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(v3.0.0.9015) plotting fix

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2025-07-19 14:06:36 +02:00
parent 49274f010b
commit 6cb724a208
5 changed files with 6 additions and 6 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.0.9014 Version: 3.0.0.9015
Date: 2025-07-18 Date: 2025-07-19
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 3.0.0.9014 # AMR 3.0.0.9015
This is primarily a bugfix release, though we added one nice feature too. This is primarily a bugfix release, though we added one nice feature too.

2
R/ggplot_sir.R
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@ -177,8 +177,8 @@ ggplot_sir <- function(data,
nrow = NULL, nrow = NULL,
colours = c( colours = c(
S = "#3CAEA3", S = "#3CAEA3",
SI = "#3CAEA3",
SDD = "#8FD6C4", SDD = "#8FD6C4",
SI = "#3CAEA3",
I = "#F6D55C", I = "#F6D55C",
IR = "#ED553B", IR = "#ED553B",
R = "#ED553B" R = "#ED553B"

2
R/plotting.R
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@ -1490,7 +1490,7 @@ labels_sir_count <- function(position = NULL,
} }
expand_SIR_colours <- function(colours_SIR, unname = TRUE) { expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
sir_order <- c("S", "SDD", "I", "R") sir_order <- c("S", "SDD", "SI", "I", "IR", "R")
if (is.null(names(colours_SIR))) { if (is.null(names(colours_SIR))) {
if (length(colours_SIR) == 1) { if (length(colours_SIR) == 1) {

2
man/ggplot_sir.Rd
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@ -9,7 +9,7 @@ ggplot_sir(data, position = NULL, x = "antibiotic",
fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1), fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE, limits = NULL, translate_ab = "name", combine_SI = TRUE,
minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
= "#3CAEA3", SI = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", IR = "#ED553B", = "#3CAEA3", SDD = "#8FD6C4", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B",
R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5, R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5,
datalabels.colour = "grey15", title = NULL, subtitle = NULL, datalabels.colour = "grey15", title = NULL, subtitle = NULL,
caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...) caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...)