mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 09:26:11 +01:00
66 lines
2.5 KiB
R
66 lines
2.5 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 Using the functions will give a warning with the name of the function it has been replaced by.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(...)
|
||
|
|
}
|
||
|
|
|
||
|
|
#' @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 %>% base::strsplit("[-,:]") %>% base::unlist() %>% base::as.double()
|
||
|
|
} else {
|
||
|
|
stop('Invalid `ratio`: ', ratio, '.')
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if (length(x) != length(ratio)) {
|
||
|
|
stop('`x` and `ratio` must be of same size.')
|
||
|
|
}
|
||
|
|
base::sum(x, na.rm = TRUE) * (ratio / base::sum(ratio, na.rm = TRUE))
|
||
|
|
}
|