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new rsi_interpretation_history

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dr. M.S. (Matthijs) Berends
2022-09-01 15:20:57 +02:00
parent a3b97a10a5
commit 63fe160322
12 changed files with 191 additions and 171 deletions
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11
man/as.rsi.Rd
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@ -10,6 +10,7 @@
\alias{as.rsi.mic}
\alias{as.rsi.disk}
\alias{as.rsi.data.frame}
\alias{rsi_interpretation_history}
\title{Interpret MIC and Disk Values, or Clean Raw R/SI Data}
\format{
An object of class \code{rsi} (inherits from \code{ordered}, \code{factor}) of length 1.
@ -56,6 +57,8 @@ is.rsi.eligible(x, threshold = 0.05)
add_intrinsic_resistance = FALSE,
reference_data = AMR::rsi_translation
)
rsi_interpretation_history(clean = FALSE)
}
\arguments{
\item{x}{vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
@ -79,6 +82,8 @@ is.rsi.eligible(x, threshold = 0.05)
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{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 \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
\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()}}.}
\item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}
}
\value{
Ordered \link{factor} with new class \verb{<rsi>}
@ -111,6 +116,8 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
}
\item For \strong{interpreting a complete data set}, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running \code{as.rsi(your_data)}.
}
For points 2, 3 and 4: Use \code{\link[=rsi_interpretation_history]{rsi_interpretation_history()}} to retrieve a \link{data.frame} (or \link[tibble:tibble]{tibble} if the \code{tibble} package is installed) with all results of the last \code{\link[=as.rsi]{as.rsi()}} call.
}
\subsection{Supported Guidelines}{
@ -172,11 +179,13 @@ df <- data.frame(
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
NIT = as.mic(32),
ERY = "R"
)
as.rsi(df)
# return a 'logbook' about the results:
rsi_interpretation_history()
# for single values
as.rsi(
x = as.mic(2),