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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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46
man/ggplot_sir.Rd
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@ -5,42 +5,18 @@
\alias{geom_sir}
\title{AMR Plots with \code{ggplot2}}
\usage{
ggplot_sir(
data,
position = NULL,
x = "antibiotic",
fill = "interpretation",
facet = NULL,
breaks = seq(0, 1, 0.1),
limits = NULL,
translate_ab = "name",
combine_SI = TRUE,
minimum = 30,
language = get_AMR_locale(),
nrow = NULL,
colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R =
"#ED553B"),
datalabels = TRUE,
datalabels.size = 2.5,
datalabels.colour = "grey15",
title = NULL,
subtitle = NULL,
caption = NULL,
x.title = "Antimicrobial",
y.title = "Proportion",
...
)
ggplot_sir(data, position = NULL, x = "antibiotic",
fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE,
minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
= "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R = "#ED553B"),
datalabels = TRUE, datalabels.size = 2.5, datalabels.colour = "grey15",
title = NULL, subtitle = NULL, caption = NULL,
x.title = "Antimicrobial", y.title = "Proportion", ...)
geom_sir(
position = NULL,
x = c("antibiotic", "interpretation"),
fill = "interpretation",
translate_ab = "name",
minimum = 30,
language = get_AMR_locale(),
combine_SI = TRUE,
...
)
geom_sir(position = NULL, x = c("antibiotic", "interpretation"),
fill = "interpretation", translate_ab = "name", minimum = 30,
language = get_AMR_locale(), combine_SI = TRUE, ...)
}
\arguments{
\item{data}{a \link{data.frame} with column(s) of class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}})}