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(v1.4.0.9031) as.ab() fix

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dr. M.S. (Matthijs) Berends
2020-12-03 22:30:14 +01:00
parent e03b3c96d3
commit fdf29e6c5b
15 changed files with 41 additions and 24 deletions
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6
R/ab.R
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@ -153,7 +153,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
}
if (isTRUE(flag_multiple_results) & x[i] %like% "[ ]") {
from_text <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]])
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]]),
error = function(e) character(0))
} else {
from_text <- character(0)
}
@ -345,7 +346,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
if (isTRUE(flag_multiple_results)) {
found <- from_text[1L]
} else {
found <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L])
found <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L]),
error = function(e) NA_character_)
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)

11
R/eucast_rules.R
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@ -38,12 +38,17 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
format_eucast_version_nr <- function(version) {
format_eucast_version_nr <- function(version, markdown = TRUE) {
# for documentation - adds title, version number, year and url in markdown language
lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
version <- format(version, nsmall = 1)
paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
" from ", lst[[version]]$year)
if (markdown == TRUE) {
paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
" from ", lst[[version]]$year)
} else {
paste0(lst[[version]]$title, " ", lst[[version]]$version_txt,
" from ", lst[[version]]$year)
}
}
#' Apply EUCAST rules

8
R/mo_property.R
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@ -386,6 +386,14 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
}
# show used version number once per session
if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) {
message_("Determining intrinsic resistance based on ",
AMR:::format_eucast_version_nr(3.2, FALSE), ". ",
font_bold("This message is shown once per session."))
options(AMR_intrinsic_resistance_note = "shown")
}
# this saves about 50% in calculation time
intrinsic_to_check <- intrinsic_resistant[which(intrinsic_resistant$microorganism %in% x |
intrinsic_resistant$antibiotic %in% ab), , drop = FALSE]