data-raw/classcodes.R

In eribul/classifyr: Deterministic Categorization of Items Based on External Code Data

# All classcodes from Excel file

rm(list = ls())

xl_path <- "data-raw/classcodes.xlsx"

# Read all classcodes from excel-file and give attributes
tibble::tibble(names = readxl::excel_sheets(xl_path)) %>%
mutate(
  data  = map(names, ~ readxl::read_excel(xl_path, .)),
  classcode = map(data, as.classcodes) %>%
              set_names(names)
) %>%
{attach(.$classcode)} # Must be able to refer to each object by name in use_data



# hip_ae ---------------------------------------------------

# There are some additional ICD-10 codes used for hip fractures.
# https://registercentrum.blob.core.windows.net/shpr/r/-rsrapport-2017-S1xKMzsAwX.pdf
# p. 149
# I do not want to make a manual copy of all those codes but simply add a
# fracture column based on existing codes.
hip_ae$icd10_fracture <-
  if_else(
    hip_ae$group == "DM1 other",
    paste0(hip_ae$icd10, "|N3(0[089]|90)"),
    hip_ae$icd10
  )
attr(hip_ae, "regexprs") <- c(attr(hip_ae, "regexprs"), "icd10_fracture")


# Elixhauser --------------------------------------------------------------

attr(elixhauser, "hierarchy") <-
  list(
    cancer   = c("metastatic cancer", "solid tumor"),
    diabetes = c("diabetes uncomplicated", "diabetes complicated")
  )

# Save all datasets. Must be referred by name directly (could use rlang maybe)
usethis::use_data(
  charlson,
  elixhauser,
  hip_ae,
  hip_ae_hailer,
  knee_ae,
  cps,
  rxriskv,
  overwrite = TRUE
)

rm(list = ls())