mirror of
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91 lines
4.1 KiB
R
Executable File
91 lines
4.1 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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# doi: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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#' Deprecated Functions
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#'
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#' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
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#' @keywords internal
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#' @name AMR-deprecated
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#' @rdname AMR-deprecated
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#' @export
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as.rsi <- function(...) {
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deprecation_warning("as.rsi", "as.sir")
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as.sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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is.rsi.eligible <- function(...) {
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deprecation_warning("is.rsi.eligible", "is_sir_eligible")
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is_sir_eligible(...)
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}
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# NAMESPACE NALOPEN
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# will be exported using s3_register() in R/zzz.R
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pillar_shaft.rsi <- function(x, ...) {
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out <- trimws(format(x))
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if (has_colour()) {
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# colours will anyway not work when has_colour() == FALSE,
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# but then the indentation should also not be applied
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out[is.na(x)] <- font_grey(" NA")
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out[x == "S"] <- font_green_bg(" S ")
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out[x == "I"] <- font_orange_bg(" I ")
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out[x == "R"] <- font_red_bg(" R ")
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}
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create_pillar_column(out, align = "left", width = 5)
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}
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type_sum.rsi <- function(x, ...) {
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deprecation_warning("as.rsi", "as.sir", "Transform your old 'rsi' class to the new 'sir' with `as.sir()` using e.g.:\n your_data %>% mutate_if(~inherits(.x, \"rsi\"), as.sir)")
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"rsi"
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}
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#' @method print rsi
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#' @export
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#' @noRd
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print.rsi <- function(x, ...) {
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deprecation_warning("as.rsi", "as.sir", "Transform your old 'rsi' class to the new 'sir' with `as.sir()`")
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print(x, ...)
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}
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deprecation_warning <- function(old, new = NULL, extra_msg = NULL) {
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env <- paste0("deprecated_", old)
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if (!env %in% names(AMR_env)) {
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AMR_env[[paste0("deprecated_", old)]] <- 1
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warning_(ifelse(is.null(new),
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paste0("The `", old, "()` function is no longer in use"),
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paste0("The `", old, "()` function has been replaced with `", new, "()`")),
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", see `?AMR-deprecated`.",
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ifelse(!is.null(extra_msg),
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paste0(" ", extra_msg),
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""),
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"\nThis warning will be shown once per session.")
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}
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}
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