scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
- ...)
+ scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
-scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
- ...)
+scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
-scale_colour_mic(keep_operators = "edges", mic_range = NULL,
- drop = FALSE, ...)
+scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
-scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
- ...)
+scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
+
+scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
# S3 method for class 'mic'
plot(x, mo = NULL, ab = NULL, guideline = "EUCAST",
@@ -154,11 +152,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
mic_range
-a manual range to limit the MIC values, e.g., mic_range = c(0.001, 32). Use NA to set no limit on one side, e.g., mic_range = c(NA, 32).
-
-
-drop
-a logical to remove intermediate MIC values, defaults to FALSE
+a manual range to limit the MIC values, e.g., mic_range = c(0.001, 32). Use NA to prevent a limit on one side, e.g., mic_range = c(NA, 32).
...
@@ -277,98 +271,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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))
-
-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")
-}
-
-
-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()
-}
-
-
-
-# }
-
+
diff --git a/reference/resistance_predict.html b/reference/resistance_predict.html
index ae7ed225c..600c4de1c 100644
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -7,7 +7,7 @@