# 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())
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