data-raw/coding-data.R

In asshah4/card: Cardiovascular Applications in Research Data

# Code to prepare `coding-data` dataset goes here

# ICD9 Procedure codes
# Most recent update is from 2014-10-01
icd9_2014 <-
	vroom::vroom_lines(system.file("data-raw", "icd9-2014-10-01.txt", package = "card")) |>
	stringr::str_split_fixed(pattern = " ", n = 2) |>
	tibble::as_tibble(.name_repair = NULL) |>
	dplyr::rename(code = V1, description = V2) |>
	dplyr::mutate(code = dplyr::if_else(nchar(code) == 3, paste0(code, "0"), code))

icd9 <- list(
	"2014" = icd9_2014
)

# ICD10 Procedure Codes
# Most recent update is from 2023-01-11
icd10_2023 <-
	vroom::vroom_lines(system.file("data-raw", "icd10-2023-01-11.txt", package = "card")) |>
	tibble::as_tibble(.name_repair = "unique") |>
	tibble::tibble(
		code = stringr::str_sub(value, 7, 13),
		description = stringr::str_sub(value, 78, nchar(value))
	) |>
	dplyr::mutate(description = tolower(description)) |>
	dplyr::select(-value)

icd10 <- list(
	"2023" = icd10_2023
)

# HCPCS codes
# Most recent update is from 2023-11-29
hcpcs_2023 <-
	vroom::vroom_lines(system.file("data-raw", "hcpcs-2023-11-29.txt", package = "card")) |>
	trimws() |>
	stringr::str_split_fixed(pattern = "\t", n = 2) |>
	tibble::as_tibble(.name_repair = NULL) |>
	dplyr::rename(code = V1, description = V2) |>
	dplyr::mutate(description = gsub("\\t", "", description)) |>
	dplyr::mutate(code = gsub("\"", "", code)) |>
	dplyr::mutate(code = gsub(" ", "", code))

hcpcs <- list(
	"2023" = hcpcs_2023
)

# CPT codes
# Most recent update is from 2023-11-29
cpt_2023 <-
	vroom::vroom(
		system.file("data-raw", "cpt-2023-11-29.txt", package = "card"),
		col_names = c("category", "code", "description"),
		delim = "\t",
		show_col_types = FALSE
	)

cpt <- list(
	"2023" = cpt_2023
)

# Combine the list of codes to be internally storied
.cms_codes <- list(
	icd9 = icd9,
	icd10 = icd10,
	hcpcs = hcpcs,
	cpt = cpt
)

# Save all this data to the package as internal data, compressed
usethis::use_data(
	.cms_codes,
	overwrite = TRUE,
	internal = TRUE
)