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(v3.0.1.9076) fix: normalise year-qualified AMR_guideline option in all affected functions
This commit is contained in:
Matthijs Berends
GitHub
@@ -1,6 +1,6 @@
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Package: AMR
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Version: 3.0.1.9077
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Date: 2026-06-26
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Version: 3.0.1.9078
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Date: 2026-06-27
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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3
NEWS.md
3
NEWS.md
@@ -1,4 +1,4 @@
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# AMR 3.0.1.9077
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# AMR 3.0.1.9078
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Planned as v3.1.0, end of June 2026.
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@@ -20,6 +20,7 @@ Planned as v3.1.0, end of June 2026.
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* New `wisca_plot()` to assess the susceptibility and incidence distributions from the Monte Carlo simulations
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### Fixed
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* Setting `options(AMR_guideline = "EUCAST 2012")` or any year-qualified value no longer causes errors or silent wrong behaviour in `interpretive_rules()`, `resistance()`, `susceptibility()`, `count_resistant()`, `count_susceptible()`, and SIR plotting/printing functions (#298)
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* `as.sir()`
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* On data frames: already-converted SIR columns no longer dropped on re-run (#278)
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* Metadata columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic columns
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10
R/count.R
10
R/count.R
@@ -126,6 +126,11 @@ count_resistant <- function(...,
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only_all_tested = FALSE,
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guideline = getOption("AMR_guideline", "EUCAST")) {
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# other arguments for meet_criteria are handled by sir_calc()
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
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message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
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@@ -150,6 +155,11 @@ count_susceptible <- function(...,
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only_all_tested = FALSE,
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guideline = getOption("AMR_guideline", "EUCAST")) {
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# other arguments for meet_criteria are handled by sir_calc()
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
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message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
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@@ -175,6 +175,11 @@ interpretive_rules <- function(x,
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...) {
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meet_criteria(x, allow_class = "data.frame")
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meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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meet_criteria(guideline, allow_class = "character", has_length = 1, is_in = c("EUCAST", "CLSI"))
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meet_criteria(info, allow_class = "logical", has_length = 1)
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meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5, 6), is_in = c("breakpoints", "expected_phenotypes", "expert", "other", "all", "custom"))
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@@ -200,12 +205,6 @@ interpretive_rules <- function(x,
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add_MO_lookup_to_AMR_env()
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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if ("custom" %in% rules && is.null(custom_rules)) {
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warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: no custom rules were set with the {.arg custom_rules} argument",
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immediate = TRUE
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@@ -482,7 +482,7 @@ scale_x_sir <- function(colours_SIR = c(
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R = "#ED553B"
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),
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language = get_AMR_locale(),
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eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
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eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
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...) {
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meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
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language <- validate_language(language)
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@@ -499,7 +499,7 @@ scale_colour_sir <- function(colours_SIR = c(
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R = "#ED553B"
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),
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language = get_AMR_locale(),
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eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
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eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
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...) {
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meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
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language <- validate_language(language)
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@@ -528,7 +528,7 @@ scale_fill_sir <- function(colours_SIR = c(
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R = "#ED553B"
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),
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language = get_AMR_locale(),
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eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
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eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
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...) {
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meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
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language <- validate_language(language)
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@@ -236,6 +236,11 @@ resistance <- function(...,
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only_all_tested = FALSE,
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guideline = getOption("AMR_guideline", "EUCAST")) {
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# other arguments for meet_criteria are handled by sir_calc()
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
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message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
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@@ -264,6 +269,11 @@ susceptibility <- function(...,
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only_all_tested = FALSE,
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guideline = getOption("AMR_guideline", "EUCAST")) {
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# other arguments for meet_criteria are handled by sir_calc()
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if (guideline %like% "EUCAST") {
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guideline <- "EUCAST"
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} else if (guideline %like% "CLSI") {
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guideline <- "CLSI"
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}
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
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message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
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2
R/sir.R
2
R/sir.R
@@ -2119,7 +2119,7 @@ pillar_shaft.sir <- function(x, ...) {
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out[is.na(x)] <- pillar::style_subtle(" NA")
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out[x == "S"] <- font_green_bg(" S ") # has font_black internally
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out[x == "SDD"] <- font_green_lighter_bg(" SDD ") # has font_black internally
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if (getOption("AMR_guideline", "EUCAST")[1] == "EUCAST") {
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if (getOption("AMR_guideline", "EUCAST")[1] %like% "EUCAST") {
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out[x == "I"] <- font_green_lighter_bg(" I ") # has font_black internally
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} else {
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out[x == "I"] <- font_orange_bg(" I ") # has font_black internally
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