fix sorting of MICs, MIC autoplot titles

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9033
-Date: 2024-05-24
+Version: 2.1.1.9034
+Date: 2024-05-30
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9033
+# AMR 2.1.1.9034
 
 *(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!)*
 
@@ -26,6 +26,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
   * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
   * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions.
   * Comparisons of MIC values are now more strict. For example, `>32` is higher than (and never equal to) `32`. Thus, `as.mic(">32") == as.mic(32)` now returns `FALSE`, and `as.mic(">32") > as.mic(32)` now returns `TRUE`.
+  * Sorting of MIC values (using `sort()`) was fixed in the same manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets sorted after `0.001`.
 * Updated `italicise_taxonomy()` to support HTML output
 * `mo_info()` now contains an extra element `group_members`, with the contents of the new `mo_group_members()` function
 * Greatly improved `vctrs` integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as `dplyr`'s `bind_rows()`, `rowwise()` and `c_across()` are now supported for e.g. columns of class `mic`. Despite this, this `AMR` package is still zero-dependent on any other package, including `dplyr` and `vctrs`.

R/eucast_rules.R

@@ -889,6 +889,7 @@ eucast_rules <- function(x,
           ),
           type = "ansi"
         ))
+        cat("\n")
         warned <- FALSE
       }
       run_changes <- edit_sir(

R/mic.R

@@ -495,12 +495,17 @@ rep.mic <- function(x, ...) {
 #' @noRd
 sort.mic <- function(x, decreasing = FALSE, ...) {
   x <- as.mic(x) # make sure that currently implemented MIC levels are used
+  dbl <- as.double(x)
+  # make sure that e.g. '<0.001' comes before '0.001', and '>0.001' comes after
+  dbl[as.character(x) %like% "<[0-9]"] <- dbl[as.character(x) %like% "<[0-9]"] - 0.000002
+  dbl[as.character(x) %like% "<="] <- dbl[as.character(x) %like% "<="] - 0.000001
+  dbl[as.character(x) %like% ">="] <- dbl[as.character(x) %like% ">="] + 0.000001
+  dbl[as.character(x) %like% ">[0-9]"] <- dbl[as.character(x) %like% ">[0-9]"] + 0.000002
   if (decreasing == TRUE) {
-    ord <- order(-as.double(x))
+    x[order(-dbl)]
   } else {
-    ord <- order(as.double(x))
+    x[order(dbl)]
   }
-  x[ord]
 }
 
 #' @method hist mic

R/plot.R

@@ -309,7 +309,6 @@ autoplot.mic <- function(object,
                          breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                          ...) {
   stop_ifnot_installed("ggplot2")
-  object <- as.mic(object) # make sure that currently implemented MIC levels are used
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
@@ -327,6 +326,7 @@ autoplot.mic <- function(object,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
 
+  object <- as.mic(object) # make sure that currently implemented MIC levels are used
   x <- range_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,

R/sir.R

@@ -884,6 +884,9 @@ as_sir_method <- function(method_short,
   if (length(mo) == 1) {
     mo <- rep(mo, length(x))
   }
+  if (length(ab) == 1) {
+    ab <- rep(ab, length(x))
+  }
   if (is.null(uti)) {
     uti <- NA
   }

R/vctrs.R

@@ -106,7 +106,7 @@ vec_ptype_full.disk <- function(x, ...) {
   "disk"
 }
 vec_ptype_abbr.disk <- function(x, ...) {
-  "disk"
+  "dsk"
 }
 vec_ptype2.disk.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x