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(v2.1.1.9127) unit tests

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dr. M.S. (Matthijs) Berends
2025-01-27 10:46:43 +01:00
parent 66833b4f5a
commit 7accf6ff13
19 changed files with 217 additions and 226 deletions
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10
man/antibiogram.Rd
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@ -3,7 +3,6 @@
\name{antibiogram}
\alias{antibiogram}
\alias{wisca}
\alias{get_long_numeric_format}
\alias{plot.antibiogram}
\alias{autoplot.antibiogram}
\alias{knit_print.antibiogram}
@ -35,8 +34,6 @@ wisca(x, antibiotics = where(is.sir), mo_transform = "shortname",
combine_SI = TRUE, sep = " + ", simulations = 1000,
info = interactive())
get_long_numeric_format(antibiogram)
\method{plot}{antibiogram}(x, ...)
\method{autoplot}{antibiogram}(object, ...)
@ -83,8 +80,6 @@ get_long_numeric_format(antibiogram)
\item{info}{a \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode}
\item{antibiogram}{the outcome of \code{\link[=antibiogram]{antibiogram()}} or \code{\link[=wisca]{wisca()}}}
\item{...}{when used in \link[knitr:kable]{R Markdown or Quarto}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)}
\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
@ -105,7 +100,7 @@ This function returns a table with values between 0 and 100 for \emph{susceptibi
For estimating antimicrobial coverage, especially when creating a WISCA, the outcome might become more reliable by only including the top \emph{n} species encountered in the data. You can filter on this top \emph{n} using \code{\link[=top_n_microorganisms]{top_n_microorganisms()}}. For example, use \code{top_n_microorganisms(your_data, n = 10)} as a pre-processing step to only include the top 10 species in the data.
Using \code{\link[=get_long_numeric_format]{get_long_numeric_format()}}, the antibiogram is converted to a long format containing numeric values. This is ideal for e.g. advanced plotting.
The numeric values of an antibiogram are stored in a long format as the \link{attribute} \code{long_numeric}. You can retrieve them using \code{attributes(x)$long_numeric}, where \code{x} is the outcome of \code{\link[=antibiogram]{antibiogram()}} or \code{\link[=wisca]{wisca()}}. This is ideal for e.g. advanced plotting.
\subsection{Formatting Type}{
The formatting of the 'cells' of the table can be set with the argument \code{formatting_type}. In these examples, \code{5} is the susceptibility percentage (for WISCA: \code{4-6} indicates the confidence level), \code{15} the numerator, and \code{300} the denominator:
@ -379,7 +374,8 @@ if (requireNamespace("knitr")) {
ab1 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain"
mo_transform = "gramstain",
wisca = TRUE
)
ab2 <- antibiogram(example_isolates,
antibiotics = c("AMC", "CIP", "TZP", "TZP+TOB"),