mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
134 lines
4.0 KiB
R
Executable File
134 lines
4.0 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Deprecated functions
|
|
#'
|
|
#' These functions are so-called '\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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @export
|
|
#' @keywords internal
|
|
#' @name AMR-deprecated
|
|
#' @rdname AMR-deprecated
|
|
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))
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
guess_mo <- function(...) {
|
|
.Deprecated(new = "as.mo", package = "AMR")
|
|
as.mo(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
guess_atc <- function(...) {
|
|
.Deprecated(new = "as.atc", package = "AMR")
|
|
as.atc(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_property <- function(...) {
|
|
.Deprecated(new = "atc_property", package = "AMR")
|
|
atc_property(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_atc <- function(...) {
|
|
.Deprecated(new = "as.atc", package = "AMR")
|
|
as.atc(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_official <- function(...) {
|
|
.Deprecated(new = "atc_official", package = "AMR")
|
|
atc_official(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_name <- function(...) {
|
|
.Deprecated(new = "atc_name", package = "AMR")
|
|
atc_name(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_trivial_nl <- function(...) {
|
|
.Deprecated(new = "atc_trivial_nl", package = "AMR")
|
|
atc_trivial_nl(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_certe <- function(...) {
|
|
.Deprecated(new = "atc_certe", package = "AMR")
|
|
atc_certe(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_umcg <- function(...) {
|
|
.Deprecated(new = "atc_umcg", package = "AMR")
|
|
atc_umcg(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
ab_tradenames <- function(...) {
|
|
.Deprecated(new = "atc_tradenames", package = "AMR")
|
|
atc_tradenames(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
atc_ddd <- function(...) {
|
|
.Deprecated(new = "atc_online_ddd", package = "AMR")
|
|
atc_online_ddd(...)
|
|
}
|
|
|
|
#' @rdname AMR-deprecated
|
|
#' @export
|
|
atc_groups <- function(...) {
|
|
.Deprecated(new = "atc_online_groups", package = "AMR")
|
|
atc_online_groups(...)
|
|
}
|
|
|