type: qs
+title: Appendix H Diagnoses Defined as Major Complications or Comorbidities 41.1
+description: Diagnoses in Appendix H Part I are considered major complications or
+  comorbidities (MCC) except when used in conjunction with the principal diagnosis
+  in the corresponding CC Exclusion List in Appendix C. In addition to the CC exclusion
+  list, the diagnoses in Part II are assigned as a major CC only for patients discharged
+  alive, otherwise they will be assigned as a non CC.
+tags: ~
+urls: ~
+created: 20240417T082757Z
+api_version: 1