AMR/R/deprecated.R

96 lines
3.2 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Deprecated functions
#'
#' These functions are \link{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 Using the functions will give a warning with the name of the function it has been replaced by.
#' @export
#' @keywords internal
#' @name AMR-deprecated
#' @rdname AMR-deprecated
as.bactid <- function(...) {
.Deprecated("as.mo", package = "AMR")
as.mo(...)
}
#' @rdname AMR-deprecated
#' @export
is.bactid <- function(...) {
.Deprecated(new = "is.mo", package = "AMR")
is.mo(...)
}
#' @rdname AMR-deprecated
#' @export
guess_bactid <- function(...) {
.Deprecated(new = "guess_mo", package = "AMR")
guess_mo(...)
}
#' @exportMethod print.bactid
#' @export
#' @noRd
print.bactid <- function(x, ...) {
cat("Class 'bactid'\n")
print.default(as.character(x), quote = FALSE)
}
#' @exportMethod as.data.frame.bactid
#' @export
#' @noRd
as.data.frame.bactid <- function (x, ...) {
# same as as.data.frame.character but with removed stringsAsFactors
nm <- paste(deparse(substitute(x), width.cutoff = 500L),
collapse = " ")
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(x, ..., nm = nm)
} else {
as.data.frame.vector(x, ...)
}
}
#' @exportMethod pull.bactid
#' @export
#' @importFrom dplyr pull
#' @noRd
pull.bactid <- function(.data, ...) {
pull(as.data.frame(.data), ...)
}
#' @rdname AMR-deprecated
#' @export
ratio <- function(x, ratio) {
.Deprecated(package = "AMR")
if (!all(is.numeric(x))) {
stop('`x` must be a vector of numeric values.')
}
if (length(ratio) == 1) {
if (ratio %like% '^([0-9]+([.][0-9]+)?[-,:])+[0-9]+([.][0-9]+)?$') {
# support for "1:2:1", "1-2-1", "1,2,1" and even "1.75:2:1.5"
ratio <- ratio %>% strsplit("[-,:]") %>% unlist() %>% as.double()
} else {
stop('Invalid `ratio`: ', ratio, '.')
}
}
if (length(x) != 1 & length(x) != length(ratio)) {
stop('`x` and `ratio` must be of same size.')
}
sum(x, na.rm = TRUE) * (ratio / sum(ratio, na.rm = TRUE))
}