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(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro

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dr. M.S. (Matthijs) Berends
2025-02-23 11:18:08 +01:00
parent 226d10f546
commit aa8f6af185
24 changed files with 481 additions and 99 deletions
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8
man/as.mic.Rd
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@@ -7,6 +7,8 @@
\alias{is.mic}
\alias{NA_mic_}
\alias{rescale_mic}
\alias{mic_p50}
\alias{mic_p90}
\alias{droplevels.mic}
\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
\usage{
@@ -18,6 +20,10 @@ NA_mic_
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
mic_p50(x, na.rm = FALSE, ...)
mic_p90(x, na.rm = FALSE, ...)
\method{droplevels}{mic}(x, as.mic = FALSE, ...)
}
\arguments{
@@ -87,6 +93,8 @@ With \code{\link[=rescale_mic]{rescale_mic()}}, existing MIC ranges can be limit
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.
\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_}}.
Use \code{\link[=mic_p50]{mic_p50()}} and \code{\link[=mic_p90]{mic_p90()}} to get the 50th and 90th percentile of MIC values. They return 'normal' \link{numeric} values.
}
\examples{
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))