mirror of https://github.com/msberends/AMR.git
228 lines
6.9 KiB
R
Executable File
228 lines
6.9 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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE 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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#' 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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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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)
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#' @rdname AMR-deprecated
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#' @export
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as.rsi <- function(x, ...) {
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deprecation_warning("as.rsi", "as.sir")
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UseMethod("as.rsi")
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}
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#' @noRd
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#' @export
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as.rsi.default <- function(...) {
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as.sir.default(...)
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}
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#' @noRd
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#' @export
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as.rsi.mic <- function(...) {
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as.sir.mic(...)
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}
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#' @noRd
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#' @export
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as.rsi.disk <- function(...) {
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as.sir.disk(...)
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}
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#' @noRd
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#' @export
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as.rsi.data.frame <- function(...) {
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as.sir.data.frame(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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facet_rsi <- function(...) {
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deprecation_warning("facet_rsi", "facet_sir")
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facet_sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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geom_rsi <- function(...) {
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deprecation_warning("geom_rsi", "geom_sir")
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geom_sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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ggplot_rsi <- function(...) {
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deprecation_warning("ggplot_rsi", "ggplot_sir")
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ggplot_sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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ggplot_rsi_predict <- function(...) {
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deprecation_warning("ggplot_rsi_predict", "ggplot_sir_predict")
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ggplot_sir_predict(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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is.rsi <- function(...) {
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# REMINDER: change as.sir() to remove the deprecation warning there
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suppressWarnings(is.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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#' @rdname AMR-deprecated
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#' @export
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labels_rsi_count <- function(...) {
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deprecation_warning("labels_rsi_count", "labels_sir_count")
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labels_sir_count(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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n_rsi <- function(...) {
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deprecation_warning("n_rsi", "n_sir")
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n_sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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random_rsi <- function(...) {
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deprecation_warning("random_rsi", "random_sir")
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random_sir(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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rsi_df <- function(...) {
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deprecation_warning("rsi_df", "sir_df")
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sir_df(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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rsi_predict <- function(...) {
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deprecation_warning("rsi_predict", "sir_predict")
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sir_predict(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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scale_rsi_colours <- function(...) {
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deprecation_warning("scale_rsi_colours", "scale_sir_colours")
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scale_sir_colours(...)
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}
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#' @rdname AMR-deprecated
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#' @export
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theme_rsi <- function(...) {
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deprecation_warning("theme_rsi", "theme_sir")
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theme_sir(...)
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}
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# will be exported using s3_register() in R/zzz.R
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pillar_shaft.rsi <- pillar_shaft.sir
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type_sum.rsi <- function(x, ...) {
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if (message_not_thrown_before("type_sum.rsi")) {
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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)")
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}
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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(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")))
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print(as.character(x), quote = FALSE)
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}
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#' @noRd
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#' @export
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`[<-.rsi` <- `[<-.sir`
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#' @noRd
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#' @export
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`[[<-.rsi` <- `[[<-.sir`
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#' @noRd
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#' @export
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barplot.rsi <- barplot.sir
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#' @noRd
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#' @export
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c.rsi <- c.sir
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#' @noRd
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#' @export
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droplevels.rsi <- droplevels.sir
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#' @noRd
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#' @export
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plot.rsi <- plot.sir
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#' @noRd
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#' @export
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rep.rsi <- rep.sir
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#' @noRd
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#' @export
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summary.rsi <- summary.sir
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#' @noRd
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#' @export
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unique.rsi <- unique.sir
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# WHEN REMOVING RSI, DON'T FORGET TO REMOVE :
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# - THE "rsi_df" CLASS FROM R/sir_calc.R
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# - 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)) {
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warning_(extra_msg)
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} else {
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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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if (isTRUE(is_function)) {
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old <- paste0(old, "()")
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new <- paste0(new, "()")
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type <- "function"
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} else {
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type <- "argument"
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}
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warning_(
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ifelse(is.null(new),
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paste0("The `", old, "` ", type, " is no longer in use"),
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paste0("The `", old, "` ", type, " has been replaced with `", new, "`")
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),
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ifelse(type == "argument",
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". While the old argument still works, it will be removed in a future version, so please update your code.",
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", see `?AMR-deprecated`."
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),
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ifelse(!is.null(extra_msg),
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paste0(" ", extra_msg),
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""
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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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}
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}
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