diff --git a/DESCRIPTION b/DESCRIPTION index 84e01ac5..b69a6bdf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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) diff --git a/NEWS.md b/NEWS.md index 55e6ba72..998f93f7 100755 --- a/NEWS.md +++ b/NEWS.md @@ -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 diff --git a/R/plot.R b/R/plot.R index 179ff836..312f0bae 100755 --- a/R/plot.R +++ b/R/plot.R @@ -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))) { diff --git a/R/sir.R b/R/sir.R index 50df07e0..5956b4ee 100755 --- a/R/sir.R +++ b/R/sir.R @@ -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 {