diff --git a/DESCRIPTION b/DESCRIPTION index 8fcb3350..3478a584 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9143 +Version: 1.8.2.9144 Date: 2023-02-24 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 1a772e11..8d10ad50 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9143 +# AMR 1.8.2.9144 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* diff --git a/R/antibiogram.R b/R/antibiogram.R index b6c3ef84..006fabde 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -50,7 +50,7 @@ #' #' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms. #' -#' All types of antibiograms as listed below can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]). The `antibiogram` object can also be used directly in R Markdown / Quarto (i.e., `knitr`) for reports. In this case, [knitr::kable()] will be applied automatically and microorganism names will even be printed in italics at default (see argument `italicise`). You can also use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. with [`as_flextable()`][flextable::as_flextable()] or [`gt()`][gt::gt()]. +#' All types of antibiograms as listed below can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]). The `antibiogram` object can also be used directly in R Markdown / Quarto (i.e., `knitr`) for reports. In this case, [knitr::kable()] will be applied automatically and microorganism names will even be printed in italics at default (see argument `italicise`). You can also use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. with `flextable::as_flextable()` or `gt::gt()`. #' #' ### Antibiogram Types #' diff --git a/man/antibiogram.Rd b/man/antibiogram.Rd index 55ca6e45..b4173217 100644 --- a/man/antibiogram.Rd +++ b/man/antibiogram.Rd @@ -87,7 +87,7 @@ This function returns a table with values between 0 and 100 for \emph{susceptibi \strong{Remember that you should filter your data to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set with one of the four available algorithms. -All types of antibiograms as listed below can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}). The \code{antibiogram} object can also be used directly in R Markdown / Quarto (i.e., \code{knitr}) for reports. In this case, \code{\link[knitr:kable]{knitr::kable()}} will be applied automatically and microorganism names will even be printed in italics at default (see argument \code{italicise}). You can also use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. with \code{\link[flextable:as_flextable]{as_flextable()}} or \code{\link[gt:gt]{gt()}}. +All types of antibiograms as listed below can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}). The \code{antibiogram} object can also be used directly in R Markdown / Quarto (i.e., \code{knitr}) for reports. In this case, \code{\link[knitr:kable]{knitr::kable()}} will be applied automatically and microorganism names will even be printed in italics at default (see argument \code{italicise}). You can also use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. with \code{flextable::as_flextable()} or \code{gt::gt()}. \subsection{Antibiogram Types}{ There are four antibiogram types, as proposed by Klinker \emph{et al.} (2021, \doi{10.1177/20499361211011373}), and they are all supported by \code{\link[=antibiogram]{antibiogram()}}: