some_mic_values <- random_mic(size = 100)
+some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
+some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
+
+
+# \donttest{
+# Plotting using ggplot2's autoplot() for MIC, disk, and SIR -----------
+if (require("ggplot2")) {
+ autoplot(some_mic_values)
+}
+
+if (require("ggplot2")) {
+ # when providing the microorganism and antibiotic, colours will show interpretations:
+ autoplot(some_mic_values, mo = "Escherichia coli", ab = "cipro")
+}
+
+if (require("ggplot2")) {
+ # support for 20 languages, various guidelines, and many options
+ autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro",
+ guideline = "CLSI 2024", language = "no",
+ title = "Disk diffusion from the North")
+}
+
+
+
+# Plotting using scale_x_mic() -----------------------------------------
+if (require("ggplot2")) {
+ mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
+ counts = c(1, 1, 2, 2, 3, 3)),
+ aes(mics, counts)) +
+ geom_col()
+ mic_plot +
+ labs(title = "without scale_x_mic()")
+}
+
+if (require("ggplot2")) {
+ mic_plot +
+ scale_x_mic() +
+ labs(title = "with scale_x_mic()")
+}
+
+if (require("ggplot2")) {
+ mic_plot +
+ scale_x_mic(keep_operators = "all") +
+ labs(title = "with scale_x_mic() keeping all operators")
+}
+
+if (require("ggplot2")) {
+ mic_plot +
+ scale_x_mic(mic_range = c(1, 16)) +
+ labs(title = "with scale_x_mic() using a manual 'within' range")
+}
+
+if (require("ggplot2")) {
+ mic_plot +
+ scale_x_mic(mic_range = c(0.032, 256)) +
+ labs(title = "with scale_x_mic() using a manual 'outside' range")
+}
+
+
+
+# Plotting using scale_y_mic() -----------------------------------------
+some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
+
+if (require("ggplot2")) {
+ ggplot(data.frame(mic = some_mic_values,
+ group = some_groups),
+ aes(group, mic)) +
+ geom_boxplot() +
+ geom_violin(linetype = 2, colour = "grey", fill = NA) +
+ scale_y_mic()
+}
+
+if (require("ggplot2")) {
+ ggplot(data.frame(mic = some_mic_values,
+ group = some_groups),
+ aes(group, mic)) +
+ geom_boxplot() +
+ geom_violin(linetype = 2, colour = "grey", fill = NA) +
+ scale_y_mic(mic_range = c(NA, 0.25))
+}
+
+
+
+# Plotting using scale_x_sir() -----------------------------------------
+if (require("ggplot2")) {
+ ggplot(data.frame(x = c("I", "R", "S"),
+ y = c(45,323, 573)),
+ aes(x, y)) +
+ geom_col() +
+ scale_x_sir()
+}
+
+
+
+# Plotting using scale_y_mic() and scale_colour_sir() ------------------
+if (require("ggplot2")) {
+ plain <- ggplot(data.frame(mic = some_mic_values,
+ group = some_groups,
+ sir = as.sir(some_mic_values,
+ mo = "E. coli",
+ ab = "cipro")),
+ aes(x = group, y = mic, colour = sir)) +
+ theme_minimal() +
+ geom_boxplot(fill = NA, colour = "grey") +
+ geom_jitter(width = 0.25)
+
+ plain
+}
+#>
+#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
+#> all the details of the breakpoint interpretations.
+#>
+#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), EUCAST 2024...
+#> NOTE
+#> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.
+
+if (require("ggplot2")) {
+ # and now with our MIC and SIR scale functions:
+ plain +
+ scale_y_mic() +
+ scale_colour_sir()
+}
+
+if (require("ggplot2")) {
+ plain +
+ scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
+ scale_colour_sir(language = "pt",
+ name = "Support in 20 languages")
+}
+
+# }
+
+# Plotting using base R's plot() ---------------------------------------
+
+plot(some_mic_values)
+
+# when providing the microorganism and antibiotic, colours will show interpretations:
+plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
+
+
+plot(some_disk_values)
+
+plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
+
+plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
+
+
+plot(some_sir_values)
+
+