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(v1.3.0.9028) eucast fix

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dr. M.S. (Matthijs) Berends
2020-09-24 12:38:13 +02:00
parent 027215ed94
commit 1d982a82b4
24 changed files with 121 additions and 88 deletions
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12
man/as.rsi.Rd
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@ -39,18 +39,18 @@ is.rsi.eligible(x, threshold = 0.05)
\method{as.rsi}{data.frame}(
x,
...,
col_mo = NULL,
guideline = "EUCAST",
uti = NULL,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
...
add_intrinsic_resistance = FALSE
)
}
\arguments{
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{...}{parameters passed on to methods}
\item{...}{for using on a \link{data.frame}: names of columns to apply \code{\link[=as.rsi]{as.rsi()}} on (supports tidy selection like \code{AMX:VAN}). Otherwise: parameters passed on to methods.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
@ -70,7 +70,7 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
}
\value{
Ordered factor with new class \code{\link{rsi}}
Ordered \link{factor} with new class \code{\link{rsi}}
}
\description{
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Values that cannot be interpreted will be returned as \code{NA} with a warning.
@ -211,7 +211,6 @@ as.rsi(x = as.disk(18),
as.rsi(c("S", "I", "R", "A", "B", "C"))
as.rsi("<= 0.002; S") # will return "S"
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
is.rsi(rsi_data)
plot(rsi_data) # for percentages
@ -221,6 +220,9 @@ barplot(rsi_data) # for frequencies
library(dplyr)
example_isolates \%>\%
mutate_at(vars(PEN:RIF), as.rsi)
# same:
example_isolates \%>\%
as.rsi(PEN:RIF)
# fastest way to transform all columns with already valid AMR results to class `rsi`:
example_isolates \%>\%