mirror of https://github.com/msberends/AMR.git
211 lines
6.5 KiB
R
Executable File
211 lines
6.5 KiB
R
Executable File
# ==================================================================== #
|
|
# 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will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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),
|
|
new_class = c("rsi", "ordered", "factor"))
|
|
#' @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(x, ...) {
|
|
# this is an exception, so mutate_if(is.rsi, as.sir) can be used
|
|
if (inherits(x, "data.frame")) {
|
|
unname(vapply(FUN.VALUE = logical(1), x, is.rsi))
|
|
} else {
|
|
inherits(x, "rsi")
|
|
}
|
|
}
|
|
#' @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, ...) {
|
|
deprecation_warning(extra_msg = "* Transform your old 'rsi' class to the new 'sir' class with `as.sir()` using e.g.:\n your_data %>% mutate_if(is.rsi, as.sir)")
|
|
paste0("rsi", font_bold(font_red("[!]")))
|
|
}
|
|
|
|
#' @method print rsi
|
|
#' @export
|
|
#' @noRd
|
|
print.rsi <- function(x, ...) {
|
|
deprecation_warning(extra_msg = "Transform your old 'rsi' class to the new 'sir' class with `as.sir()`")
|
|
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
|
|
|
|
deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL) {
|
|
if (is.null(old)) {
|
|
warning_(extra_msg)
|
|
} else {
|
|
env <- paste0("deprecated_", old)
|
|
if (!env %in% names(AMR_env)) {
|
|
AMR_env[[paste0("deprecated_", old)]] <- 1
|
|
warning_(ifelse(is.null(new),
|
|
paste0("The `", old, "()` function is no longer in use"),
|
|
paste0("The `", old, "()` function has been replaced with `", new, "()`")),
|
|
", see `?AMR-deprecated`.",
|
|
ifelse(!is.null(extra_msg),
|
|
paste0(" ", extra_msg),
|
|
""),
|
|
"\nThis warning will be shown once per session.")
|
|
}
|
|
}
|
|
}
|