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(v2.1.1.9144) new MIC scales and fix for rescale_mic()
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@ -1,6 +1,6 @@
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This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
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First and foremost, you are trained on version 2.1.1.9143. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9144. Remember this whenever someone asks which AMR package version you’re at.
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Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
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----------------------------------------------------------------------------------------------------
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@ -332,6 +332,7 @@ export(resistance_predict)
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export(retrieve_wisca_parameters)
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export(rifamycins)
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export(right_join_microorganisms)
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export(scale_color_mic)
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export(scale_colour_mic)
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export(scale_fill_mic)
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export(scale_sir_colours)
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@ -2875,9 +2876,9 @@ rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
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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{mic_range}{a manual range to limit the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent a 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{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}.}
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\item{...}{arguments passed on to methods}
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}
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@ -7330,6 +7331,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
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\alias{scale_x_mic}
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\alias{scale_y_mic}
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\alias{scale_colour_mic}
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\alias{scale_color_mic}
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\alias{scale_fill_mic}
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\alias{plot.mic}
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\alias{autoplot.mic}
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@ -7347,17 +7349,15 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/plot.Rd':
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\alias{labels_sir_count}
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\title{Plotting Helpers for AMR Data Analysis}
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\usage{
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scale_x_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL,
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drop = FALSE, ...)
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scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE,
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...)
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scale_color_mic(keep_operators = "edges", mic_range = NULL, ...)
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scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
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\method{plot}{mic}(x, mo = NULL, ab = NULL, guideline = "EUCAST",
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main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
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@ -7428,9 +7428,7 @@ labels_sir_count(position = NULL, x = "antibiotic",
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\arguments{
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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{drop}{a \link{logical} to remove intermediate MIC values, defaults to \code{FALSE}}
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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 prevent a limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
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\item{...}{arguments passed on to methods}
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@ -7521,7 +7519,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
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# Plotting using scale_x_mic() ---------------------------------------------
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# Plotting using scale_x_mic() -----------------------------------------
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\donttest{
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if (require("ggplot2")) {
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mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
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@ -7552,6 +7550,37 @@ if (require("ggplot2")) {
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labs(title = "with scale_x_mic() using a manual 'outside' range")
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}
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# Plotting using scale_y_mic() -----------------------------------------
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some_groups <- sample(LETTERS[1:5], 20, replace = TRUE)
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if (require("ggplot2")) {
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ggplot(data.frame(mic = some_mic_values,
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group = some_groups),
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aes(group, mic)) +
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geom_boxplot() +
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geom_violin(linetype = 2, colour = "grey", fill = NA) +
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scale_y_mic()
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}
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if (require("ggplot2")) {
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ggplot(data.frame(mic = some_mic_values,
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group = some_groups),
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aes(group, mic)) +
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geom_boxplot() +
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geom_violin(linetype = 2, colour = "grey", fill = NA) +
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scale_y_mic(mic_range = c(NA, 2))
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}
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# Plotting using scale_fill_mic() -----------------------------------------
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some_counts <- as.integer(runif(20, 5, 50))
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if (require("ggplot2")) {
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ggplot(data.frame(mic = some_mic_values,
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group = some_groups,
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counts = some_counts,
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aes(group, counts, fill = mic)) +
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geom_col() +
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scale_fill_mic(mic_range = c(0.5, 16))
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}
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# Auto plotting --------------------------------------------------------
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if (require("ggplot2")) {
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autoplot(some_mic_values)
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}
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@ -7562,7 +7591,7 @@ if (require("ggplot2")) {
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autoplot(some_sir_values)
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}
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# Plotting using scale_y_percent() -----------------------------------------
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# Plotting using scale_y_percent() -------------------------------------
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if (require("ggplot2")) {
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p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
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counts = c(1, 1, 2, 2, 3, 3)),
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