P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-20 23:33:16 +02:00
Code Releases Activity

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-07-17 17:05:41 +02:00
parent 8dab0a3730
commit d94bdd2c6a
23 changed files with 237 additions and 164 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
man/plot.Rd
View File

@ -33,25 +33,25 @@ scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_x_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#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("#3CAEA3", "#F6D55C", "#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("#3CAEA3", "#F6D55C", "#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,
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("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(), expand = TRUE,
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"), ...)
@ -60,8 +60,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
language = language),
xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(), expand = TRUE,
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"), ...)
@ -69,8 +69,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(), expand = TRUE,
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"), ...)
@ -78,8 +78,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(), expand = TRUE,
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"), ...)
@ -90,8 +90,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
\method{autoplot}{sir}(object, title = deparse(substitute(object)),
xlab = translate_AMR("Antimicrobial Interpretation", language = language),
ylab = translate_AMR("Frequency", language = language),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
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)
@ -99,8 +99,8 @@ 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_sir_colours(..., aesthetics, colours_SIR = c("#3CAEA3", "#F6D55C",
"#ED553B"))
scale_sir_colours(..., aesthetics, colours_SIR = c(S = "#3CAEA3", SDD =
"#8FD6C4", I = "#F6D55C", R = "#ED553B"))
theme_sir()