data-raw/04_seer-icd-o-3.R

In GerkeLab/fcds: Process Data from the Florida Cancer Data System

fcds:::requires_package(c("here", "rvest", "readxl"), "icd-o-3 import")

library(rvest)
library(readxl)
library(dplyr)

seer_icdo3_base_url <- "https://seer.cancer.gov/icd-o-3"
seer_icdo3 <- read_html(seer_icdo3_base_url)

seer_icdo3_xls <-
  seer_icdo3 %>%
  xml_nodes("a") %>%
  xml_attr("href") %>%
  grep("icdo3.+xlsx?$", ., value = TRUE) %>%
  file.path(seer_icdo3_base_url, .)

# seer_icdo3_xls <- "sitetype.icdo3.20180323.xls"
seer_icdo3_file <- here::here("data-raw", basename(seer_icdo3_xls))
download.file(seer_icdo3_xls, seer_icdo3_file)

seer_icd_o_3_raw <- read_excel(seer_icdo3_file)

seer_icd_o_3 <-
  seer_icd_o_3_raw %>%
  rename_all(fcds:::to_snake_case) %>%
  select(-site_recode) %>%
  # Rename columns to match FCDS data names
  rename(
    site_group = site_description,
    morphology = histology_behavior,
    morphology_description = histology_behavior_description
  ) %>%
  mutate(
    histology_detail = substr(morphology, 4, 4),
    histology = paste0(histology, histology_detail)
  ) %>%
  select(-histology_detail) %>%
  mutate_at(quos(site_group, contains("description")), ~ {
    x <- tolower(purrr::set_names(unique(.x)))
    x <- tools::toTitleCase(x)
    x <- sub("\\b[Nn]os", "NOS", x)
    factor(x[.x])
  })

usethis::use_data(seer_icd_o_3, compress = "xz", overwrite = TRUE)