mirror of https://github.com/msberends/AMR.git
136 lines
5.6 KiB
R
136 lines
5.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mic.R
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\docType{data}
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\name{as.mic}
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\alias{as.mic}
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\alias{mic}
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\alias{is.mic}
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\alias{NA_mic_}
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\alias{limit_mic_range}
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\alias{droplevels.mic}
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\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
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\usage{
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as.mic(x, na.rm = FALSE, keep_operators = "all")
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is.mic(x)
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NA_mic_
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limit_mic_range(x, mic_range, keep_operators = "edges", as.mic = TRUE)
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\method{droplevels}{mic}(x, as.mic = FALSE, ...)
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}
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\arguments{
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\item{x}{a \link{character} or \link{numeric} vector}
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\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
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\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
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\item{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
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\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
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\item{...}{arguments passed on to methods}
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}
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\value{
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Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as a \link{numeric} vector. Bear in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
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}
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\description{
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This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
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}
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\details{
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To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2011-2023) and CLSI (2011-2023).
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This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- random_mic(10)
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x
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#> Class 'mic'
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#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
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is.factor(x)
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#> [1] TRUE
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x[1] * 2
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#> [1] 32
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median(x)
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#> [1] 26
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}\if{html}{\out{</div>}}
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This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.:
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\if{html}{\out{<div class="sourceCode">}}\preformatted{x[x > 4]
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#> Class 'mic'
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#> [1] 16 8 8 64 >=128 32 32 16
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df <- data.frame(x, hospital = "A")
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subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
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#> x hospital
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#> 1 16 A
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#> 5 64 A
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#> 6 >=128 A
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#> 8 32 A
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#> 9 32 A
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#> 10 16 A
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}\if{html}{\out{</div>}}
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All so-called \link[=groupGeneric]{group generic functions} are implemented for the MIC class (such as \code{!}, \code{!=}, \code{<}, \code{>=}, \code{\link[=exp]{exp()}}, \code{\link[=log2]{log2()}}). Some functions of the \code{stats} package are also implemented (such as \code{\link[=quantile]{quantile()}}, \code{\link[=median]{median()}}, \code{\link[=fivenum]{fivenum()}}). Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
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Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numeric()}} on MIC values will remove the operators and return a numeric vector. Do \strong{not} use \code{\link[=as.integer]{as.integer()}} on MIC values as by the \R convention on \link{factor}s, it will return the index of the factor levels (which is often useless for regular users).
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Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \code{mic} class.
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With \code{\link[=limit_mic_range]{limit_mic_range()}}, existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.
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For \code{ggplot2}, use one of the \code{\link[=scale_x_mic]{scale_*_mic()}} functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
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\code{NA_mic_} is a missing value of the new \code{mic} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
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}
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\examples{
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mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
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mic_data
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is.mic(mic_data)
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# this can also coerce combined MIC/SIR values:
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as.mic("<=0.002; S")
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# mathematical processing treats MICs as numeric values
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fivenum(mic_data)
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quantile(mic_data)
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all(mic_data < 512)
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# limit MICs using limit_mic_range()
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limit_mic_range(mic_data, mic_range = c(4, 16))
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# interpret MIC values
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as.sir(
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x = as.mic(2),
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mo = as.mo("Streptococcus pneumoniae"),
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ab = "AMX",
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guideline = "EUCAST"
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)
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as.sir(
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x = as.mic(c(0.01, 2, 4, 8)),
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mo = as.mo("Streptococcus pneumoniae"),
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ab = "AMX",
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guideline = "EUCAST"
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)
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# plot MIC values, see ?plot
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plot(mic_data)
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plot(mic_data, mo = "E. coli", ab = "cipro")
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if (require("ggplot2")) {
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autoplot(mic_data, mo = "E. coli", ab = "cipro")
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}
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if (require("ggplot2")) {
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autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
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}
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}
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\seealso{
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\code{\link[=as.sir]{as.sir()}}
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}
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\keyword{datasets}
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