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AMR
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dr. M.S. (Matthijs) Berends 2023-07-10 17:02:28 +02:00
parent a4e2e25e3f
commit 1b499bf012
4 changed files with 15 additions and 13 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.0.0.9030
Version: 2.0.0.9031
Date: 2023-07-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.0.0.9030
# AMR 2.0.0.9031
## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

11
R/plot.R
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@ -763,6 +763,12 @@ plot_name_of_I <- function(guideline) {
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, fn, language, method, breakpoint_type, include_PKPD, ...) {
guideline <- get_guideline(guideline, AMR::clinical_breakpoints)
# store previous interpretations to backup
sir_history <- AMR_env$sir_interpretation_history
# and clear previous interpretations
AMR_env$sir_interpretation_history <- AMR_env$sir_interpretation_history[0, , drop = FALSE]
if (!is.null(mo) && !is.null(ab)) {
# interpret and give colour based on MIC values
mo <- as.mo(mo)
@ -770,11 +776,6 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
ab <- as.ab(ab)
abname <- ab_name(ab, language = language)
# store previous interpretations to backup
sir_history <- AMR_env$sir_interpretation_history
# and clear previous interpretations
AMR_env$sir_interpretation_history <- AMR_env$sir_interpretation_history[0, , drop = FALSE]
sir <- suppressWarnings(suppressMessages(as.sir(fn(names(x)), mo = mo, ab = ab, guideline = guideline, include_screening = FALSE, include_PKPD = include_PKPD, breakpoint_type = breakpoint_type, ...)))
guideline_txt <- guideline
if (all(is.na(sir))) {

13
R/sir.R
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@ -911,11 +911,12 @@ as_sir_method <- function(method_short,
msgs <- character(0)
if (nrow(breakpoints) == 0) {
# apparently no breakpoints found
msg_note(paste0(
"No ", method_coerced, " breakpoints available for ",
suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
" (", ab_coerced, ")"
))
message(
paste0(font_rose_bg(" WARNING "), "\n"),
font_black(paste0(" ", AMR_env$bullet_icon, " No ", method_coerced, " breakpoints available for ",
suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
" (", ab_coerced, ")")))
load_mo_uncertainties(metadata_mo)
return(rep(NA_sir_, nrow(df)))
}
@ -1090,7 +1091,7 @@ as_sir_method <- function(method_short,
message_(intro_txt, appendLF = FALSE, as_note = FALSE)
}
if (isTRUE(rise_warning)) {
message(font_rose_bg(" * WARNING *"))
message(font_rose_bg(" WARNING "))
} else if (length(msgs) == 0) {
message(font_green_bg(" OK "))
} else {