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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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