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fix for antibiograms on R < 3.5

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dr. M.S. (Matthijs) Berends
2023-02-24 09:43:10 +01:00
parent e70f2cd32c
commit 049baf0a71
13 changed files with 108 additions and 101 deletions
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11
man/antibiogram.Rd
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@ -35,7 +35,7 @@ antibiogram(
\method{autoplot}{antibiogram}(object, ...)
knit_print.antibiogram(
\method{knit_print}{antibiogram}(
x,
italicise = TRUE,
na = getOption("knitr.kable.NA", default = ""),
@ -75,7 +75,7 @@ knit_print.antibiogram(
\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
\item{italicise}{a \link{logical} to indicate whether the microorganism names in the \link[knitr:kable]{knitr} table should be made italic, using \code{\link[=italicise_taxonomy]{italicise_taxonomy()}}. This only works when the output format is markdown, such as in HTML output.}
\item{italicise}{a \link{logical} to indicate whether the microorganism names in the \link[knitr:kable]{knitr} table should be made italic, using \code{\link[=italicise_taxonomy]{italicise_taxonomy()}}.}
\item{na}{character to use for showing \code{NA} values}
}
@ -87,6 +87,9 @@ 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()}}.
\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()}}:
\enumerate{
\item \strong{Traditional Antibiogram}
@ -134,8 +137,6 @@ your_data \%>\%
}\if{html}{\out{</div>}}
}
All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}) or directly used into R Markdown / Quarto formats for reports (in the last case, \code{\link[knitr:kable]{knitr::kable()}} will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. \code{flextable::as_flextable()} or \code{gt::gt()}.
Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the \code{only_all_tested} argument (default is \code{FALSE}). See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=antibiogram]{antibiogram()}} works to calculate the \%SI:
\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
@ -156,6 +157,7 @@ Note that for combination antibiograms, it is important to realise that suscepti
--------------------------------------------------------------------
}\if{html}{\out{</div>}}
}
}
\examples{
# example_isolates is a data set available in the AMR package.
# run ?example_isolates for more info.
@ -233,6 +235,7 @@ antibiogram(example_isolates,
)
)
# Print the output for R Markdown / Quarto -----------------------------
ureido <- antibiogram(example_isolates,