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Remove RSI from package, add extra MIC scale functions

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dr. M.S. (Matthijs) Berends
2023-12-03 11:34:48 +01:00
parent 6f417d0ef2
commit c7461766ce
21 changed files with 260 additions and 580 deletions
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14
man/as.mic.Rd
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@ -4,16 +4,19 @@
\name{as.mic}
\alias{as.mic}
\alias{mic}
\alias{NA_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_
is.mic(x)
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
\method{droplevels}{mic}(x, as.mic = FALSE, ...)
}
@ -24,6 +27,8 @@ is.mic(x)
\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}
@ -77,6 +82,8 @@ Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numer
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{
@ -92,6 +99,9 @@ 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),