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(v2.1.1.9160) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-26 20:28:33 +01:00
parent 0c3ea4b538
commit 22e66741cc
13 changed files with 38 additions and 50 deletions
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45
R/ab.R
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@ -106,10 +106,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
))
}
loop_time <- list(...)$loop_time
if (is.null(loop_time)) {
loop_time <- 1
}
already_regex <- isTRUE(list(...)$already_regex)
fast_mode <- isTRUE(list(...)$fast_mode)
@ -134,8 +130,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_unknown_ATCs <- character(0)
note_if_more_than_one_found <- function(found, index, from_text) {
if (loop_time == 1 && isTRUE(length(from_text) > 1)) {
abnames <- ab_name(from_text, tolower = TRUE, loop_time = loop_time + 1)
if (isTRUE(length(from_text) > 1)) {
abnames <- ab_name(from_text, tolower = TRUE)
if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|(avi|tazo|mono|vabor)bactam)") {
abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam", "tazobactam", "vaborbactam", "monobactam")]
}
@ -190,15 +186,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[is.na(x)] <- NA
already_known[is.na(x)] <- FALSE
if (loop_time == 1 && sum(already_known) < length(x)) {
if (sum(already_known) < length(x)) {
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress))
}
for (i in which(!already_known)) {
if (loop_time == 1) {
progress$tick()
}
progress$tick()
if (is.na(x[i]) || is.null(x[i])) {
next
@ -218,7 +212,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
}
if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 1, translate_ab = FALSE)[[1]]),
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
error = function(e) character(0)
)
} else {
@ -331,9 +325,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
# INITIAL SEARCH - More uncertain results ----
if (loop_time == 1 && fast_mode == FALSE) {
# only run on first and second try
# More uncertain results ----
if (fast_mode == FALSE) {
ab_df <- AMR_env$AB_lookup
ab_df$length_name <- nchar(ab_df$generalised_name)
@ -391,23 +384,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}
if (loop_time == 1 && sum(already_known) < length(x)) {
if (sum(already_known) < length(x)) {
close(progress)
}
# save to package env to save time for next time
if (loop_time == 1) {
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$ab_previously_coerced <- unique(rbind_AMR(
AMR_env$ab_previously_coerced,
data.frame(
x = x,
ab = x_new,
x_bak = x_bak[match(x, x_bak_clean)],
stringsAsFactors = FALSE
)
))
}
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$ab_previously_coerced <- unique(rbind_AMR(
AMR_env$ab_previously_coerced,
data.frame(
x = x,
ab = x_new,
x_bak = x_bak[match(x, x_bak_clean)],
stringsAsFactors = FALSE
)
))
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {

10
R/custom_antimicrobials.R
View File

@ -69,11 +69,8 @@
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning (which is suppressed here):
#' suppressWarnings(
#' as.ab("testab")
#' )
#' # returns a wildly guessed result:
#' as.ab("testab")
#'
#' # now add a custom entry - it will be considered by as.ab() and
#' # all ab_*() functions
@ -109,6 +106,7 @@
#' ab_name("J01CR50")
#'
#' # even antimicrobial selectors work
#' # see ?amr_selector
#' x <- data.frame(
#' random_column = "some value",
#' coflu = as.sir("S"),
@ -155,7 +153,7 @@ add_custom_antimicrobials <- function(x) {
}
AMR_env$AB_lookup <- unique(rbind_AMR(AMR_env$AB_lookup, new_df))
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% x$ab), , drop = FALSE]
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE]
class(AMR_env$AB_lookup$ab) <- c("ab", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
}