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https://github.com/msberends/AMR.git
synced 2025-07-10 22:22:19 +02:00
revised as.rsi()
, fix for mdro()
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@ -36,7 +36,7 @@ is.rsi.eligible(x, threshold = 0.05)
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x,
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mo = NULL,
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ab = deparse(substitute(x)),
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guideline = "EUCAST",
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guideline = getOption("AMR_guideline", "EUCAST"),
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uti = NULL,
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conserve_capped_values = FALSE,
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add_intrinsic_resistance = FALSE,
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@ -48,7 +48,7 @@ is.rsi.eligible(x, threshold = 0.05)
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x,
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mo = NULL,
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ab = deparse(substitute(x)),
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guideline = "EUCAST",
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guideline = getOption("AMR_guideline", "EUCAST"),
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uti = NULL,
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add_intrinsic_resistance = FALSE,
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reference_data = AMR::rsi_translation,
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@ -59,7 +59,7 @@ is.rsi.eligible(x, threshold = 0.05)
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x,
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...,
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col_mo = NULL,
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guideline = "EUCAST",
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guideline = getOption("AMR_guideline", "EUCAST"),
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uti = NULL,
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conserve_capped_values = FALSE,
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add_intrinsic_resistance = FALSE,
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@ -79,7 +79,7 @@ rsi_interpretation_history(clean = FALSE)
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\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}}
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\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), but can be set with the \link[=options]{option} \code{AMR_guideline}. Supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}.}
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\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
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@ -109,8 +109,8 @@ The \code{\link[=as.rsi]{as.rsi()}} function works in four ways:
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\itemize{
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
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your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.mic, as.rsi)
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your_data \%>\% mutate(across(where(is.mic), as.rsi))
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}\if{html}{\out{</div>}}
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\item Operators like "<=" will be stripped before interpretation. When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
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}
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@ -118,8 +118,8 @@ your_data \%>\% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
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\itemize{
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\item Using \code{dplyr}, R/SI interpretation can be done very easily with either:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
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your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
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\if{html}{\out{<div class="sourceCode">}}\preformatted{your_data \%>\% mutate_if(is.disk, as.rsi)
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your_data \%>\% mutate(across(where(is.disk), as.rsi))
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}\if{html}{\out{</div>}}
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}
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\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)}.
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@ -133,6 +133,15 @@ For points 2, 3 and 4: Use \code{\link[=rsi_interpretation_history]{rsi_interpre
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For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).
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Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
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You can set the default guideline with the \code{AMR_guideline} \link[=options]{option} (e.g. in your \code{.Rprofile} file), such as:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{ options(AMR_guideline = "CLSI")
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options(AMR_guideline = "CLSI 2018")
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options(AMR_guideline = "EUCAST 2020")
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# or to reset:
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options(AMR_guideline = NULL)
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}\if{html}{\out{</div>}}
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}
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\subsection{After Interpretation}{
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