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rename limit_mic_range() to rescale_mic()

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dr. M.S. (Matthijs) Berends
2024-05-24 15:07:41 +02:00
parent d214f74e25
commit c3ce1b551d
8 changed files with 22 additions and 22 deletions
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8
R/mic.R
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@@ -96,7 +96,7 @@ VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)),
#'
#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class.
#'
#' With [limit_mic_range()], existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.
#' With [rescale_mic()], existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.
#'
#' For `ggplot2`, use one of the [`scale_*_mic()`][scale_x_mic()] functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as a [numeric] vector. Bear in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
@@ -116,8 +116,8 @@ VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)),
#' quantile(mic_data)
#' all(mic_data < 512)
#'
#' # limit MICs using limit_mic_range()
#' limit_mic_range(mic_data, mic_range = c(4, 16))
#' # limit MICs using rescale_mic()
#' rescale_mic(mic_data, mic_range = c(4, 16))
#'
#' # interpret MIC values
#' as.sir(
@@ -270,7 +270,7 @@ NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE)
#' @rdname as.mic
#' @param mic_range a manual range to limit the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to set no limit on one side, e.g., `mic_range = c(NA, 32)`.
#' @export
limit_mic_range <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
stop_ifnot(all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
"Values in `mic_range` must be valid MIC values. Unvalid: ", vector_and(mic_range[mic_range %in% c(VALID_MIC_LEVELS, NA)]))

8
R/plot.R
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@@ -117,7 +117,7 @@ scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE
meet_criteria(drop, allow_class = "logical", has_length = 1)
scale <- ggplot2::scale_x_discrete(drop = drop, ...)
scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
}
scale
}
@@ -130,7 +130,7 @@ scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE
meet_criteria(drop, allow_class = "logical", has_length = 1)
scale <- ggplot2::scale_y_discrete(drop = drop, ...)
scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
}
scale
}
@@ -143,7 +143,7 @@ scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, drop =
meet_criteria(drop, allow_class = "logical", has_length = 1)
scale <- ggplot2::scale_colour_discrete(drop = drop, ...)
scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
}
scale
}
@@ -156,7 +156,7 @@ scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FA
meet_criteria(drop, allow_class = "logical", has_length = 1)
scale <- ggplot2::scale_fill_discrete(drop = drop, ...)
scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
}
scale
}

2
R/sir.R
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@@ -323,7 +323,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
#' @rdname as.sir
#' @export
#' @param S,I,R,N,SDD a case-indepdendent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters are removed from the input.
#' @param S,I,R,N,SDD a case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters are removed from the input.
# extra param: warn (logical, to never throw a warning)
as.sir.default <- function(x, S = "^(S|U)+$", I = "^(I|H)+$", R = "^(R)+$", N = "^(N|V)+$", SDD = "^(SDD|D)+$", ...) {
if (inherits(x, "sir")) {