mirror of
https://github.com/msberends/AMR.git
synced 2026-06-29 10:56:21 +02:00
(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 @@
|
||||
Package: AMR
|
||||
Version: 3.0.1.9077
|
||||
Date: 2026-06-26
|
||||
Version: 3.0.1.9078
|
||||
Date: 2026-06-27
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
|
||||
3
NEWS.md
3
NEWS.md
@@ -1,4 +1,4 @@
|
||||
# AMR 3.0.1.9077
|
||||
# AMR 3.0.1.9078
|
||||
|
||||
Planned as v3.1.0, end of June 2026.
|
||||
|
||||
@@ -20,6 +20,7 @@ Planned as v3.1.0, end of June 2026.
|
||||
* New `wisca_plot()` to assess the susceptibility and incidence distributions from the Monte Carlo simulations
|
||||
|
||||
### Fixed
|
||||
* 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)
|
||||
* `as.sir()`
|
||||
* On data frames: already-converted SIR columns no longer dropped on re-run (#278)
|
||||
* Metadata columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic columns
|
||||
|
||||
10
R/count.R
10
R/count.R
@@ -126,6 +126,11 @@ count_resistant <- function(...,
|
||||
only_all_tested = FALSE,
|
||||
guideline = getOption("AMR_guideline", "EUCAST")) {
|
||||
# other arguments for meet_criteria are handled by sir_calc()
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
|
||||
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
|
||||
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)}.")
|
||||
@@ -150,6 +155,11 @@ count_susceptible <- function(...,
|
||||
only_all_tested = FALSE,
|
||||
guideline = getOption("AMR_guideline", "EUCAST")) {
|
||||
# other arguments for meet_criteria are handled by sir_calc()
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
|
||||
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
|
||||
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)}.")
|
||||
|
||||
@@ -175,6 +175,11 @@ interpretive_rules <- function(x,
|
||||
...) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1, is_in = c("EUCAST", "CLSI"))
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
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"))
|
||||
@@ -200,12 +205,6 @@ interpretive_rules <- function(x,
|
||||
|
||||
add_MO_lookup_to_AMR_env()
|
||||
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
|
||||
if ("custom" %in% rules && is.null(custom_rules)) {
|
||||
warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: no custom rules were set with the {.arg custom_rules} argument",
|
||||
immediate = TRUE
|
||||
|
||||
@@ -482,7 +482,7 @@ scale_x_sir <- function(colours_SIR = c(
|
||||
R = "#ED553B"
|
||||
),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
|
||||
...) {
|
||||
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
|
||||
language <- validate_language(language)
|
||||
@@ -499,7 +499,7 @@ scale_colour_sir <- function(colours_SIR = c(
|
||||
R = "#ED553B"
|
||||
),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
|
||||
...) {
|
||||
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
|
||||
language <- validate_language(language)
|
||||
@@ -528,7 +528,7 @@ scale_fill_sir <- function(colours_SIR = c(
|
||||
R = "#ED553B"
|
||||
),
|
||||
language = get_AMR_locale(),
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
|
||||
eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
|
||||
...) {
|
||||
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
|
||||
language <- validate_language(language)
|
||||
|
||||
@@ -236,6 +236,11 @@ resistance <- function(...,
|
||||
only_all_tested = FALSE,
|
||||
guideline = getOption("AMR_guideline", "EUCAST")) {
|
||||
# other arguments for meet_criteria are handled by sir_calc()
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
|
||||
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
|
||||
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)}.")
|
||||
@@ -264,6 +269,11 @@ susceptibility <- function(...,
|
||||
only_all_tested = FALSE,
|
||||
guideline = getOption("AMR_guideline", "EUCAST")) {
|
||||
# other arguments for meet_criteria are handled by sir_calc()
|
||||
if (guideline %like% "EUCAST") {
|
||||
guideline <- "EUCAST"
|
||||
} else if (guideline %like% "CLSI") {
|
||||
guideline <- "CLSI"
|
||||
}
|
||||
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
|
||||
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
|
||||
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)}.")
|
||||
|
||||
2
R/sir.R
2
R/sir.R
@@ -2119,7 +2119,7 @@ pillar_shaft.sir <- function(x, ...) {
|
||||
out[is.na(x)] <- pillar::style_subtle(" NA")
|
||||
out[x == "S"] <- font_green_bg(" S ") # has font_black internally
|
||||
out[x == "SDD"] <- font_green_lighter_bg(" SDD ") # has font_black internally
|
||||
if (getOption("AMR_guideline", "EUCAST")[1] == "EUCAST") {
|
||||
if (getOption("AMR_guideline", "EUCAST")[1] %like% "EUCAST") {
|
||||
out[x == "I"] <- font_green_lighter_bg(" I ") # has font_black internally
|
||||
} else {
|
||||
out[x == "I"] <- font_orange_bg(" I ") # has font_black internally
|
||||
|
||||
Reference in New Issue
Block a user