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(v1.5.0.9025) big plot and ggplot generics update

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dr. M.S. (Matthijs) Berends
2021-02-25 10:33:08 +01:00
parent 31ceba5441
commit a673407904
42 changed files with 1058 additions and 842 deletions
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57
R/mic.R
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@ -53,8 +53,9 @@
#' ab = "AMX",
#' guideline = "EUCAST")
#'
#' # plot MIC values, see ?plot
#' plot(mic_data)
#' barplot(mic_data)
#' plot(mic_data, mo = "E. coli", ab = "cipro")
as.mic <- function(x, na.rm = FALSE) {
meet_criteria(x, allow_class = c("mic", "character", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
@ -175,9 +176,11 @@ as.numeric.mic <- function(x, ...) {
#' @method droplevels mic
#' @export
#' @noRd
droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, ...) {
droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = TRUE, ...) {
x <- droplevels.factor(x, exclude = exclude, ...)
class(x) <- c("mic", "ordered", "factor")
if (as.mic == TRUE) {
class(x) <- c("mic", "ordered", "factor")
}
x
}
@ -221,54 +224,6 @@ summary.mic <- function(object, ...) {
value
}
#' @method plot mic
#' @export
#' @importFrom graphics barplot axis
#' @rdname plot
plot.mic <- function(x,
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "MIC value",
axes = FALSE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(axes, allow_class = "logical", has_length = 1)
barplot(table(as.double(x)),
ylab = ylab,
xlab = xlab,
axes = axes,
main = main,
...)
axis(2, seq(0, max(table(as.double(x)))))
}
#' @method barplot mic
#' @export
#' @importFrom graphics barplot axis
#' @rdname plot
barplot.mic <- function(height,
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "MIC value",
axes = FALSE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(axes, allow_class = "logical", has_length = 1)
barplot(table(as.double(height)),
ylab = ylab,
xlab = xlab,
axes = axes,
main = main,
...)
axis(2, seq(0, max(table(as.double(height)))))
}
#' @method [ mic
#' @export
#' @noRd