added appendix D pin (#2)

NAMESPACE

@@ -4,6 +4,7 @@ export(add_dot)
 export(appendix_A)
 export(appendix_B)
 export(appendix_C)
+export(appendix_D)
 export(apply_age_edits)
 export(case_chapter_icd10)
 export(ex_data)

R/appendices.R

@@ -65,8 +65,8 @@ appendix_B <- function() {
 #' complication or comorbidity (CC) or a major complication or comorbidity (MCC)
 #' when used as a secondary diagnosis.
 #'
-#' Part 1 lists these codes. Each code is indicated as CC or MCC. A link is given
-#' to a collection of diagnosis codes which, when used as the principal
+#' Part 1 lists these codes. Each code is indicated as CC or MCC. A link is
+#' given to a collection of diagnosis codes which, when used as the principal
 #' diagnosis, will cause the CC or MCC to be considered as only a non-CC.
 #'
 #' Part 2 lists codes which are assigned as a Major CC only for patients
@@ -75,12 +75,15 @@ appendix_B <- function() {
 #' Part 3 lists diagnosis codes that are designated as a complication or
 #' comorbidity (CC) or major complication or comorbidity (MCC) and included in
 #' the definition of the logic for the listed DRGs. When reported as a secondary
-#' diagnosis and grouped to one of the listed DRGs the diagnosis is excluded from
-#' acting as a CC/MCC for severity in DRG assignment.
+#' diagnosis and grouped to one of the listed DRGs the diagnosis is excluded
+#' from acting as a CC/MCC for severity in DRG assignment.
 #'
 #' @template args-icd_code
 #'
-#' @param pdx `<chr>` 4-digit Principal Diagnosis (PDX) Group number
+#' @param pdx `<chr>` 4-digit Principal Diagnosis (PDX) Group number, e.g.,
+#'   `0011` (~ 2,040 in total)
+#'
+#' @param unnest `<lgl>` Unnest the `pdx_icd` column
 #'
 #' @template args-dots
 #'
@@ -96,6 +99,7 @@ appendix_B <- function() {
 #' @export
 appendix_C <- function(icd = NULL,
                        pdx = NULL,
+                       unnest = FALSE,
                        ...) {
 
   mcc <- pins::pin_read(mount_board(), "msdrg_ccmcc_41.1")
@@ -106,3 +110,53 @@ appendix_C <- function(icd = NULL,
 
   return(mcc)
 }
+
+
+#' 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
+#' hierarchical order.
+#'
+#' Patients with multiple procedures are assigned to the highest surgical class
+#' in the hierarchy to which one of the procedures is assigned. Thus, if a
+#' patient receives both a D&C and a hysterectomy, the patient is assigned to the
+#' hysterectomy surgical class because a hysterectomy is higher in the hierarchy
+#' than a D&C. Because of the surgical hierarchy, ordering of the surgical
+#' procedures on the patient abstract or claim has no influence on the assignment
+#' of the surgical class and the MS-DRG. The surgical hierarchy for each MDC
+#' reflects the relative resource requirements of various surgical procedures.
+#'
+#' In some cases a surgical class in the hierarchy is actually an MS-DRG. For
+#' example, Arthroscopy is both a surgical class in the hierarchy and MS-DRG 509
+#' in MDC 8, Diseases and Disorders of the Musculoskeletal System and Connective
+#' Tissue.
+#'
+#' In other cases the surgical class in the hierarchy is further partitioned
+#' based on other variables such as complications and comorbidities, or principal
+#' diagnosis to form multiple MS-DRGs. As an example, in MDC 5, Diseases and
+#' Disorders of the Circulatory System, the surgical class for permanent
+#' pacemaker implantation is divided into three MS-DRGs (242-244) based on
+#' whether or not the patient had no CCs, a CC or an MCC.
+#'
+#' Appendix D presents the surgical hierarchy for each MDC. Appendix D is
+#' organized by MDC with a list of the surgical classes associated with that MDC
+#' listed in hierarchical order as well as the MS-DRGs that are included in each
+#' surgical class.
+#'
+#' The names given to the surgical classes in the hierarchy correspond to the
+#' names used in the MS-DRG logic tables and in the body of the Definitions
+#' Manual.
+#'
+#' @template returns
+#'
+#' @examples
+#' head(appendix_D())
+#'
+#' @autoglobal
+#'
+#' @export
+appendix_D <- function() {
+  pins::pin_read(mount_board(), "msdrg_drg_groups_41.1")
+}

data-raw/appendixD.R

@@ -35,15 +35,97 @@
 # names used in the MS-DRG logic tables and in the body of the Definitions
 # Manual.
 
+library(tidyverse)
+
 path_d <- "C:/Users/Andrew/Desktop/payer_guidelines/data/MSDRG/MSDRGv41.1ICD10_R0_DefinitionsManual_TEXT_0/appendix_D.txt"
 
+dfile <- readr::read_table(
+  path_d,
+  skip = 27,
+  col_names = FALSE) |>
+  dplyr::mutate(row = dplyr::row_number(), .before = 1) |>
+  dplyr::slice(2:dplyr::n()) |>
+  tidyr::unite("drg_group_description", X2:X12, na.rm = TRUE, sep = " ") |>
+  dplyr::rename(drg_groups = X1)
+
+
+drows <- dfile |>
+  dplyr::filter(drg_groups == "MDC") |>
+  dplyr::mutate(end = lead(row) - 1,
+                drg_groups = NULL) |>
+  dplyr::mutate(mdc_group = substr(drg_group_description, 1, 2),
+                mdc_group_description = substr(drg_group_description, 4, 100),
+                drg_group_description = NULL)
+
+
+
+dfinal <- dfile |>
+  dplyr::left_join(drows) |>
+  dplyr::mutate(end = NULL) |>
+  tidyr::fill(mdc_group, mdc_group_description) |>
+  tidyr::separate_longer_delim(cols = drg_groups, delim = "-") |>
+  dplyr::select(
+    mdc = mdc_group,
+    mdc_description = mdc_group_description,
+    drg_group = drg_groups,
+    drg_group_description = drg_group_description
+    ) |>
+  dplyr::filter(drg_group != "MDC")
+
+
+# Update Pin
+board <- pins::board_folder(here::here("inst/extdata/pins"))
+
+board |> pins::pin_write(
+  dfinal,
+  name = "msdrg_drg_groups_41.1",
+  title = "Appendix D MS-DRG Surgical Hierarchy by MDC and MS-DRG 41.1",
+  description = c(
+    "Appendix D presents the surgical hierarchy for each MDC. Appendix D is organized by MDC with a list of the surgical classes associated with that MDC listed in hierarchical order as well as the MS-DRGs that are included in each surgical class."
+  ),
+  type = "qs"
+)
+
+board |> pins::write_board_manifest()
+
+
+mdcs <- dplyr::tribble(
+  ~mdc, ~mdc_description,
+  "00", "Pre-MDC",
+  "01", "Diseases and disorders of the nervous system",
+  "02", "Diseases and disorders of the eye",
+  "03", "Diseases and disorders of the ear, nose, mouth, and throat",
+  "04", "Diseases and disorders of the respiratory system",
+  "05", "Diseases and disorders of the circulatory system",
+  "06", "Diseases and disorders of the digestive system",
+  "07", "Diseases and disorders of the hepatobiliary system and pancreas",
+  "08", "Diseases and disorders of the musculoskeletal system and connective tissue",
+  "09", "Diseases and disorders of the skin, subcutaneous tissue, and breast",
+  "10", "Endocrine, nutritional and metabolic diseases and disorders",
+  "11", "Diseases and disorders of the kidney and urinary tract",
+  "12", "Diseases and disorders of the male reproductive system",
+  "13", "Diseases and disorders of the female reproductive system",
+  "14", "Pregnancy, childbirth and the puerperium",
+  "15", "Newborns and other neonates with conditions originating in the perinatal period",
+  "16", "Diseases and disorders of blood, blood forming organs and immunological disorders",
+  "17", "Myeloproliferative diseases and disorders, poor blood cell formation",
+  "18", "Infectious and parasitic diseases",
+  "19", "Mental diseases and disorders",
+  "20", "Alcohol/drug use and alcohol/drug induced organic mental disorders",
+  "21", "Injuries, poisonings and toxic effects of drugs",
+  "22", "Burns",
+  "23", "Factors influencing health status and other contacts with health services",
+  "24", "Multiple significant trauma",
+  "25", "Human immunodeficiency virus infections",
+)
+
 readr::read_fwf(
   path_d,
   readr::fwf_cols(
     icd_code = c(1, 7),
     cc_mcc = c(9, 12),
     pdx_group = c(14, sum(14 + 5)),
-    icd_description = c(31, 500)
+    icd_description = c(31, 500),
   )
 ) |>
   tidyr::separate_wider_delim(

inst/extdata/pins/_pins.yaml

@@ -10,5 +10,7 @@ msdrg_41.1:
 - msdrg_41.1/20240405T103411Z-1ed8e/
 msdrg_ccmcc_41.1:
 - msdrg_ccmcc_41.1/20240415T024824Z-61fa0/
+msdrg_drg_groups_41.1:
+- msdrg_drg_groups_41.1/20240417T055023Z-5ae76/
 msdrg_index_41.1:
 - msdrg_index_41.1/20240405T103150Z-3ca9d/

inst/extdata/pins/msdrg_drg_groups_41.1/20240417T055023Z-5ae76/data.txt

@@ -0,0 +1,13 @@
+file: msdrg_drg_groups_41.qs
+file_size: 4153
+pin_hash: 5ae76dedd2b23d07
+type: qs
+title: Appendix D MS-DRG Surgical Hierarchy by MDC and MS-DRG 41.1
+description: Appendix D presents the surgical hierarchy for each MDC. Appendix D is
+  organized by MDC with a list of the surgical classes associated with that MDC listed
+  in hierarchical order as well as the MS-DRGs that are included in each surgical
+  class.
+tags: ~
+urls: ~
+created: 20240417T055023Z
+api_version: 1