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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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8
man/as.mic.Rd
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@@ -12,13 +12,15 @@
\alias{droplevels.mic}
\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
\usage{
as.mic(x, na.rm = FALSE, keep_operators = "all")
as.mic(x, na.rm = FALSE, keep_operators = "all",
round_to_next_log2 = FALSE)
is.mic(x)
NA_mic_
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE,
round_to_next_log2 = FALSE)
mic_p50(x, na.rm = FALSE, ...)
@@ -33,6 +35,8 @@ mic_p90(x, na.rm = FALSE, ...)
\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{round_to_next_log2}{A \link{logical} to round up all values to the next log2 level, that are not either 0.0001, 0.0002, 0.0005, 0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, or 4096. Values that are already in this list (with or without operators), are left unchanged (including any operators).}
\item{mic_range}{A manual range to rescale the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling 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{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}