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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
parent 8d8444c607
commit 4dc4398ad1
23 changed files with 543 additions and 440 deletions
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31
data-raw/extractATCs.R
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@ -19,8 +19,10 @@ for (Jxx in c("J01", "J02", "J04")) {
complete_vector <- c(complete_vector, out)
}
complete_vector.bak <- complete_vector
next_codes <- gsub("(.*?) .*", "\\1", complete_vector)
for (Jxxx in next_codes) {
message("Checking ", Jxxx)
site <- gsub("{code}", Jxxx, url, fixed = TRUE)
tbl <- site |>
read_html() |>
@ -36,7 +38,7 @@ for (Jxxx in next_codes) {
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)
message("Checking ", Jxxxxx)
site <- gsub("{code}", Jxxxxx, url, fixed = TRUE)
tbl <- site |>
read_html() |>
@ -66,20 +68,37 @@ new_ab <- complete_tbl |>
) |>
mutate(name = paste0(substr(toupper(name), 1, 1), substr(name, 2, 999))) |>
mutate(name = gsub(" and ", "/", name)) |>
filter(name %unlike% "^Combinations") |>
filter(name %unlike% "^Combinations",
name %unlike% "/beta[-]lactamase inhibitor",
name %unlike% "combinations") |>
arrange(name)
new_atcs <- new_ab |>
mutate(name_gen = generalise_antibiotic_name(name)) |>
filter(name_gen %in% AMR_env$AB_lookup$generalised_name) |>
mutate(ab = as.ab(name_gen))
new_atcs$atc_group1 <- complete_vector
for (i in seq_len(nrow(new_atcs))) {
# fill in DDDs and ATC code
antimicrobials$oral_ddd[which(antimicrobials$ab == new_atcs$ab[i])] <- new_atcs$oral_ddd[i]
antimicrobials$oral_units[which(antimicrobials$ab == new_atcs$ab[i])] <- new_atcs$oral_units[i]
antimicrobials$iv_ddd[which(antimicrobials$ab == new_atcs$ab[i])] <- new_atcs$iv_ddd[i]
antimicrobials$iv_units[which(antimicrobials$ab == new_atcs$ab[i])] <- new_atcs$iv_units[i]
antimicrobials$atc[which(antimicrobials$ab == new_atcs$ab[i])] <- list(c(antimicrobials$atc[which(antimicrobials$ab == new_atcs$ab[i])][[1]], new_atcs$atc[i]))
}
# check these - any new?
new_ab |>
filter(!name %in% antibiotics$name | !atc %in% unlist(antibiotics$atc)) |>
filter(!name %in% antimicrobials$name | !atc %in% unlist(antimicrobials$atc)) |>
mutate(
name_old = ab_name(atc, language = NULL),
new = !atc %in% unlist(antibiotics$atc)
new = !atc %in% unlist(antimicrobials$atc)
) |>
View()
atc_ref <- antibiotics |>
atc_ref <- antimicrobials |>
select(ab, group, atc_group1, atc_group2) |>
mutate(atc = ab_atc(ab, only_first = TRUE)) |>
filter(!is.na(atc)) |>
@ -91,7 +110,7 @@ atc_ref <- atc_ref |>
arrange(atc, group, atc_group1, atc_group2) |>
distinct(atc, .keep_all = TRUE)
antibiotics |>
antimicrobials |>
bind_rows(new |>
select(-group, -atc_group1, -atc_group2) |>
left_join(atc_ref, by = c("atc_part" = "atc")) %>%