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(v1.8.1.9006) added EUCAST 2022 and CLSI 2022

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dr. M.S. (Matthijs) Berends
2022-05-10 21:34:30 +02:00
parent 680e8e7a41
commit 859224e9d0
30 changed files with 3464 additions and 3392 deletions
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18
R/plot.R
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@ -79,7 +79,7 @@ plot.mic <- function(x,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -166,7 +166,7 @@ barplot.mic <- function(height,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(height))),
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -299,7 +299,7 @@ fortify.mic <- function(object, ...) {
#' @importFrom graphics barplot axis mtext legend
#' @rdname plot
plot.disk <- function(x,
main = paste("Disk zones of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -386,7 +386,7 @@ plot.disk <- function(x,
#' @export
#' @noRd
barplot.disk <- function(height,
main = paste("Disk zones of", deparse(substitute(height))),
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -525,7 +525,7 @@ fortify.disk <- function(object, ...) {
plot.rsi <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = paste("Resistance Overview of", deparse(substitute(x))),
main = deparse(substitute(x)),
...) {
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
@ -576,7 +576,7 @@ plot.rsi <- function(x,
#' @export
#' @noRd
barplot.rsi <- function(height,
main = paste("Resistance Overview of", deparse(substitute(height))),
main = deparse(substitute(height)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -738,7 +738,11 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
guideline_txt <- ""
} else {
guideline_txt <- paste0("(", guideline, ")")
guideline_txt <- guideline
if (isTRUE(list(...)$uti)) {
guideline_txt <- paste("UTIs,", guideline_txt)
}
guideline_txt <- paste0("(", guideline_txt, ")")
}
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
} else {