completely updated antibiotics

data-raw/extractATCs.R

@@ -0,0 +1,105 @@
+library(rvest)
+library(dplyr)
+library(tidyr)
+library(AMR)
+# we need J01, J02 and J04 (J03 does not exist)
+
+url <- "https://www.whocc.no/atc_ddd_index/?code={code}&showdescription=no"
+complete_vector <- character(0)
+for (Jxx in c("J01", "J02", "J04")) {
+  site <- gsub("{code}", Jxx, url, fixed = TRUE)
+  tbl <- site |>
+    read_html() |>
+    html_element("#content") |>
+    html_text() |>
+    strsplit(Jxx, fixed = TRUE)
+  out <- paste0(Jxx, tbl[[1]])
+  out <- out[out %like% paste0(Jxx, "[A-Z0-9]")]
+  out <- gsub("(.*?)\n.*", "\\1", out)
+  complete_vector <- c(complete_vector, out)
+}
+
+next_codes <- gsub("(.*?) .*", "\\1", complete_vector)
+for (Jxxx in next_codes) {
+  site <- gsub("{code}", Jxxx, url, fixed = TRUE)
+  tbl <- site |>
+    read_html() |>
+    html_element("#content") |>
+    html_text() |>
+    strsplit(Jxxx, fixed = TRUE)
+  out <- paste0(Jxxx, tbl[[1]])
+  out <- out[out %like% paste0(Jxxx, "[A-Z0-9]")]
+  out <- gsub("(.*?)\n.*", "\\1", out)
+  complete_vector <- c(complete_vector, out)
+}
+
+next_codes <- gsub("(.*?) .*", "\\1", complete_vector[complete_vector %like% "[A-Z][0-9][0-9][A-Z][A-Z]"])
+complete_tbl <- NULL
+for (Jxxxxx in next_codes) {
+  message(Jxxxxx)
+  site <- gsub("{code}", Jxxxxx, url, fixed = TRUE)
+  tbl <- site |>
+    read_html() |>
+    html_element("table") |>
+    html_table(header = TRUE) |>
+    mutate_if(is.character, function(x) ifelse(x == "", NA_character_, x)) |>
+    fill(`ATC code`, Name, .direction = "down")
+  if (is.null(complete_tbl)) {
+    complete_tbl <- tbl
+  } else {
+    complete_tbl <- bind_rows(complete_tbl, tbl)
+  }
+}
+
+new_ab <- complete_tbl |>
+  select(atc = `ATC code`, name = Name, ddd = DDD, ddd_units = U, route = Adm.R) |>
+  filter(route %in% c("O", "P", NA)) |>
+  mutate(route = case_when(
+    route == "O" ~ "oral",
+    route == "P" ~ "iv",
+    TRUE ~ NA_character_
+  )) |>
+  pivot_wider(names_from = route, values_from = c(ddd, ddd_units), values_fn = first) |>
+  select(atc, name,
+    oral_ddd = ddd_oral, oral_units = ddd_units_oral,
+    iv_ddd = ddd_iv, iv_units = ddd_units_iv
+  ) |>
+  mutate(name = paste0(substr(toupper(name), 1, 1), substr(name, 2, 999))) |>
+  mutate(name = gsub(" and ", "/", name)) |>
+  filter(name %unlike% "^Combinations") |>
+  arrange(name)
+
+# check these - any new?
+new_ab |>
+  filter(!name %in% antibiotics$name | !atc %in% unlist(antibiotics$atc)) |>
+  mutate(
+    name_old = ab_name(atc, language = NULL),
+    new = !atc %in% unlist(antibiotics$atc)
+  ) |>
+  View()
+
+
+atc_ref <- antibiotics |>
+  select(ab, group, atc_group1, atc_group2) |>
+  mutate(atc = ab_atc(ab, only_first = TRUE)) |>
+  filter(!is.na(atc)) |>
+  mutate(atc = substr(atc, 1, 5)) |>
+  select(atc, everything(), -ab) |>
+  distinct() |>
+  arrange(atc)
+atc_ref <- atc_ref |>
+  arrange(atc, group, atc_group1, atc_group2) |>
+  distinct(atc, .keep_all = TRUE)
+
+antibiotics |>
+  bind_rows(new |>
+    select(-group, -atc_group1, -atc_group2) |>
+    left_join(atc_ref, by = c("atc_part" = "atc")) %>%
+    mutate(
+      atc = as.list(atc),
+      loinc = as.list(character(nrow(.))),
+      abbreviations = loinc,
+      synonyms = loinc
+    ) |>
+    select(-atc_part)) |>
+  View()