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