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()