mirror of https://github.com/msberends/AMR.git
134 lines
6.9 KiB
R
134 lines
6.9 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/mic.R
|
|
\docType{data}
|
|
\name{as.mic}
|
|
\alias{as.mic}
|
|
\alias{mic}
|
|
\alias{is.mic}
|
|
\alias{NA_mic_}
|
|
\alias{rescale_mic}
|
|
\alias{droplevels.mic}
|
|
\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
|
|
\usage{
|
|
as.mic(x, na.rm = FALSE, keep_operators = "all")
|
|
|
|
is.mic(x)
|
|
|
|
NA_mic_
|
|
|
|
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
|
|
|
|
\method{droplevels}{mic}(x, as.mic = FALSE, ...)
|
|
}
|
|
\arguments{
|
|
\item{x}{a \link{character} or \link{numeric} vector}
|
|
|
|
\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
|
|
|
|
\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.}
|
|
|
|
\item{mic_range}{a manual range to plot 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)}.}
|
|
|
|
\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
|
|
|
|
\item{...}{arguments passed on to methods}
|
|
}
|
|
\value{
|
|
Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
|
|
}
|
|
\description{
|
|
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.
|
|
}
|
|
\details{
|
|
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).
|
|
|
|
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:
|
|
|
|
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- random_mic(10)
|
|
x
|
|
#> Class 'mic'
|
|
#> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
|
|
|
|
is.factor(x)
|
|
#> [1] TRUE
|
|
|
|
x[1] * 2
|
|
#> [1] 32
|
|
|
|
median(x)
|
|
#> [1] 26
|
|
}\if{html}{\out{</div>}}
|
|
|
|
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.:
|
|
|
|
\if{html}{\out{<div class="sourceCode">}}\preformatted{x[x > 4]
|
|
#> Class 'mic'
|
|
#> [1] 16 8 8 64 >=128 32 32 16
|
|
|
|
df <- data.frame(x, hospital = "A")
|
|
subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
|
|
#> x hospital
|
|
#> 1 16 A
|
|
#> 5 64 A
|
|
#> 6 >=128 A
|
|
#> 8 32 A
|
|
#> 9 32 A
|
|
#> 10 16 A
|
|
}\if{html}{\out{</div>}}
|
|
|
|
The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. 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.
|
|
|
|
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).
|
|
|
|
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.
|
|
|
|
With \code{\link[=rescale_mic]{rescale_mic()}}, existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.
|
|
|
|
\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_}}.
|
|
}
|
|
\examples{
|
|
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
|
|
mic_data
|
|
is.mic(mic_data)
|
|
|
|
# this can also coerce combined MIC/SIR values:
|
|
as.mic("<=0.002; S")
|
|
|
|
# mathematical processing treats MICs as numeric values
|
|
fivenum(mic_data)
|
|
quantile(mic_data)
|
|
all(mic_data < 512)
|
|
|
|
# rescale MICs using rescale_mic()
|
|
rescale_mic(mic_data, mic_range = c(4, 16))
|
|
|
|
# interpret MIC values
|
|
as.sir(
|
|
x = as.mic(2),
|
|
mo = as.mo("Streptococcus pneumoniae"),
|
|
ab = "AMX",
|
|
guideline = "EUCAST"
|
|
)
|
|
as.sir(
|
|
x = as.mic(c(0.01, 2, 4, 8)),
|
|
mo = as.mo("Streptococcus pneumoniae"),
|
|
ab = "AMX",
|
|
guideline = "EUCAST"
|
|
)
|
|
|
|
# plot MIC values, see ?plot
|
|
plot(mic_data)
|
|
plot(mic_data, mo = "E. coli", ab = "cipro")
|
|
|
|
if (require("ggplot2")) {
|
|
autoplot(mic_data, mo = "E. coli", ab = "cipro")
|
|
}
|
|
if (require("ggplot2")) {
|
|
autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
|
|
}
|
|
}
|
|
\seealso{
|
|
\code{\link[=as.sir]{as.sir()}}
|
|
}
|
|
\keyword{datasets}
|