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(v2.1.1.9080) fix rescale_mic() for an outside MIC range
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Package: AMR
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Version: 2.1.1.9079
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Version: 2.1.1.9080
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Date: 2024-09-24
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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
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# AMR 2.1.1.9079
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# AMR 2.1.1.9080
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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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6
R/mic.R
6
R/mic.R
@ -304,9 +304,9 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
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# create a manual factor with levels only within desired range
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expanded <- plotrange_as_table(x,
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expand = TRUE,
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keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
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mic_range = mic_range)
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expand = TRUE,
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keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
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mic_range = mic_range)
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if (keep_operators == "edges") {
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names(expanded)[1] <- paste0("<=", names(expanded)[1])
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names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])
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@ -73,7 +73,7 @@
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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(0.125, "<=4", 4, 8, 32, ">=32")),
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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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@ -92,8 +92,13 @@
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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, 128)) +
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#' labs(title = "with scale_x_mic() using a manual range")
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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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#'
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#' if (require("ggplot2")) {
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@ -795,7 +800,14 @@ plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NU
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x <- as.mic(x, keep_operators = keep_operators)
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if (expand == TRUE) {
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# expand range for MIC by adding common intermediate factors levels
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extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
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if (!is.null(mic_range) && !all(is.na(mic_range))) {
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# base on mic_range
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`%na_or%` <- function(x, y) if (is.na(x)) y else x
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extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES >= (mic_range[1] %na_or% min(x, na.rm = TRUE)) & COMMON_MIC_VALUES <= (mic_range[2] %na_or% max(x, na.rm = TRUE))]
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} else {
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# base on x
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extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
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}
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# remove the ones that are in 25% range of user values
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extra_range <- extra_range[!vapply(FUN.VALUE = logical(1), extra_range, function(r) any(abs(r - x) / x < 0.25, na.rm = TRUE))]
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nms <- extra_range
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2
R/sir.R
2
R/sir.R
@ -1376,7 +1376,7 @@ as_sir_method <- function(method_short,
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} else {
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site <- paste0("body site '", site, "'")
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}
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if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
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if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && is.na(uti_current) && message_not_thrown_before("as.sir", "uti", ab_current)) {
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# only UTI breakpoints available
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notes_current <- c(notes_current, paste0("Breakpoints for ", font_bold(ab_formatted), " in ", mo_formatted, " are only available for (uncomplicated) urinary tract infections (UTI); assuming `uti = TRUE`."))
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} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {
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13
man/plot.Rd
13
man/plot.Rd
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/plot.R
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% Please edit documentation in R/plotting.R
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\name{plot}
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\alias{plot}
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\alias{scale_x_mic}
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@ -180,7 +180,7 @@ 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(0.125, "<=4", 4, 8, 32, ">=32")),
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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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@ -199,8 +199,13 @@ if (require("ggplot2")) {
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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, 128)) +
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labs(title = "with scale_x_mic() using a manual range")
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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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if (require("ggplot2")) {
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