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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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174
R/ab.R
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@ -97,21 +97,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
meet_criteria(flag_multiple_results, allow_class = "logical", has_length = 1)
language <- validate_language(language)
meet_criteria(info, allow_class = "logical", has_length = 1)
if (is.ab(x) || all(x %in% c(AMR_env$AB_lookup$ab, NA))) {
# all valid AB codes, but not yet right class or might have additional attributes as AMR selector
attributes(x) <- NULL
return(set_clean_class(x,
new_class = c("ab", "character")
new_class = c("ab", "character")
))
}
already_regex <- isTRUE(list(...)$already_regex)
fast_mode <- isTRUE(list(...)$fast_mode)
x_bak <- x
x <- toupper(x)
# remove diacritics
x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
x <- gsub('"', "", x, fixed = TRUE)
@ -122,13 +122,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
if (already_regex == FALSE) {
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
}
x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
x_new <- rep(NA_character_, length(x))
x_uncertain <- character(0)
x_unknown <- character(0)
x_unknown_ATCs <- character(0)
note_if_more_than_one_found <- function(found, index, from_text) {
if (isTRUE(length(from_text) > 1)) {
abnames <- ab_name(from_text, tolower = TRUE)
@ -149,7 +149,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
}
found[1L]
}
# Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
known_names <- x %in% AMR_env$AB_lookup$generalised_name
x_new[known_names] <- AMR_env$AB_lookup$ab[match(x[known_names], AMR_env$AB_lookup$generalised_name)]
@ -179,27 +179,27 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
" for ", vector_and(prev), ". Run `ab_reset_session()` to reset this. This note will be shown once per session for this input."
)
}
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid | previously_coerced
# fix for NAs
x_new[is.na(x)] <- NA
already_known[is.na(x)] <- FALSE
if (sum(already_known) < length(x)) {
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress))
}
for (i in which(!already_known)) {
progress$tick()
if (is.na(x[i]) || is.null(x[i])) {
next
}
if (identical(x[i], "") ||
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it:
identical(tolower(x[i]), "bacteria")) {
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it:
identical(tolower(x[i]), "bacteria")) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
next
}
@ -210,21 +210,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[i] <- NA_character_
next
}
if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
error = function(e) character(0)
error = function(e) character(0)
)
} else {
from_text <- character(0)
}
# old code for phenoxymethylpenicillin (Peni V)
if (x[i] == "PNV") {
x_new[i] <- "PHN"
next
}
# exact LOINC code
loinc_found <- unlist(lapply(
AMR_env$AB_lookup$generalised_loinc,
@ -235,7 +235,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact synonym
synonym_found <- unlist(lapply(
AMR_env$AB_lookup$generalised_synonyms,
@ -246,7 +246,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact abbreviation
abbr_found <- unlist(lapply(
AMR_env$AB_lookup$generalised_abbreviations,
@ -258,7 +258,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# length of input is quite long, and Levenshtein distance is only max 2
if (nchar(x[i]) >= 10) {
levenshtein <- as.double(utils::adist(x[i], AMR_env$AB_lookup$generalised_name))
@ -268,7 +268,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
}
# allow characters that resemble others, but only continue when having more than 3 characters
if (nchar(x[i]) <= 3) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
@ -298,22 +298,22 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_spelling <- gsub("(O|0)", "(O|0)+", x_spelling, perl = TRUE)
x_spelling <- gsub("++", "+", x_spelling, fixed = TRUE)
}
# try if name starts with it
found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0("^", x_spelling)), "ab", drop = TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try if name ends with it
found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# and try if any synonym starts with it
synonym_found <- unlist(lapply(
AMR_env$AB_lookup$generalised_synonyms,
@ -324,38 +324,46 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# More uncertain results ----
if (fast_mode == FALSE) {
ab_df <- AMR_env$AB_lookup
ab_df$length_name <- nchar(ab_df$generalised_name)
# now retrieve Levensthein distance for name, synonyms, and translated names
ab_df$lev_name <- as.double(utils::adist(x[i], ab_df$generalised_name,
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE))
ab_df$lev_syn <- vapply(FUN.VALUE = double(1),
ab_df$generalised_synonyms,
function(y) ifelse(length(y[nchar(y) >= 5]) == 0,
999,
min(as.double(utils::adist(x[i], y[nchar(y) >= 5], ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE)), na.rm = TRUE)),
USE.NAMES = FALSE)
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE
))
ab_df$lev_syn <- vapply(
FUN.VALUE = double(1),
ab_df$generalised_synonyms,
function(y) {
ifelse(length(y[nchar(y) >= 5]) == 0,
999,
min(as.double(utils::adist(x[i], y[nchar(y) >= 5],
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE
)), na.rm = TRUE)
)
},
USE.NAMES = FALSE
)
if (!is.null(language) && language != "en") {
ab_df$trans <- generalise_antibiotic_name(translate_AMR(ab_df$name, language = language))
ab_df$lev_trans <- as.double(utils::adist(x[i], ab_df$trans,
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE))
ignore.case = FALSE,
fixed = TRUE,
costs = c(insertions = 1, deletions = 1, substitutions = 2),
counts = FALSE
))
} else {
ab_df$lev_trans <- ab_df$lev_name
}
if (any(ab_df$lev_name < 5, na.rm = TRUE)) {
x_new[i] <- ab_df$ab[order(ab_df$lev_name)][1]
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
@ -379,15 +387,15 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
}
}
}
# nothing found
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}
if (sum(already_known) < length(x)) {
close(progress)
}
# save to package env to save time for next time
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$ab_previously_coerced <- unique(rbind_AMR(
@ -399,7 +407,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
stringsAsFactors = FALSE
)
))
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
warning_(
@ -407,7 +415,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
vector_and(x_unknown_ATCs), "."
)
}
# Throw note about uncertainties
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
x_unknown <- c(
@ -421,7 +429,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
vector_and(x_unknown), "."
)
}
# Throw note about uncertainties
if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
x_uncertain <- unique(x_uncertain)
@ -429,25 +437,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
if (length(x_uncertain) <= 3) {
examples <- vector_and(
paste0(
'"', x_uncertain, '" (assumed ',
'"', x_uncertain, '" (assumed ',
ab_name(AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], language = NULL, tolower = TRUE),
", ", AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], ")"),
quotes = FALSE)
", ", AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], ")"
),
quotes = FALSE
)
} else {
examples <- paste0(nr2char(length(x_uncertain)), " antimicrobials")
}
message_("Antimicrobial translation was uncertain for ", examples,
". If required, use `add_custom_antimicrobials()` to add custom entries.")
message_(
"Antimicrobial translation was uncertain for ", examples,
". If required, use `add_custom_antimicrobials()` to add custom entries."
)
}
}
x_result <- x_new[match(x_bak_clean, x)]
if (length(x_result) == 0) {
x_result <- NA_character_
}
set_clean_class(x_result,
new_class = c("ab", "character")
new_class = c("ab", "character")
)
}
@ -473,13 +485,15 @@ ab_reset_session <- function() {
pillar_shaft.ab <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_na(NA)
# add the names to the drugs as mouse-over!
if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
out[!is.na(x)] <- font_url(url = paste0(x[!is.na(x)], ": ", ab_name(x[!is.na(x)])),
txt = out[!is.na(x)])
out[!is.na(x)] <- font_url(
url = paste0(x[!is.na(x)], ": ", ab_name(x[!is.na(x)])),
txt = out[!is.na(x)]
)
}
create_pillar_column(out, align = "left", min_width = 4)
}
@ -494,12 +508,14 @@ type_sum.ab <- function(x, ...) {
print.ab <- function(x, ...) {
if (!is.null(attributes(x)$amr_selector)) {
function_name <- attributes(x)$amr_selector
message_("This 'ab' vector was retrieved using `" , function_name, "()`, which should normally be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
" ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
" ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
" ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]")
message_(
"This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
" ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
" ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
" ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
)
}
cat("Class 'ab'\n")
print(as.character(x), quote = FALSE)
@ -614,9 +630,9 @@ get_translate_ab <- function(translate_ab) {
} else {
translate_ab <- tolower(translate_ab)
stop_ifnot(translate_ab %in% colnames(AMR::antibiotics),
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
"invalid value for 'translate_ab', this must be a column name of the antibiotics data set\n",
"or TRUE (equals 'name') or FALSE to not translate at all.",
call = FALSE
)
translate_ab
}
@ -633,11 +649,11 @@ create_AB_AV_lookup <- function(df) {
new_df$generalised_all <- unname(lapply(
as.list(as.data.frame(
t(new_df[,
c(
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
colnames(new_df)[colnames(new_df) %like% "generalised"]
),
drop = FALSE
c(
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
colnames(new_df)[colnames(new_df) %like% "generalised"]
),
drop = FALSE
]),
stringsAsFactors = FALSE
)),