AMR/R/zz_deprecated.R

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# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Deprecated Functions
#'
#' 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will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
#' @keywords internal
#' @name AMR-deprecated
#' @rdname AMR-deprecated
#' @export
NA_rsi_ <- set_clean_class(factor(NA_character_, levels = c("S", "I", "R"), ordered = TRUE),
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new_class = c("rsi", "ordered", "factor")
)
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#' @rdname AMR-deprecated
#' @export
as.rsi <- function(x, ...) {
deprecation_warning("as.rsi", "as.sir")
UseMethod("as.rsi")
}
#' @noRd
#' @export
as.rsi.default <- function(...) {
as.sir.default(...)
}
#' @noRd
#' @export
as.rsi.mic <- function(...) {
as.sir.mic(...)
}
#' @noRd
#' @export
as.rsi.disk <- function(...) {
as.sir.disk(...)
}
#' @noRd
#' @export
as.rsi.data.frame <- function(...) {
as.sir.data.frame(...)
}
#' @rdname AMR-deprecated
#' @export
facet_rsi <- function(...) {
deprecation_warning("facet_rsi", "facet_sir")
facet_sir(...)
}
#' @rdname AMR-deprecated
#' @export
geom_rsi <- function(...) {
deprecation_warning("geom_rsi", "geom_sir")
geom_sir(...)
}
#' @rdname AMR-deprecated
#' @export
ggplot_rsi <- function(...) {
deprecation_warning("ggplot_rsi", "ggplot_sir")
ggplot_sir(...)
}
#' @rdname AMR-deprecated
#' @export
ggplot_rsi_predict <- function(...) {
deprecation_warning("ggplot_rsi_predict", "ggplot_sir_predict")
ggplot_sir_predict(...)
}
#' @rdname AMR-deprecated
#' @export
is.rsi <- function(...) {
# REMINDER: change as.sir() to remove the deprecation warning there
suppressWarnings(is.sir(...))
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}
#' @rdname AMR-deprecated
#' @export
is.rsi.eligible <- function(...) {
deprecation_warning("is.rsi.eligible", "is_sir_eligible")
is_sir_eligible(...)
}
#' @rdname AMR-deprecated
#' @export
labels_rsi_count <- function(...) {
deprecation_warning("labels_rsi_count", "labels_sir_count")
labels_sir_count(...)
}
#' @rdname AMR-deprecated
#' @export
n_rsi <- function(...) {
deprecation_warning("n_rsi", "n_sir")
n_sir(...)
}
#' @rdname AMR-deprecated
#' @export
random_rsi <- function(...) {
deprecation_warning("random_rsi", "random_sir")
random_sir(...)
}
#' @rdname AMR-deprecated
#' @export
rsi_df <- function(...) {
deprecation_warning("rsi_df", "sir_df")
sir_df(...)
}
#' @rdname AMR-deprecated
#' @export
rsi_predict <- function(...) {
deprecation_warning("rsi_predict", "sir_predict")
sir_predict(...)
}
#' @rdname AMR-deprecated
#' @export
scale_rsi_colours <- function(...) {
deprecation_warning("scale_rsi_colours", "scale_sir_colours")
scale_sir_colours(...)
}
#' @rdname AMR-deprecated
#' @export
theme_rsi <- function(...) {
deprecation_warning("theme_rsi", "theme_sir")
theme_sir(...)
}
# will be exported using s3_register() in R/zzz.R
pillar_shaft.rsi <- pillar_shaft.sir
type_sum.rsi <- function(x, ...) {
if (message_not_thrown_before("type_sum.rsi")) {
deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns to 'sir' with `as.sir()`, e.g.:\n your_data %>% mutate_if(is.rsi, as.sir)")
}
"rsi"
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}
#' @method print rsi
#' @export
#' @noRd
print.rsi <- function(x, ...) {
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deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir' - transform your 'rsi' data with `as.sir()`")
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cat("Class 'rsi'", font_bold(font_red("[!]\n")))
print(as.character(x), quote = FALSE)
}
#' @noRd
#' @export
`[<-.rsi` <- `[<-.sir`
#' @noRd
#' @export
`[[<-.rsi` <- `[[<-.sir`
#' @noRd
#' @export
barplot.rsi <- barplot.sir
#' @noRd
#' @export
c.rsi <- c.sir
#' @noRd
#' @export
droplevels.rsi <- droplevels.sir
#' @noRd
#' @export
plot.rsi <- plot.sir
#' @noRd
#' @export
rep.rsi <- rep.sir
#' @noRd
#' @export
summary.rsi <- summary.sir
#' @noRd
#' @export
unique.rsi <- unique.sir
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# WHEN REMOVING RSI, DON'T FORGET TO REMOVE :
# - THE "rsi_df" CLASS FROM R/sir_calc.R
# - CODE CONTAINING only_rsi_columns, colours_RSI, include_untested_rsi, prob_RSI
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deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE) {
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if (is.null(old)) {
warning_(extra_msg)
} else {
env <- paste0("deprecated_", old)
if (!env %in% names(AMR_env)) {
AMR_env[[paste0("deprecated_", old)]] <- 1
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if (isTRUE(is_function)) {
old <- paste0(old, "()")
new <- paste0(new, "()")
type <- "function"
} else {
type <- "argument"
}
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warning_(
ifelse(is.null(new),
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paste0("The `", old, "` ", type, " is no longer in use"),
paste0("The `", old, "` ", type, " has been replaced with `", new, "`")
),
ifelse(type == "argument",
". While the old argument still works, it will be removed in a future version, so please update your code.",
", see `?AMR-deprecated`."
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),
ifelse(!is.null(extra_msg),
paste0(" ", extra_msg),
""
),
"\nThis warning will be shown once per session."
)
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}
}
}