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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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157
man/plot.Rd
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@@ -33,80 +33,135 @@ scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_x_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
= "#ED553B"), language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
scale_x_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
...
)
scale_colour_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I =
"#F6D55C", R = "#ED553B"), language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
scale_colour_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
...
)
scale_fill_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C",
R = "#ED553B"), language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
scale_fill_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
...
)
\method{plot}{mic}(x, mo = NULL, ab = NULL,
\method{plot}{mic}(
x,
mo = NULL,
ab = NULL,
guideline = getOption("AMR_guideline", "EUCAST"),
main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
= language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
= "#ED553B"), language = get_AMR_locale(), expand = TRUE,
main = deparse(substitute(x)),
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
\method{autoplot}{mic}(object, mo = NULL, ab = NULL,
\method{autoplot}{mic}(
object,
mo = NULL,
ab = NULL,
guideline = getOption("AMR_guideline", "EUCAST"),
title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
= "#ED553B"), language = get_AMR_locale(), expand = TRUE,
title = deparse(substitute(object)),
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
\method{plot}{disk}(x, main = deparse(substitute(x)),
\method{plot}{disk}(
x,
main = deparse(substitute(x)),
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
mo = NULL, ab = NULL, guideline = getOption("AMR_guideline", "EUCAST"),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
"#ED553B"), language = get_AMR_locale(), expand = TRUE,
mo = NULL,
ab = NULL,
guideline = getOption("AMR_guideline", "EUCAST"),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
\method{autoplot}{disk}(object, mo = NULL, ab = NULL,
title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
language = language), guideline = getOption("AMR_guideline", "EUCAST"),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
"#ED553B"), language = get_AMR_locale(), expand = TRUE,
\method{autoplot}{disk}(
object,
mo = NULL,
ab = NULL,
title = deparse(substitute(object)),
ylab = translate_AMR("Frequency", language = language),
xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
guideline = getOption("AMR_guideline", "EUCAST"),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
\method{plot}{sir}(x, ylab = translate_AMR("Percentage", language =
language), xlab = translate_AMR("Antimicrobial Interpretation", language =
language), main = deparse(substitute(x)), language = get_AMR_locale(),
...)
\method{autoplot}{sir}(object, title = deparse(substitute(object)),
\method{plot}{sir}(
x,
ylab = translate_AMR("Percentage", language = language),
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
ylab = translate_AMR("Frequency", language = language), colours_SIR = c(S
= "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(), ...)
main = deparse(substitute(x)),
language = get_AMR_locale(),
...
)
\method{autoplot}{sir}(
object,
title = deparse(substitute(object)),
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
ylab = translate_AMR("Frequency", language = language),
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
...
)
facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
limits = c(0, NA))
scale_y_percent(
breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
limits = c(0, NA)
)
scale_sir_colours(..., aesthetics, colours_SIR = c(S = "#3CAEA3", SDD =
"#8FD6C4", I = "#F6D55C", R = "#ED553B"))
scale_sir_colours(
...,
aesthetics,
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B")
)
theme_sir()
labels_sir_count(position = NULL, x = "antibiotic",
translate_ab = "name", minimum = 30, language = get_AMR_locale(),
combine_SI = TRUE, datalabels.size = 3, datalabels.colour = "grey15")
labels_sir_count(
position = NULL,
x = "antibiotic",
translate_ab = "name",
minimum = 30,
language = get_AMR_locale(),
combine_SI = TRUE,
datalabels.size = 3,
datalabels.colour = "grey15"
)
}
\arguments{
\item{keep_operators}{A \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}