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 Using the functions will give a warning with the name of the function it has been replaced by.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