Remove RSI from package, add extra MIC scale functions

R/zz_deprecated.R

@@ -27,171 +27,14 @@
 # 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will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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(...) {
-  # REMINDER: change as.sir() to remove the deprecation warning there
-  suppressWarnings(is.sir(...))
-}
-#' @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"
-}
-
-#' @method print rsi
-#' @export
-#' @noRd
-print.rsi <- function(x, ...) {
-  deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir' - transform your 'rsi' data 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
-
-# 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
+# #' 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
+# NULL
 
 deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE) {
   if (is.null(old)) {