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(v2.1.1.9154) documentation fix
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 2.1.1.9153
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Version: 2.1.1.9154
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Date: 2025-02-22
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9153
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# AMR 2.1.1.9154
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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@ -1,6 +1,6 @@
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Metadata-Version: 2.2
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Name: AMR
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Version: 2.1.1.9153
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Version: 2.1.1.9154
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Summary: A Python wrapper for the AMR R package
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Home-page: https://github.com/msberends/AMR
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Author: Matthijs Berends
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
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setup(
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name='AMR',
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version='2.1.1.9153',
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version='2.1.1.9154',
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packages=find_packages(),
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install_requires=[
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'rpy2',
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84
R/plotting.R
84
R/plotting.R
@ -81,20 +81,24 @@
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#' some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
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#'
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#'
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#' # Plotting using base R's plot() ---------------------------------------
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#'
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#' plot(some_mic_values)
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#' plot(some_disk_values)
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#' plot(some_sir_values)
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#'
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#' # when providing the microorganism and antibiotic, colours will show interpretations:
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#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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#' 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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#' \donttest{
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#' # Plotting using ggplot2's autoplot() for MIC, disk, and SIR -----------
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#' if (require("ggplot2")) {
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#' autoplot(some_mic_values)
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#' }
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#' if (require("ggplot2")) {
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#' # when providing the microorganism and antibiotic, colours will show interpretations:
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#' autoplot(some_mic_values, mo = "Escherichia coli", ab = "cipro")
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#' }
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#' if (require("ggplot2")) {
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#' # support for 20 languages, various guidelines, and many options
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#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro",
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#' guideline = "CLSI 2024", language = "no",
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#' title = "Disk diffusion from the North")
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#' }
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#'
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#'
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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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#' counts = c(1, 1, 2, 2, 3, 3)),
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@ -142,22 +146,10 @@
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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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#' scale_y_mic(mic_range = c(NA, 0.25))
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#' }
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#'
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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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#'
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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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#'
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#' # Plotting using scale_x_sir() -----------------------------------------
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#' if (require("ggplot2")) {
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#' ggplot(data.frame(x = c("I", "R", "S"),
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@ -191,42 +183,22 @@
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#' if (require("ggplot2")) {
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#' plain +
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#' scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
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#' scale_colour_sir(language = "nl", eucast_I = FALSE,
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#' name = "In Dutch!")
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#' scale_colour_sir(language = "pt",
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#' name = "Support in 20 languages")
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#' }
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#'
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#'
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#' # Plotting using ggplot2's autoplot() ----------------------------------
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#' if (require("ggplot2")) {
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#' autoplot(some_mic_values)
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#' }
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#' if (require("ggplot2")) {
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#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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#' }
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#' if (require("ggplot2")) {
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#' autoplot(some_sir_values)
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#' }
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#' # Plotting using base R's plot() ---------------------------------------
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#'
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#' plot(some_mic_values)
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#' # when providing the microorganism and antibiotic, colours will show interpretations:
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#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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#'
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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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#' aes(mics, counts / sum(counts))) +
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#' geom_col()
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#' print(p)
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#' plot(some_disk_values)
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#' 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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#'
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#' p2 <- p +
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#' scale_y_percent() +
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#' theme_sir()
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#' print(p2)
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#'
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#' p +
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#' scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
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#' limits = c(0, 1)) +
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#' theme_sir()
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#' }
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#' }
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#' plot(some_sir_values)
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NULL
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create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
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@ -243,12 +215,12 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
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scale$mic_limits_set <- limits_set
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scale$transform <- function(x) {
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as.double(rescale_mic(x = as.double(x), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
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as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
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}
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scale$transform_df <- function(self, df) {
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stop_if(all(is.na(df[[aest]])),
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"`scale_", aest, "_mic()`: All MIC values are `NA`. Check your input data.", call = FALSE)
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self$mic_values_rescaled <- rescale_mic(x = as.double(df[[aest]]), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
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self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
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# create new breaks and labels here
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lims <- range(self$mic_values_rescaled, na.rm = TRUE)
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# support inner and outer mic_range settings (e.g., data ranges 0.5-8 and mic_range is set to 0.025-64)
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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 2.1.1.9153. Remember this whenever someone asks which AMR package version you’re at.
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First and foremost, you are trained on version 2.1.1.9154. 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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@ -7540,159 +7540,6 @@ The interpretation of "I" will be named "Increased exposure" for all EUCAST guid
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For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
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}
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}
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\examples{
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some_mic_values <- random_mic(size = 100)
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some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
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some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
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# Plotting using base R's plot() ---------------------------------------
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plot(some_mic_values)
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plot(some_disk_values)
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plot(some_sir_values)
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# when providing the microorganism and antibiotic, colours will show interpretations:
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plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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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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\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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counts = c(1, 1, 2, 2, 3, 3)),
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aes(mics, counts)) +
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geom_col()
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mic_plot +
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labs(title = "without scale_x_mic()")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic() +
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labs(title = "with scale_x_mic()")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(keep_operators = "all") +
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labs(title = "with scale_x_mic() keeping all operators")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(mic_range = c(1, 16)) +
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labs(title = "with scale_x_mic() using a manual 'within' range")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(mic_range = c(0.032, 256)) +
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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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# Plotting using scale_x_sir() -----------------------------------------
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if (require("ggplot2")) {
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ggplot(data.frame(x = c("I", "R", "S"),
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y = c(45,323, 573)),
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aes(x, y)) +
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geom_col() +
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scale_x_sir()
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}
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# Plotting using scale_y_mic() and scale_colour_sir() ------------------
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if (require("ggplot2")) {
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plain <- ggplot(data.frame(mic = some_mic_values,
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group = some_groups,
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sir = as.sir(some_mic_values,
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mo = "E. coli",
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ab = "cipro")),
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aes(x = group, y = mic, colour = sir)) +
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theme_minimal() +
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geom_boxplot(fill = NA, colour = "grey") +
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geom_jitter(width = 0.25)
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plain
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}
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if (require("ggplot2")) {
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# and now with our MIC and SIR scale functions:
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plain +
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scale_y_mic() +
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scale_colour_sir()
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}
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if (require("ggplot2")) {
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plain +
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scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
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scale_colour_sir(language = "nl", eucast_I = FALSE,
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name = "In Dutch!")
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}
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# Plotting using ggplot2's autoplot() ----------------------------------
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if (require("ggplot2")) {
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autoplot(some_mic_values)
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}
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if (require("ggplot2")) {
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autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
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}
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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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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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aes(mics, counts / sum(counts))) +
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geom_col()
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print(p)
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p2 <- p +
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scale_y_percent() +
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theme_sir()
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print(p2)
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p +
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scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
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limits = c(0, 1)) +
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theme_sir()
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}
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}
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}
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153
man/plot.Rd
153
man/plot.Rd
@ -196,156 +196,3 @@ The interpretation of "I" will be named "Increased exposure" for all EUCAST guid
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For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
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}
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}
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\examples{
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some_mic_values <- random_mic(size = 100)
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some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
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some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
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# Plotting using base R's plot() ---------------------------------------
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plot(some_mic_values)
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plot(some_disk_values)
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plot(some_sir_values)
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# when providing the microorganism and antibiotic, colours will show interpretations:
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plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
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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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\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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counts = c(1, 1, 2, 2, 3, 3)),
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aes(mics, counts)) +
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geom_col()
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mic_plot +
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labs(title = "without scale_x_mic()")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic() +
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labs(title = "with scale_x_mic()")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(keep_operators = "all") +
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labs(title = "with scale_x_mic() keeping all operators")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(mic_range = c(1, 16)) +
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labs(title = "with scale_x_mic() using a manual 'within' range")
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}
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if (require("ggplot2")) {
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mic_plot +
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scale_x_mic(mic_range = c(0.032, 256)) +
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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))
|
||||
|
||||
if (require("ggplot2")) {
|
||||
ggplot(data.frame(mic = some_mic_values,
|
||||
group = some_groups,
|
||||
counts = some_counts),
|
||||
aes(group, counts, fill = mic)) +
|
||||
geom_col() +
|
||||
scale_fill_mic(mic_range = c(0.5, 16))
|
||||
}
|
||||
|
||||
# Plotting using scale_x_sir() -----------------------------------------
|
||||
if (require("ggplot2")) {
|
||||
ggplot(data.frame(x = c("I", "R", "S"),
|
||||
y = c(45,323, 573)),
|
||||
aes(x, y)) +
|
||||
geom_col() +
|
||||
scale_x_sir()
|
||||
}
|
||||
|
||||
|
||||
# Plotting using scale_y_mic() and scale_colour_sir() ------------------
|
||||
if (require("ggplot2")) {
|
||||
plain <- ggplot(data.frame(mic = some_mic_values,
|
||||
group = some_groups,
|
||||
sir = as.sir(some_mic_values,
|
||||
mo = "E. coli",
|
||||
ab = "cipro")),
|
||||
aes(x = group, y = mic, colour = sir)) +
|
||||
theme_minimal() +
|
||||
geom_boxplot(fill = NA, colour = "grey") +
|
||||
geom_jitter(width = 0.25)
|
||||
|
||||
plain
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
# and now with our MIC and SIR scale functions:
|
||||
plain +
|
||||
scale_y_mic() +
|
||||
scale_colour_sir()
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
plain +
|
||||
scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
|
||||
scale_colour_sir(language = "nl", eucast_I = FALSE,
|
||||
name = "In Dutch!")
|
||||
}
|
||||
|
||||
|
||||
# Plotting using ggplot2's autoplot() ----------------------------------
|
||||
if (require("ggplot2")) {
|
||||
autoplot(some_mic_values)
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
|
||||
}
|
||||
if (require("ggplot2")) {
|
||||
autoplot(some_sir_values)
|
||||
}
|
||||
|
||||
|
||||
# Plotting using scale_y_percent() -------------------------------------
|
||||
if (require("ggplot2")) {
|
||||
p <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
|
||||
counts = c(1, 1, 2, 2, 3, 3)),
|
||||
aes(mics, counts / sum(counts))) +
|
||||
geom_col()
|
||||
print(p)
|
||||
|
||||
p2 <- p +
|
||||
scale_y_percent() +
|
||||
theme_sir()
|
||||
print(p2)
|
||||
|
||||
p +
|
||||
scale_y_percent(breaks = seq(from = 0, to = 1, by = 0.1),
|
||||
limits = c(0, 1)) +
|
||||
theme_sir()
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user