(v1.8.1.9004) fix for table() on MICs

R/mic.R

@@ -47,7 +47,7 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' @rdname as.mic
 #' @param x a [character] or [numeric] vector
 #' @param na.rm a [logical] indicating whether missing values should be removed
-#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
+#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
 #' 
 #' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
 #' 
@@ -86,6 +86,10 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' ```
 #' 
 #' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
+#' 
+#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
+#' 
+#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `<mic>` class.
 #' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
 #' @aliases mic
 #' @export
@@ -196,7 +200,8 @@ all_valid_mics <- function(x) {
 }
 
 #' @rdname as.mic
-#' @details `NA_mic_` is a missing value of the new `<mic>` class.
+#' @details `NA_mic_` is a missing value of the new `<mic>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
 #' @export
 NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
                            new_class =  c("mic", "ordered", "factor"))
@@ -221,9 +226,11 @@ as.numeric.mic <- function(x, ...) {
   as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
 }
 
+#' @rdname as.mic
 #' @method droplevels mic
+#' @param exclude factor levels which should be excluded from the result even if present, see [droplevels()][base::droplevels()]
+#' @param as.mic a [logical] to indicate whether the `<mic>` class should be kept, defaults to `FALSE`
 #' @export
-#' @noRd
 droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = FALSE, ...) {
   x <- droplevels.factor(x, exclude = exclude, ...)
   if (as.mic == TRUE) {
@@ -253,7 +260,9 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat("Class <mic>\n")
+  cat("Class <mic>",
+      ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
+      "\n", sep = "")
   print(as.character(x), quote = FALSE)
   att <- attributes(x)
   if ("na.action" %in% names(att)) {

R/rsi.R

@@ -33,7 +33,7 @@
 #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
 #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
 #' @inheritParams first_isolate
-#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
+#' @param guideline defaults to the latest included EUCAST guideline, supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
@@ -179,7 +179,7 @@
 #'   example_isolates %>%
 #'     mutate_if(is.rsi.eligible, as.rsi)
 #'     
-#'   # note: from dplyr 1.0.0 on, this will be: 
+#'   # since dplyr 1.0.0, this can also be: 
 #'   # example_isolates %>%
 #'   #   mutate(across(where(is.rsi.eligible), as.rsi))
 #' }
@@ -189,7 +189,7 @@ as.rsi <- function(x, ...) {
 }
 
 #' @rdname as.rsi
-#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
+#' @details `NA_rsi_` is a missing value of the new `<rsi>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
 #' @export
 NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
                            new_class =  c("rsi", "ordered", "factor"))