diff --git a/DESCRIPTION b/DESCRIPTION index 783dda02..09a56025 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.1.9003 +Version: 1.8.1.9004 Date: 2022-05-09 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 9a683ff0..3a626846 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.8.1.9003 +# `AMR` 1.8.1.9004 ## Last updated: 9 May 2022 ### Changed diff --git a/R/mic.R b/R/mic.R index 0b077ad2..d5a9e938 100755 --- a/R/mic.R +++ b/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 `` 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 `` class. +#' @details `NA_mic_` is a missing value of the new `` 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 `` 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 \n") + cat("Class ", + 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)) { diff --git a/R/rsi.R b/R/rsi.R index 24772746..a80326cb 100755 --- a/R/rsi.R +++ b/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 `` class. +#' @details `NA_rsi_` is a missing value of the new `` 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")) diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index f98e02ae..7739bac9 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index d0e3cfb3..38bd6720 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,7 +43,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 12c4f12c..1ab18143 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index e9bbe351..ee823ef9 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/docs/authors.html b/docs/authors.html index 43af78f6..b47ce57e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/docs/index.html b/docs/index.html index 9ca96788..76d7b387 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/docs/news/index.html b/docs/news/index.html index 314cf777..44c34afc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 @@ -157,12 +157,12 @@
-

-AMR 1.8.1.9003

+

+AMR 1.8.1.9004

-

Last updated: 9 May 2022

+

Last updated: 9 May 2022

-

Changed

+

Changed

  • Removed as.integer() for MIC values, since MIC are not integer values and running table() on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally as.integer() on factors work)
  • droplevels() on MIC will now return a common factor at default and will lose the <mic> class. Use droplevels(..., as.mic = TRUE) to keep the <mic> class.
    • diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index 0daf4317..7a523999 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1 + 1.8.1.9004
@@ -30,7 +30,7 @@
  • -
    • droplevels( + x, + exclude = if (any(is.na(levels(x)))) NULL else NA, + as.mic = FALSE, + ... +)
    -
    -

    Format

    -

    An object of class mic (inherits from ordered, factor) of length 1.

    -

    Arguments

    x

    a character or numeric vector

    na.rm

    a logical indicating whether missing values should be removed

    +
    exclude
    +

    factor levels which should be excluded from the result even if present, see droplevels()

    +
    as.mic
    +

    a logical to indicate whether the <mic> class should be kept, defaults to FALSE

    Value

    @@ -186,7 +194,7 @@

    Details

    -

    To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST and CLSI.

    +

    To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021).

    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:

    x <- random_mic(10)
 x
 #> Class <mic>
@@ -216,7 +224,9 @@
 #> 10    16        A

    The following generic functions 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.

    -

    NA_mic_ is a missing value of the new <mic> class.

    +

    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 factors, 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.

    +

    NA_mic_ is a missing value of the new <mic> class, analogous to e.g. base R's NA_character_.

    Stable Lifecycle

    @@ -277,7 +287,7 @@ The lifecycle of this function is stable
    -

    Site built with pkgdown 2.0.2.

    +

    Site built with pkgdown 2.0.3.

    diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index c3e7efb6..62cb372d 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9002 + 1.8.1.9004 @@ -225,7 +225,7 @@
    ab

    any (vector of) text that can be coerced to a valid antimicrobial code with as.ab()

    guideline
    -

    defaults to the latest included EUCAST guideline, see Details for all options

    +

    defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see Details

    uti

    (Urinary Tract Infection) A vector with logicals (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 logicals 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.

    conserve_capped_values
    @@ -289,7 +289,7 @@

    The function is.rsi.eligible() returns TRUE when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and FALSE otherwise. The threshold of 5% can be set with the threshold argument. If the input is a data.frame, it iterates over all columns and returns a logical vector.

    -

    NA_rsi_ is a missing value of the new <rsi> class.

    +

    NA_rsi_ is a missing value of the new <rsi> class, analogous to e.g. base R's NA_character_.

    Interpretation of R and S/I

    @@ -408,7 +408,7 @@ The lifecycle of this function is stableexample_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)) } diff --git a/docs/reference/index.html b/docs/reference/index.html index 5e8e510e..ec796c07 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004
    @@ -200,7 +200,7 @@

    Interpret MIC and Disk Values, or Clean Raw R/SI Data

    -

    as.mic() NA_mic_ is.mic()

    +

    as.mic() NA_mic_ is.mic() droplevels(<mic>)

    Transform Input to Minimum Inhibitory Concentrations (MIC)

    diff --git a/docs/survey.html b/docs/survey.html index f0faa2df..eef75c52 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.1.9003 + 1.8.1.9004 diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R index a82a992d..714bf5dd 100755 --- a/inst/tinytest/test-mic.R +++ b/inst/tinytest/test-mic.R @@ -33,7 +33,9 @@ expect_true(is.mic(as.mic(8))) expect_equal(as.double(as.mic(">=32")), 32) expect_equal(as.numeric(as.mic(">=32")), 32) -expect_equal(as.integer(as.mic(">=32")), 32) +expect_equal(as.integer(as.mic(">=32")), # should be factor level, not the MIC + as.integer(factor(as.character(">=32"), + levels = levels(as.mic(">=32"))))) expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA) # all levels should be valid MICs diff --git a/man/as.mic.Rd b/man/as.mic.Rd index 71c7126d..185aa44e 100755 --- a/man/as.mic.Rd +++ b/man/as.mic.Rd @@ -6,21 +6,30 @@ \alias{mic} \alias{NA_mic_} \alias{is.mic} +\alias{droplevels.mic} \title{Transform Input to Minimum Inhibitory Concentrations (MIC)} -\format{ -An object of class \code{mic} (inherits from \code{ordered}, \code{factor}) of length 1. -} \usage{ as.mic(x, na.rm = FALSE) NA_mic_ is.mic(x) + +\method{droplevels}{mic}( + x, + exclude = if (any(is.na(levels(x)))) NULL else NA, + as.mic = FALSE, + ... +) } \arguments{ \item{x}{a \link{character} or \link{numeric} vector} \item{na.rm}{a \link{logical} indicating whether missing values should be removed} + +\item{exclude}{factor levels which should be excluded from the result even if present, see \link[base:droplevels]{droplevels()}} + +\item{as.mic}{a \link{logical} to indicate whether the \verb{} class should be kept, defaults to \code{FALSE}} } \value{ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value. @@ -29,7 +38,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology. } \details{ -To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI. +To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021). This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10) x @@ -63,7 +72,11 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4) The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values. -\code{NA_mic_} is a missing value of the new \verb{} class. +Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numeric()}} on MIC values will remove the operators and return a numeric vector. Do \strong{not} use \code{\link[=as.integer]{as.integer()}} on MIC values as by the \R convention on \link{factor}s, it will return the index of the factor levels (which is often useless for regular users). + +Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \verb{} class. + +\code{NA_mic_} is a missing value of the new \verb{} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. } \section{Stable Lifecycle}{ diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index d73402cf..c8dfcc04 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -68,7 +68,7 @@ is.rsi.eligible(x, threshold = 0.05) \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}} -\item{guideline}{defaults to the latest included EUCAST guideline, see \emph{Details} for all options} +\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see \emph{Details}} \item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{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 \emph{Examples}.} @@ -133,7 +133,7 @@ The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector. } -\code{NA_rsi_} is a missing value of the new \verb{} class. +\code{NA_rsi_} is a missing value of the new \verb{} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. } \section{Interpretation of R and S/I}{ @@ -247,7 +247,7 @@ if (require("dplyr")) { 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)) }