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(v3.0.1.9001) fix antibiogram
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@@ -1,6 +1,6 @@
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Package: AMR
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Version: 3.0.1
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Date: 2025-09-20
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Version: 3.0.1.9001
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Date: 2025-09-30
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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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data analysis and to work with microbial and antimicrobial properties by
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@@ -27,10 +27,10 @@ Authors@R: c(
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person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
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person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
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person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
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person(given = c("Matthew"), family = "Saab", role = "ctb"),
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person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
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person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
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person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(given = c("Rogier", "P."), family = "Schade", role = "ctb"),
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person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
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person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
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person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
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6
NEWS.md
6
NEWS.md
@@ -1,3 +1,9 @@
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# AMR 3.0.1.9001
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### Changed
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* Fixed a bug in `antibiogram()` for when no antimicrobials are set
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# AMR 3.0.1
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This is a bugfix release following the release of v3.0.0 in June 2025.
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@@ -1620,8 +1620,8 @@ get_n_cores <- function(max_cores = Inf) {
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# Support `where()` if tidyselect not installed ----
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if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
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# tidyselect::where() exists, load the namespace to make `where()`s work across the package in default arguments
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loadNamespace("tidyselect")
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# tidyselect::where() exists, retrieve from their namespace to make `where()`s work across the package in default arguments
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where <- tidyselect::where
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} else {
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where <- function(fn) {
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# based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
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@@ -453,7 +453,7 @@ antibiogram.default <- function(x,
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deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
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antimicrobials <- list(...)$antibiotics
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}
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meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
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meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer", "function"), allow_NA = FALSE, allow_NULL = FALSE)
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if (!is.function(mo_transform)) {
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meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
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}
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@@ -518,6 +518,10 @@ antibiogram.default <- function(x,
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# get antimicrobials
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ab_trycatch <- tryCatch(colnames(suppressWarnings(x[, antimicrobials, drop = FALSE])), error = function(e) NULL)
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if (is.null(ab_trycatch)) {
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# try with tidyverse
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ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
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}
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if (is.null(ab_trycatch)) {
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stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
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antimicrobials.bak <- antimicrobials
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10
R/plotting.R
10
R/plotting.R
@@ -53,17 +53,17 @@
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#' ### The `scale_*_mic()` Functions
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#'
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#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
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#'
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#'
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#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [mic][as.mic()].
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#'
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#'
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#' When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as `>=`). Missing intermediate log2 levels will always be plotted too.
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#'
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#' ### The `scale_*_sir()` Functions
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#'
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#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
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#'
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#'
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#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [sir][as.sir()].
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#'
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#'
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#' At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
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#'
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#' ### Additional `ggplot2` Functions
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@@ -201,7 +201,7 @@
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#' geom_boxplot(fill = NA, colour = "grey30") +
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#' geom_jitter(width = 0.25)
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#' labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
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#'
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#'
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#' mic_sir_plot
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#' }
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#' if (require("ggplot2")) {
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@@ -83,10 +83,10 @@ Other contributors:
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\item Judith M. Fonville [contributor]
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\item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
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\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
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\item Matthew Saab [contributor]
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\item Matthew Saab (\href{https://orcid.org/0009-0008-6626-7919}{ORCID}) [contributor]
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\item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
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\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
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\item Rogier P. Schade [contributor]
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\item Rogier P. Schade (\href{https://orcid.org/0000-0002-9487-4467}{ORCID}) [contributor]
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\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
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\item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
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\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
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@@ -322,7 +322,7 @@ if (require("ggplot2")) {
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geom_boxplot(fill = NA, colour = "grey30") +
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geom_jitter(width = 0.25)
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labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
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mic_sir_plot
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}
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if (require("ggplot2")) {
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@@ -32,6 +32,9 @@ test_that("test-antibiogram.R", {
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# Traditional antibiogram ----------------------------------------------
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ab0 <- antibiogram(example_isolates)
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ab1 <- antibiogram(example_isolates,
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antimicrobials = c(aminoglycosides(), carbapenems())
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)
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