(v2.1.1.9080) fix `rescale_mic()` for an outside MIC range

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9079
+Version: 2.1.1.9080
 Date: 2024-09-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9079
+# AMR 2.1.1.9080
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

R/mic.R

@@ -304,9 +304,9 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
   
   # create a manual factor with levels only within desired range
   expanded <- plotrange_as_table(x,
-                             expand = TRUE,
-                             keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
-                             mic_range = mic_range)
+                                 expand = TRUE,
+                                 keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
+                                 mic_range = mic_range)
   if (keep_operators == "edges") {
     names(expanded)[1] <- paste0("<=", names(expanded)[1])
     names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])

R/plotting.R

@@ -73,7 +73,7 @@
 #' # Plotting using scale_x_mic()
 #' \donttest{
 #' if (require("ggplot2")) {
-#'   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
+#'   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()
@@ -92,8 +92,13 @@
 #' }
 #' if (require("ggplot2")) {
 #'   mic_plot +
-#'     scale_x_mic(mic_range = c(1, 128)) +
-#'     labs(title = "with scale_x_mic() using a manual range")
+#'     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")) {
@@ -795,7 +800,14 @@ plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NU
     x <- as.mic(x, keep_operators = keep_operators)
     if (expand == TRUE) {
       # expand range for MIC by adding common intermediate factors levels
-      extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
+      if (!is.null(mic_range) && !all(is.na(mic_range))) {
+        # base on mic_range
+        `%na_or%` <- function(x, y) if (is.na(x)) y else x
+        extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES >= (mic_range[1] %na_or% min(x, na.rm = TRUE)) & COMMON_MIC_VALUES <= (mic_range[2] %na_or% max(x, na.rm = TRUE))]
+      } else {
+        # base on x
+        extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
+      }
       # remove the ones that are in 25% range of user values
       extra_range <- extra_range[!vapply(FUN.VALUE = logical(1), extra_range, function(r) any(abs(r - x) / x < 0.25, na.rm = TRUE))]
       nms <- extra_range

R/sir.R

@@ -1376,7 +1376,7 @@ as_sir_method <- function(method_short,
     } else {
       site <- paste0("body site '", site, "'")
     }
-    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
+    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && is.na(uti_current) && message_not_thrown_before("as.sir", "uti", ab_current)) {
       # only UTI breakpoints available
       notes_current <- c(notes_current, paste0("Breakpoints for ", font_bold(ab_formatted), " in ", mo_formatted, " are only available for (uncomplicated) urinary tract infections (UTI); assuming `uti = TRUE`."))
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {

man/plot.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/plotting.R
 \name{plot}
 \alias{plot}
 \alias{scale_x_mic}
@@ -180,7 +180,7 @@ 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(0.125, "<=4", 4, 8, 32, ">=32")),
+  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()
@@ -199,8 +199,13 @@ if (require("ggplot2")) {
 }
 if (require("ggplot2")) {
   mic_plot +
-    scale_x_mic(mic_range = c(1, 128)) +
-    labs(title = "with scale_x_mic() using a manual range")
+    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")) {