data-raw/CCSR_DX.R

In vcastro/CCS: HCUP Clinical Classification Software (CCS) Mapping to Common Diagnosis and Procedure Codes

options(tidyverse.quiet = TRUE)
library(tidyverse)
source('data-raw/util.R')


##########################################################
###
### CCSR DX ICD-10
###
##########################################################

download_extract(url = "https://hcup-us.ahrq.gov/toolssoftware/ccsr/DXCCSR_v2025-1.zip",
                 exdir = "data-raw",
                 files = c("DXCCSR-Reference-File-v2025-1.xlsx"))


CCSR_DX_src <- readxl::read_xlsx("data-raw/DXCCSR-Reference-File-v2025-1.xlsx", 
                                 sheet = "CCSR_Categories",
                                 skip = 1)


# CCSR_DX_chapters <- tibble::tribble(
#   ~chapter_number, ~chapter_desc, ~chapter_abbr, 
#   1, "Certain infectious and parasitic diseases", "INF",
#   2, "Neoplasms", "NEO",
#   3, "Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism", "BLD",
#   4, "Endocrine, nutritional and metabolic diseases", "END",
#   5, "Mental, behavioral and neurodevelopmental disorders", "MBD",
#   6, "Diseases of the nervous system", "NVS",
#   7, "Diseases of the eye and adnexa", "EYE",
#   8, "Diseases of the ear and mastoid process", "EAR",
#   9, "Diseases of the circulatory system", "CIR",
#   10, "Diseases of the respiratory system", "RSP",
#   11, "Diseases of the digestive system", "DIG",
#   12, "Diseases of the skin and subcutaneous tissue", "SKN",
#   13, "Diseases of the musculoskeletal system and connective tissue", "MUS",
#   14, "Diseases of the genitourinary system", "GEN",
#   15, "Pregnancy, childbirth and the puerperium", "PRG",
#   16, "Certain conditions originating in the perinatal period", "PNL",
#   17, "Congenital malformations, deformations and chromosomal abnormalities", "MAL",
#   18, "Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified", "SYM",
#   19, "Injury, poisoning and certain other consequences of external causes", "INJ",
#   20, "External causes of morbidity", "EXT",
#   21, "Factors influencing health status and contact with health services", "FAC"
# )


CCSR_DX_chapters <- readxl::read_xlsx("data-raw/DXCCSR-Reference-File-v2025-1.xlsx", 
                                 sheet = "Naming_Conventions",
                                 skip = 1) %>% 
  mutate(chapter_number = row_number()) %>% 
  select(chapter_number,
         chapter_desc = `CCSR for ICD-10-CM Body System`,
         chapter_abbr = `3-Character Abbreviation`)


CCSR_DX_categories <- CCSR_DX_src %>% 
  mutate(chapter_abbr = substr(`CCSR Category`, 1, 3)) %>% 
  left_join(CCSR_DX_chapters, by="chapter_abbr") %>% 
  select(chapter_abbr, chapter_number, chapter_desc, 
         CCSR_category_code = `CCSR Category`, 
         CCSR_category_desc = `CCSR Category Description`) |> 
  filter(!grepl("XXX", CCSR_category_code))


CCSR_DX_map_src <- readxl::read_xlsx("data-raw/DXCCSR-Reference-File-v2025-1.xlsx", 
                                 sheet = "DX_to_CCSR_Mapping",
                                 skip = 1)


CCSR_DX_mapping <- CCSR_DX_map_src %>% 
  mutate(vocabulary_id = 'ICD10CM') %>% 
  select(CCSR_category_code = `CCSR Category`, vocabulary_id, 
         code = `ICD-10-CM Code`, 
         code_description = `ICD-10-CM Code Description` )





usethis::use_data(CCSR_DX_categories, overwrite=TRUE)
usethis::use_data(CCSR_DX_mapping, overwrite=TRUE)

# 
# QA
# CCSR_DX_mapping %>%
#   anti_join(CCSR_DX_categories, by = "CCSR_category_code")
# 
# CCSR_DX_categories %>%
#   anti_join(CCSR_DX_mapping, by = "CCSR_category_code")