mirror of https://github.com/msberends/AMR.git
258 lines
6.4 KiB
R
258 lines
6.4 KiB
R
# ==================================================================== #
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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) 2018-2020 Berends MS, Luz CF et al. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Methods for tidyverse
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#'
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#' These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.
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#' @inheritSection lifecycle Stable lifecycle
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#' @inheritSection AMR Read more on our website!
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#' @keywords internal
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#' @name AMR-tidyverse
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NULL
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#' @rdname AMR-tidyverse
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#' @exportMethod scale_type.mo
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#' @export
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scale_type.mo <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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#' @rdname AMR-tidyverse
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#' @exportMethod scale_type.ab
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#' @export
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scale_type.ab <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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# Class mo ----------------------------------------------------------------
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#' @exportMethod vec_ptype_abbr.mo
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#' @importFrom vctrs vec_ptype_abbr
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#' @export
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vec_ptype_abbr.mo <- function(x, ...) {
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"mo"
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}
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#' @exportMethod vec_ptype_full.mo
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#' @importFrom vctrs vec_ptype_full
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#' @export
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vec_ptype_full.mo <- function(x, ...) {
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"mo"
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}
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#' @rdname AMR-tidyverse
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#' @export
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vec_ptype2.mo <- function(x, y, ...) {
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UseMethod("vec_ptype2.mo", y)
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}
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#' @method vec_ptype2.mo default
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#' @export
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vec_ptype2.mo.default <- function(x, y, ..., x_arg = "x", y_arg = "y") {
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vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
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}
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#' @method vec_ptype2.mo character
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#' @export
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vec_ptype2.mo.character <- function(x, y, ...) {
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x
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}
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#' @method vec_ptype2.character mo
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#' @exportMethod vec_ptype2.character.mo
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#' @importFrom vctrs vec_ptype2.character
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#' @export
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vec_ptype2.character.mo <- function(x, y, ...) {
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y
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}
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#' @rdname AMR-tidyverse
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#' @export
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vec_cast.mo <- function(x, to, ...) {
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UseMethod("vec_cast.mo")
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}
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#' @method vec_cast.mo mo
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#' @export
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vec_cast.mo.mo <- function(x, to, ...) {
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as.mo(x)
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}
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#' @method vec_cast.mo character
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#' @export
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vec_cast.mo.character <- function(x, to, ...) {
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as.mo(x)
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}
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#' @method vec_cast.mo default
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#' @importFrom vctrs vec_default_cast
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#' @export
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vec_cast.mo.default <- function(x, to, ...) {
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vec_default_cast(x, to)
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}
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#' @method vec_cast.character mo
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#' @exportMethod vec_cast.character.mo
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#' @importFrom vctrs vec_cast vec_cast.character
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#' @export
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vec_cast.character.mo <- function(x, to, ...) {
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unclass(x)
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}
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# Class ab ----------------------------------------------------------------
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#' @exportMethod vec_ptype_abbr.ab
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#' @importFrom vctrs vec_ptype_abbr
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#' @export
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vec_ptype_abbr.ab <- function(x, ...) {
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"ab"
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}
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#' @exportMethod vec_ptype_full.ab
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#' @importFrom vctrs vec_ptype_full
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#' @export
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vec_ptype_full.ab <- function(x, ...) {
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"ab"
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}
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#' @rdname AMR-tidyverse
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#' @export
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vec_ptype2.ab <- function(x, y, ...) {
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UseMethod("vec_ptype2.ab", y)
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}
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#' @method vec_ptype2.ab default
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#' @export
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vec_ptype2.ab.default <- function(x, y, ..., x_arg = "x", y_arg = "y") {
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vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
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}
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#' @method vec_ptype2.ab character
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#' @export
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vec_ptype2.ab.character <- function(x, y, ...) {
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x
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}
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#' @method vec_ptype2.character ab
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#' @exportMethod vec_ptype2.character.ab
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#' @importFrom vctrs vec_ptype2.character
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#' @export
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vec_ptype2.character.ab <- function(x, y, ...) {
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y
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}
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#' @rdname AMR-tidyverse
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#' @export
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vec_cast.ab <- function(x, to, ...) {
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UseMethod("vec_cast.ab")
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}
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#' @method vec_cast.ab ab
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#' @export
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vec_cast.ab.ab <- function(x, to, ...) {
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as.ab(x)
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}
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#' @method vec_cast.ab character
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#' @export
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vec_cast.ab.character <- function(x, to, ...) {
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as.ab(x)
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}
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#' @method vec_cast.ab default
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#' @importFrom vctrs vec_default_cast
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#' @export
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vec_cast.ab.default <- function(x, to, ...) {
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vec_default_cast(x, to)
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}
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#' @method vec_cast.character ab
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#' @exportMethod vec_cast.character.ab
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#' @importFrom vctrs vec_cast vec_cast.character
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#' @export
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vec_cast.character.ab <- function(x, to, ...) {
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unclass(x)
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}
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# Class disk --------------------------------------------------------------
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#' @exportMethod vec_ptype_abbr.disk
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#' @importFrom vctrs vec_ptype_abbr
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#' @export
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vec_ptype_abbr.disk <- function(x, ...) {
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"disk"
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}
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#' @exportMethod vec_ptype_full.disk
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#' @importFrom vctrs vec_ptype_full
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#' @export
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vec_ptype_full.disk <- function(x, ...) {
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"disk"
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}
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# Class rsi --------------------------------------------------------------
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#' @exportMethod vec_ptype_abbr.rsi
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#' @importFrom vctrs vec_ptype_abbr
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#' @export
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vec_ptype_abbr.rsi <- function(x, ...) {
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"rsi"
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}
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#' @exportMethod vec_ptype_full.rsi
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#' @importFrom vctrs vec_ptype_full
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#' @export
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vec_ptype_full.rsi <- function(x, ...) {
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"rsi"
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}
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# Class mic --------------------------------------------------------------
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#' @exportMethod vec_ptype_abbr.mic
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#' @importFrom vctrs vec_ptype_abbr
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#' @export
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vec_ptype_abbr.mic <- function(x, ...) {
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"mic"
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}
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#' @exportMethod vec_ptype_full.mic
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#' @importFrom vctrs vec_ptype_full
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#' @export
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vec_ptype_full.mic <- function(x, ...) {
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"mic"
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}
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