(v3.0.1.9152) Let a named colours_SIR without S, I or R use the default colours for these, which fixes the example of ggplot_sir() with colours = c(SI = "yellow"), let ggplot_sir() pass the facet as a value to facet_sir(), and make the test of the eucast_I default independent of the AMR_guideline option

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9151
+Version: 3.0.1.9152
 Date: 2026-10-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9151
+# AMR 3.0.1.9152
 
 Planned as v3.1.0, mid October 2026.
 
@@ -136,7 +136,7 @@ Planned as v3.1.0, mid October 2026.
   * Fixed `barplot()` for SIR values, which gave NI, WT, and NWT the wrong colours, and always showed empty bars for WT, NWT, and NS. `barplot()` and `autoplot()` for SIR values now always show S and R, and all other values (such as SDD, I, WT, NWT, and NS) only when they occur. Data with only WT and NWT shows these two.
   * `autoplot()` for disk diffusion values now validates `include_PKPD` and `breakpoint_type`, and `plot()` and `autoplot()` for SIR values now validate `language`
   * The y axis of `plot()` and `barplot()` now has a readable number of tick marks for large counts, instead of one per count
-  * A named `colours_SIR` is now matched by name in all plotting functions, and needs at least the names S, I and R. SDD gets the colour of S if not set. Previously, the colours of S/I and I/R were taken by position, and a named vector of three colours gave missing colours.
+  * A named `colours_SIR` is now matched by name in all plotting functions, and S, I and R get their default colour if not set. SDD gets the colour of S if not set. Previously, the colours of S/I and I/R were taken by position, and a named vector of three colours gave missing colours.
   * `keep_operators = TRUE` and `FALSE` in the `scale_*_mic()` functions now behave like `"all"` and `"none"`, as in `as.mic()`
   * Fixed the `scale_*_sir()` functions failing when `values` was set. A named `values` (e.g., `values = c(S = "green")`) now replaces the colours of the SIR values it names, and `scale_x_sir()` warns that it ignores `values`.
   * Fixed `scale_x_sir()` ignoring other arguments, such as `name`

R/ggplot_sir.R

@@ -271,7 +271,8 @@ ggplot_sir <- function(data,
   }
 
   if (!is.null(facet)) {
-    p <- p + facet_sir(facet = facet, nrow = nrow)
+    # pass the value, as facet_sir() takes an unquoted name as column name
+    p <- p + do.call(facet_sir, list(facet = facet, nrow = nrow))
   }
 
   p <- p + ggplot2::labs(

R/plotting.R

@@ -39,7 +39,7 @@
 #' @param guideline Interpretation guideline to use - the default is the latest included EUCAST guideline, see *Details*.
 #' @param main,title Title of the plot.
 #' @param xlab,ylab Axis title.
-#' @param colours_SIR Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.
+#' @param colours_SIR Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with any of the names S, SDD, I, R, SI and IR. Missing names S, I and R get the default colour, and with three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.
 #' @param language Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the package option [`AMR_locale`][AMR-options], e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` to prevent translation.
 #' @param expand A [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
 #' @param aesthetics Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size".
@@ -1484,10 +1484,9 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
       all(names(colours_SIR) %in% sir_order),
       "Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(sir_order, quotes = FALSE, sort = FALSE), "."
     )
-    stop_ifnot(
-      all(c("S", "I", "R") %in% names(colours_SIR)),
-      "A named {.arg colours_SIR} must contain at least the names S, I and R."
-    )
+    # S, I and R get the default colours, unless set, e.g. for ggplot_sir(colours = c(SI = "yellow"))
+    default_colours <- c(S = "#3CAEA3", I = "#F6D55C", R = "#ED553B")
+    colours_SIR[setdiff(names(default_colours), names(colours_SIR))] <- default_colours[setdiff(names(default_colours), names(colours_SIR))]
   }
   # SDD and SI get the colour of S, and IR gets the colour of R, unless set
   colours_SIR[setdiff(c("SDD", "SI"), names(colours_SIR))] <- colours_SIR[["S"]]

man/plot.Rd

@@ -158,7 +158,7 @@ theme_sir()
 
 \item{...}{Arguments passed on to methods.}
 
-\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.}
+\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with any of the names S, SDD, I, R, SI and IR. Missing names S, I and R get the default colour, and with three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.}
 
 \item{language}{Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} to prevent translation.}
 

tests/testthat/test-ggplot_sir.R

@@ -59,6 +59,13 @@ test_that("test-ggplot_sir.R", {
         ggplot_sir(x = "antibiotic", facet = "interpretation"),
       "gg"
     )
+    # the facet is passed on as value, so the plot can be built
+    expect_inherits(
+      ggplot_build(example_isolates %>%
+        select(AMC, CIP) %>%
+        ggplot_sir(x = "interpretation", facet = "antibiotic")),
+      "ggplot_built"
+    )
 
     expect_equal(
       (example_isolates %>%

tests/testthat/test-plotting.R

@@ -120,6 +120,8 @@ test_that("test-plotting.R", {
     expect_identical(AMR:::expand_SIR_colours(c(S = "s", I = "i", R = "r")), c("s", "s", "i", "r", "s", "r"))
     expect_identical(AMR:::expand_SIR_colours(c("s", "i", "r")), c("s", "s", "i", "r", "s", "r"))
     expect_error(AMR:::expand_SIR_colours(c(S = "s", I = "i", X = "r")))
+    # missing names S, I and R get the default colours, as in the example of ggplot_sir()
+    expect_identical(AMR:::expand_SIR_colours(c(SI = "y")), c("#3CAEA3", "#3CAEA3", "#F6D55C", "#ED553B", "y", "#ED553B"))
 
     # colours of SIR bar plots follow the SIR values
     sir_values <- as.sir(c("S", "S", "R", "NI", "NS"))
@@ -153,8 +155,11 @@ test_that("test-plotting.R", {
     expect_identical(facet_sir(antibiotic)$params$facets, facet_sir("antibiotic")$params$facets)
 
     # the default of eucast_I follows the guideline option
+    old_option <- options(AMR_guideline = "EUCAST")
     expect_identical(scale_fill_sir(language = "en")$labels("I"), "(I) Susceptible, incr. exp.")
-    old_option <- options(AMR_guideline = "EUCAST 2018")
+    options(AMR_guideline = "EUCAST 2018")
+    expect_identical(scale_fill_sir(language = "en")$labels("I"), "(I) Intermediate")
+    options(AMR_guideline = "CLSI")
     expect_identical(scale_fill_sir(language = "en")$labels("I"), "(I) Intermediate")
     options(old_option)