(v2.1.1.9154) documentation fix

man/plot.Rd

@@ -196,156 +196,3 @@ The interpretation of "I" will be named "Increased exposure" for all EUCAST guid
 For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
 }
 }
-\examples{
-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))
-
-
-# Plotting using base R's plot() ---------------------------------------
-
-plot(some_mic_values)
-plot(some_disk_values)
-plot(some_sir_values)
-
-# when providing the microorganism and antibiotic, colours will show interpretations:
-plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
-plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
-plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
-
-
-# Plotting using scale_x_mic() -----------------------------------------
-\donttest{
-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, 2))
-}
-
-
-# Plotting using scale_fill_mic() -----------------------------------------
-some_counts <- as.integer(runif(20, 5, 50))
-
-if (require("ggplot2")) {
-  ggplot(data.frame(mic = some_mic_values,
-                   group = some_groups,
-                   counts = some_counts),
-         aes(group, counts, fill = mic)) +
-    geom_col() +
-    scale_fill_mic(mic_range = c(0.5, 16))
-}
-
-# 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
-}
-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 = "nl", eucast_I = FALSE,
-                     name = "In Dutch!")
-}
-
-
-# Plotting using ggplot2's autoplot() ----------------------------------
-if (require("ggplot2")) {
-  autoplot(some_mic_values)
-}
-if (require("ggplot2")) {
-  autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
-}
-if (require("ggplot2")) {
-  autoplot(some_sir_values)
-}
-
-
-# Plotting using scale_y_percent() -------------------------------------
-if (require("ggplot2")) {
-  p <- 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 / sum(counts))) +
-    geom_col()
-  print(p)
-  
-  p2 <- p +
-    scale_y_percent() +
-    theme_sir()
-  print(p2)
-  
-  p +
-    scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
-                    limits = c(0, 1)) +
-    theme_sir()
-}
-}
-}