mirror of https://github.com/msberends/AMR.git
861 lines
22 KiB
R
Executable File
861 lines
22 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# these are allowed MIC values and will become [factor] levels
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operators <- c("<", "<=", "", ">=", ">")
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valid_mic_levels <- c(
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c(t(vapply(
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FUN.VALUE = character(6), operators,
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function(x) paste0(x, "0.000", c(1:4, 6, 8))
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))),
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c(t(vapply(
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FUN.VALUE = character(90), operators,
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function(x) paste0(x, "0.00", c(1:9, 11:19, 21:29, 31:39, 41:49, 51:59, 61:69, 71:79, 81:89, 91:99))
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))),
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unique(c(t(vapply(
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FUN.VALUE = character(106), operators,
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function(x) {
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paste0(x, sort(as.double(paste0(
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"0.0",
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sort(c(1:99, 125, 128, 156, 165, 256, 512, 625))
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))))
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}
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)))),
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unique(c(t(vapply(
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FUN.VALUE = character(103), operators,
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function(x) {
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paste0(x, sort(as.double(paste0(
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"0.",
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c(1:99, 125, 128, 256, 512)
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))))
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}
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)))),
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c(t(vapply(
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FUN.VALUE = character(10), operators,
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function(x) paste0(x, sort(c(1:9, 1.5)))
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))),
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c(t(vapply(
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FUN.VALUE = character(45), operators,
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function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])
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))),
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c(t(vapply(
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FUN.VALUE = character(17), operators,
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function(x) paste0(x, sort(c(2^c(7:11), 192, 80 * c(2:12))))
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)))
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)
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#' Transform Input to Minimum Inhibitory Concentrations (MIC)
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#'
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#' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
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#' @rdname as.mic
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#' @param x a [character] or [numeric] vector
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#' @param na.rm a [logical] indicating whether missing values should be removed
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#' @param ... arguments passed on to methods
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#' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
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#'
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#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
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#'
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#' ```
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#' x <- random_mic(10)
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#' x
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#' #> Class 'mic'
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#' #> [1] 16 1 8 8 64 >=128 0.0625 32 32 16
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#'
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#' is.factor(x)
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#' #> [1] TRUE
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#'
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#' x[1] * 2
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#' #> [1] 32
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#'
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#' median(x)
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#' #> [1] 26
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#' ```
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#'
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#' This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using [numeric] values in data analysis, e.g.:
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#'
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#' ```
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#' x[x > 4]
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#' #> Class 'mic'
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#' #> [1] 16 8 8 64 >=128 32 32 16
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#'
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#' df <- data.frame(x, hospital = "A")
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#' subset(df, x > 4) # or with dplyr: df %>% filter(x > 4)
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#' #> x hospital
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#' #> 1 16 A
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#' #> 5 64 A
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#' #> 6 >=128 A
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#' #> 8 32 A
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#' #> 9 32 A
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#' #> 10 16 A
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#' ```
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#'
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#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
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#'
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#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
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#'
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#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class.
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#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
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#' @aliases mic
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#' @export
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#' @seealso [as.sir()]
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#' @examples
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#' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
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#' mic_data
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#' is.mic(mic_data)
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#'
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#' # this can also coerce combined MIC/SIR values:
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#' as.mic("<=0.002; S")
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#'
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#' # mathematical processing treats MICs as numeric values
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#' fivenum(mic_data)
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#' quantile(mic_data)
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#' all(mic_data < 512)
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#'
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#' # interpret MIC values
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#' as.sir(
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#' x = as.mic(2),
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#' mo = as.mo("Streptococcus pneumoniae"),
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#' ab = "AMX",
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#' guideline = "EUCAST"
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#' )
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#' as.sir(
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#' x = as.mic(c(0.01, 2, 4, 8)),
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#' mo = as.mo("Streptococcus pneumoniae"),
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#' ab = "AMX",
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#' guideline = "EUCAST"
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#' )
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#'
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#' # plot MIC values, see ?plot
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#' plot(mic_data)
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#' plot(mic_data, mo = "E. coli", ab = "cipro")
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#'
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#' if (require("ggplot2")) {
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#' autoplot(mic_data, mo = "E. coli", ab = "cipro")
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#' }
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#' if (require("ggplot2")) {
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#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
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#' }
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#' if (require("ggplot2")) {
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#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk") # Ukrainian
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#' }
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as.mic <- function(x, na.rm = FALSE) {
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meet_criteria(x, allow_class = c("mic", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
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meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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if (is.mic(x)) {
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x
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} else {
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if (is.numeric(x)) {
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x <- format(x, scientific = FALSE)
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} else {
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x <- as.character(unlist(x))
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}
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if (isTRUE(na.rm)) {
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x <- x[!is.na(x)]
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}
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x[trimws2(x) == ""] <- NA
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x.bak <- x
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# comma to period
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x <- gsub(",", ".", x, fixed = TRUE)
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# transform Unicode for >= and <=
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x <- gsub("\u2264", "<=", x, fixed = TRUE)
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x <- gsub("\u2265", ">=", x, fixed = TRUE)
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# remove other invalid characters
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x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE)
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# remove space between operator and number ("<= 0.002" -> "<=0.002")
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x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
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# transform => to >= and =< to <=
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x <- gsub("=<", "<=", x, fixed = TRUE)
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x <- gsub("=>", ">=", x, fixed = TRUE)
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# dots without a leading zero must start with 0
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x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
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# values like "<=0.2560.512" should be 0.512
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x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
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# remove ending .0
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x <- gsub("[.]+0$", "", x, perl = TRUE)
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# remove all after last digit
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x <- gsub("[^0-9]+$", "", x, perl = TRUE)
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# keep only one zero before dot
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x <- gsub("0+[.]", "0.", x, perl = TRUE)
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# starting 00 is probably 0.0 if there's no dot yet
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x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
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# remove last zeroes
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x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
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x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
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# remove ending .0 again
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x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
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# never end with dot
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x <- gsub("[.]$", "", x, perl = TRUE)
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# trim it
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x <- trimws2(x)
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## previously unempty values now empty - should return a warning later on
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x[x.bak != "" & x == ""] <- "invalid"
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na_before <- x[is.na(x) | x == ""] %pm>% length()
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x[!x %in% valid_mic_levels] <- NA
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na_after <- x[is.na(x) | x == ""] %pm>% length()
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if (na_before != na_after) {
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list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
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unique() %pm>%
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sort() %pm>%
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vector_and(quotes = TRUE)
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cur_col <- get_current_column()
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warning_("in `as.mic()`: ", na_after - na_before, " result",
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ifelse(na_after - na_before > 1, "s", ""),
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ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
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" truncated (",
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round(((na_after - na_before) / length(x)) * 100),
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"%) that were invalid MICs: ",
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list_missing,
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call = FALSE
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)
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}
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set_clean_class(factor(x, levels = valid_mic_levels, ordered = TRUE),
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new_class = c("mic", "ordered", "factor")
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)
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}
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}
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all_valid_mics <- function(x) {
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if (!inherits(x, c("mic", "character", "factor", "numeric", "integer"))) {
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return(FALSE)
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}
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x_mic <- tryCatch(suppressWarnings(as.mic(x[!is.na(x)])),
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error = function(e) NA
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)
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!any(is.na(x_mic)) && !all(is.na(x))
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}
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#' @rdname as.mic
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#' @details `NA_mic_` is a missing value of the new `mic` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
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#' @format NULL
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#' @export
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NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
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new_class = c("mic", "ordered", "factor")
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)
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#' @rdname as.mic
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#' @export
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is.mic <- function(x) {
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inherits(x, "mic")
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}
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#' @method as.double mic
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#' @export
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#' @noRd
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as.double.mic <- function(x, ...) {
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as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
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}
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#' @method as.numeric mic
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#' @export
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#' @noRd
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as.numeric.mic <- function(x, ...) {
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as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
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}
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#' @rdname as.mic
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#' @method droplevels mic
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#' @param as.mic a [logical] to indicate whether the `mic` class should be kept - the default is `FALSE`
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#' @export
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droplevels.mic <- function(x, as.mic = FALSE, ...) {
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x <- droplevels.factor(x, ...)
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if (as.mic == TRUE) {
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class(x) <- c("mic", "ordered", "factor")
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}
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x
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}
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# will be exported using s3_register() in R/zzz.R
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pillar_shaft.mic <- function(x, ...) {
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crude_numbers <- as.double(x)
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operators <- gsub("[^<=>]+", "", as.character(x))
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operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
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out <- trimws(paste0(operators, trimws(format(crude_numbers))))
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out[is.na(x)] <- font_na(NA)
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# maketrailing zeroes almost invisible
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out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
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create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
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}
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# will be exported using s3_register() in R/zzz.R
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type_sum.mic <- function(x, ...) {
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"mic"
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}
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#' @method print mic
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#' @export
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#' @noRd
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print.mic <- function(x, ...) {
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cat("Class 'mic'",
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ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
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"\n",
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sep = ""
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)
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print(as.character(x), quote = FALSE)
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att <- attributes(x)
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if ("na.action" %in% names(att)) {
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cat(font_silver(paste0("(NA ", class(att$na.action), ": ", paste0(att$na.action, collapse = ", "), ")\n")))
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}
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}
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#' @method summary mic
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#' @export
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#' @noRd
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summary.mic <- function(object, ...) {
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summary(as.double(object), ...)
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}
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#' @method as.matrix mic
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#' @export
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#' @noRd
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as.matrix.mic <- function(x, ...) {
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as.matrix(as.double(x), ...)
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}
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#' @method [ mic
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#' @export
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#' @noRd
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"[.mic" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method [[ mic
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#' @export
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#' @noRd
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"[[.mic" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method [<- mic
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#' @export
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#' @noRd
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"[<-.mic" <- function(i, j, ..., value) {
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value <- as.mic(value)
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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}
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#' @method [[<- mic
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#' @export
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#' @noRd
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"[[<-.mic" <- function(i, j, ..., value) {
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value <- as.mic(value)
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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}
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#' @method c mic
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#' @export
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#' @noRd
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c.mic <- function(...) {
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as.mic(unlist(lapply(list(...), as.character)))
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}
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#' @method unique mic
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#' @export
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#' @noRd
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unique.mic <- function(x, incomparables = FALSE, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method rep mic
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#' @export
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#' @noRd
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rep.mic <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method sort mic
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#' @export
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#' @noRd
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sort.mic <- function(x, decreasing = FALSE, ...) {
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if (decreasing == TRUE) {
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ord <- order(-as.double(x))
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} else {
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ord <- order(as.double(x))
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}
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x[ord]
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}
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#' @method hist mic
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#' @importFrom graphics hist
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#' @export
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#' @noRd
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hist.mic <- function(x, ...) {
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warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
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hist(log2(x))
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}
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# will be exported using s3_register() in R/zzz.R
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get_skimmers.mic <- function(column) {
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skimr::sfl(
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skim_type = "mic",
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p0 = ~ stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
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p25 = ~ stats::quantile(., probs = 0.25, na.rm = TRUE, names = FALSE),
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p50 = ~ stats::quantile(., probs = 0.5, na.rm = TRUE, names = FALSE),
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p75 = ~ stats::quantile(., probs = 0.75, na.rm = TRUE, names = FALSE),
|
|
p100 = ~ stats::quantile(., probs = 1, na.rm = TRUE, names = FALSE),
|
|
hist = ~ skimr::inline_hist(log2(stats::na.omit(.)), 5)
|
|
)
|
|
}
|
|
|
|
# Miscellaneous mathematical functions ------------------------------------
|
|
|
|
#' @method mean mic
|
|
#' @export
|
|
#' @noRd
|
|
mean.mic <- function(x, trim = 0, na.rm = FALSE, ...) {
|
|
mean(as.double(x), trim = trim, na.rm = na.rm, ...)
|
|
}
|
|
|
|
#' @method median mic
|
|
#' @importFrom stats median
|
|
#' @export
|
|
#' @noRd
|
|
median.mic <- function(x, na.rm = FALSE, ...) {
|
|
median(as.double(x), na.rm = na.rm, ...)
|
|
}
|
|
|
|
#' @method quantile mic
|
|
#' @importFrom stats quantile
|
|
#' @export
|
|
#' @noRd
|
|
quantile.mic <- function(x, probs = seq(0, 1, 0.25), na.rm = FALSE,
|
|
names = TRUE, type = 7, ...) {
|
|
quantile(as.double(x), probs = probs, na.rm = na.rm, names = names, type = type, ...)
|
|
}
|
|
|
|
# Math (see ?groupGeneric) ----------------------------------------------
|
|
|
|
#' @method abs mic
|
|
#' @export
|
|
#' @noRd
|
|
abs.mic <- function(x) {
|
|
abs(as.double(x))
|
|
}
|
|
#' @method sign mic
|
|
#' @export
|
|
#' @noRd
|
|
sign.mic <- function(x) {
|
|
sign(as.double(x))
|
|
}
|
|
#' @method sqrt mic
|
|
#' @export
|
|
#' @noRd
|
|
sqrt.mic <- function(x) {
|
|
sqrt(as.double(x))
|
|
}
|
|
#' @method floor mic
|
|
#' @export
|
|
#' @noRd
|
|
floor.mic <- function(x) {
|
|
floor(as.double(x))
|
|
}
|
|
#' @method ceiling mic
|
|
#' @export
|
|
#' @noRd
|
|
ceiling.mic <- function(x) {
|
|
ceiling(as.double(x))
|
|
}
|
|
#' @method trunc mic
|
|
#' @export
|
|
#' @noRd
|
|
trunc.mic <- function(x, ...) {
|
|
trunc(as.double(x), ...)
|
|
}
|
|
#' @method round mic
|
|
#' @export
|
|
#' @noRd
|
|
round.mic <- function(x, digits = 0) {
|
|
round(as.double(x), digits = digits)
|
|
}
|
|
#' @method signif mic
|
|
#' @export
|
|
#' @noRd
|
|
signif.mic <- function(x, digits = 6) {
|
|
signif(as.double(x), digits = digits)
|
|
}
|
|
#' @method exp mic
|
|
#' @export
|
|
#' @noRd
|
|
exp.mic <- function(x) {
|
|
exp(as.double(x))
|
|
}
|
|
#' @method log mic
|
|
#' @export
|
|
#' @noRd
|
|
log.mic <- function(x, base = exp(1)) {
|
|
log(as.double(x), base = base)
|
|
}
|
|
#' @method log10 mic
|
|
#' @export
|
|
#' @noRd
|
|
log10.mic <- function(x) {
|
|
log10(as.double(x))
|
|
}
|
|
#' @method log2 mic
|
|
#' @export
|
|
#' @noRd
|
|
log2.mic <- function(x) {
|
|
log2(as.double(x))
|
|
}
|
|
#' @method expm1 mic
|
|
#' @export
|
|
#' @noRd
|
|
expm1.mic <- function(x) {
|
|
expm1(as.double(x))
|
|
}
|
|
#' @method log1p mic
|
|
#' @export
|
|
#' @noRd
|
|
log1p.mic <- function(x) {
|
|
log1p(as.double(x))
|
|
}
|
|
#' @method cos mic
|
|
#' @export
|
|
#' @noRd
|
|
cos.mic <- function(x) {
|
|
cos(as.double(x))
|
|
}
|
|
#' @method sin mic
|
|
#' @export
|
|
#' @noRd
|
|
sin.mic <- function(x) {
|
|
sin(as.double(x))
|
|
}
|
|
#' @method tan mic
|
|
#' @export
|
|
#' @noRd
|
|
tan.mic <- function(x) {
|
|
tan(as.double(x))
|
|
}
|
|
#' @method cospi mic
|
|
#' @export
|
|
#' @noRd
|
|
cospi.mic <- function(x) {
|
|
cospi(as.double(x))
|
|
}
|
|
#' @method sinpi mic
|
|
#' @export
|
|
#' @noRd
|
|
sinpi.mic <- function(x) {
|
|
sinpi(as.double(x))
|
|
}
|
|
#' @method tanpi mic
|
|
#' @export
|
|
#' @noRd
|
|
tanpi.mic <- function(x) {
|
|
tanpi(as.double(x))
|
|
}
|
|
#' @method acos mic
|
|
#' @export
|
|
#' @noRd
|
|
acos.mic <- function(x) {
|
|
acos(as.double(x))
|
|
}
|
|
#' @method asin mic
|
|
#' @export
|
|
#' @noRd
|
|
asin.mic <- function(x) {
|
|
asin(as.double(x))
|
|
}
|
|
#' @method atan mic
|
|
#' @export
|
|
#' @noRd
|
|
atan.mic <- function(x) {
|
|
atan(as.double(x))
|
|
}
|
|
#' @method cosh mic
|
|
#' @export
|
|
#' @noRd
|
|
cosh.mic <- function(x) {
|
|
cosh(as.double(x))
|
|
}
|
|
#' @method sinh mic
|
|
#' @export
|
|
#' @noRd
|
|
sinh.mic <- function(x) {
|
|
sinh(as.double(x))
|
|
}
|
|
#' @method tanh mic
|
|
#' @export
|
|
#' @noRd
|
|
tanh.mic <- function(x) {
|
|
tanh(as.double(x))
|
|
}
|
|
#' @method acosh mic
|
|
#' @export
|
|
#' @noRd
|
|
acosh.mic <- function(x) {
|
|
acosh(as.double(x))
|
|
}
|
|
#' @method asinh mic
|
|
#' @export
|
|
#' @noRd
|
|
asinh.mic <- function(x) {
|
|
asinh(as.double(x))
|
|
}
|
|
#' @method atanh mic
|
|
#' @export
|
|
#' @noRd
|
|
atanh.mic <- function(x) {
|
|
atanh(as.double(x))
|
|
}
|
|
#' @method lgamma mic
|
|
#' @export
|
|
#' @noRd
|
|
lgamma.mic <- function(x) {
|
|
lgamma(as.double(x))
|
|
}
|
|
#' @method gamma mic
|
|
#' @export
|
|
#' @noRd
|
|
gamma.mic <- function(x) {
|
|
gamma(as.double(x))
|
|
}
|
|
#' @method digamma mic
|
|
#' @export
|
|
#' @noRd
|
|
digamma.mic <- function(x) {
|
|
digamma(as.double(x))
|
|
}
|
|
#' @method trigamma mic
|
|
#' @export
|
|
#' @noRd
|
|
trigamma.mic <- function(x) {
|
|
trigamma(as.double(x))
|
|
}
|
|
#' @method cumsum mic
|
|
#' @export
|
|
#' @noRd
|
|
cumsum.mic <- function(x) {
|
|
cumsum(as.double(x))
|
|
}
|
|
#' @method cumprod mic
|
|
#' @export
|
|
#' @noRd
|
|
cumprod.mic <- function(x) {
|
|
cumprod(as.double(x))
|
|
}
|
|
#' @method cummax mic
|
|
#' @export
|
|
#' @noRd
|
|
cummax.mic <- function(x) {
|
|
cummax(as.double(x))
|
|
}
|
|
#' @method cummin mic
|
|
#' @export
|
|
#' @noRd
|
|
cummin.mic <- function(x) {
|
|
cummin(as.double(x))
|
|
}
|
|
|
|
# Ops (see ?groupGeneric) -----------------------------------------------
|
|
|
|
is_greater <- function(el) {
|
|
el %like_case% ">[0-9]"
|
|
}
|
|
is_lower <- function(el) {
|
|
el %like_case% "<[0-9]"
|
|
}
|
|
|
|
#' @method + mic
|
|
#' @export
|
|
#' @noRd
|
|
`+.mic` <- function(e1, e2) {
|
|
as.double(e1) + as.double(e2)
|
|
}
|
|
|
|
#' @method - mic
|
|
#' @export
|
|
#' @noRd
|
|
`-.mic` <- function(e1, e2) {
|
|
as.double(e1) - as.double(e2)
|
|
}
|
|
|
|
#' @method * mic
|
|
#' @export
|
|
#' @noRd
|
|
`*.mic` <- function(e1, e2) {
|
|
as.double(e1) * as.double(e2)
|
|
}
|
|
|
|
#' @method / mic
|
|
#' @export
|
|
#' @noRd
|
|
`/.mic` <- function(e1, e2) {
|
|
as.double(e1) / as.double(e2)
|
|
}
|
|
|
|
#' @method ^ mic
|
|
#' @export
|
|
#' @noRd
|
|
`^.mic` <- function(e1, e2) {
|
|
as.double(e1)^as.double(e2)
|
|
}
|
|
|
|
#' @method %% mic
|
|
#' @export
|
|
#' @noRd
|
|
`%%.mic` <- function(e1, e2) {
|
|
as.double(e1) %% as.double(e2)
|
|
}
|
|
|
|
#' @method %/% mic
|
|
#' @export
|
|
#' @noRd
|
|
`%/%.mic` <- function(e1, e2) {
|
|
as.double(e1) %/% as.double(e2)
|
|
}
|
|
|
|
#' @method & mic
|
|
#' @export
|
|
#' @noRd
|
|
`&.mic` <- function(e1, e2) {
|
|
as.double(e1) & as.double(e2)
|
|
}
|
|
|
|
#' @method | mic
|
|
#' @export
|
|
#' @noRd
|
|
`|.mic` <- function(e1, e2) {
|
|
as.double(e1) | as.double(e2)
|
|
}
|
|
|
|
#' @method ! mic
|
|
#' @export
|
|
#' @noRd
|
|
`!.mic` <- function(x) {
|
|
!as.double(x)
|
|
}
|
|
|
|
#' @method == mic
|
|
#' @export
|
|
#' @noRd
|
|
`==.mic` <- function(e1, e2) {
|
|
as.double(e1) == as.double(e2)
|
|
}
|
|
|
|
#' @method != mic
|
|
#' @export
|
|
#' @noRd
|
|
`!=.mic` <- function(e1, e2) {
|
|
as.double(e1) != as.double(e2)
|
|
}
|
|
|
|
#' @method < mic
|
|
#' @export
|
|
#' @noRd
|
|
`<.mic` <- function(e1, e2) {
|
|
as.double(e1) < as.double(e2)
|
|
}
|
|
|
|
#' @method <= mic
|
|
#' @export
|
|
#' @noRd
|
|
`<=.mic` <- function(e1, e2) {
|
|
as.double(e1) <= as.double(e2)
|
|
}
|
|
|
|
#' @method >= mic
|
|
#' @export
|
|
#' @noRd
|
|
`>=.mic` <- function(e1, e2) {
|
|
as.double(e1) >= as.double(e2)
|
|
}
|
|
|
|
#' @method > mic
|
|
#' @export
|
|
#' @noRd
|
|
`>.mic` <- function(e1, e2) {
|
|
as.double(e1) > as.double(e2)
|
|
# doesn't work...
|
|
# nolint start
|
|
# as.double(e1) > as.double(e2) |
|
|
# (as.double(e1) == as.double(e2) & is_lower(e2) & !is_lower(e1)) |
|
|
# (as.double(e1) == as.double(e2) & is_greater(e1) & !is_greater(e2))
|
|
# nolint end
|
|
}
|
|
|
|
# Summary (see ?groupGeneric) -------------------------------------------
|
|
|
|
#' @method all mic
|
|
#' @export
|
|
#' @noRd
|
|
all.mic <- function(..., na.rm = FALSE) {
|
|
all(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method any mic
|
|
#' @export
|
|
#' @noRd
|
|
any.mic <- function(..., na.rm = FALSE) {
|
|
any(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method sum mic
|
|
#' @export
|
|
#' @noRd
|
|
sum.mic <- function(..., na.rm = FALSE) {
|
|
sum(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method prod mic
|
|
#' @export
|
|
#' @noRd
|
|
prod.mic <- function(..., na.rm = FALSE) {
|
|
prod(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method min mic
|
|
#' @export
|
|
#' @noRd
|
|
min.mic <- function(..., na.rm = FALSE) {
|
|
min(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method max mic
|
|
#' @export
|
|
#' @noRd
|
|
max.mic <- function(..., na.rm = FALSE) {
|
|
max(as.double(c(...)), na.rm = na.rm)
|
|
}
|
|
#' @method range mic
|
|
#' @export
|
|
#' @noRd
|
|
range.mic <- function(..., na.rm = FALSE) {
|
|
range(as.double(c(...)), na.rm = na.rm)
|
|
}
|