(v1.1.0.9000) CLSI as.rsi() fix, better vctrs support, new CI

R/vctrs.R

@@ -0,0 +1,235 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it 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.gitlab.io/AMR.    #
+# ==================================================================== #
+
+#' `vctrs` methods
+#' 
+#' These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.
+#' @inheritSection lifecycle Stable lifecycle
+#' @inheritSection AMR Read more on our website!
+#' @keywords internal
+#' @name AMR-vctrs
+NULL
+
+
+# Class mo ----------------------------------------------------------------
+
+
+#' @exportMethod vec_ptype_abbr.mo
+#' @importFrom vctrs vec_ptype_abbr
+#' @export
+vec_ptype_abbr.mo <- function(x, ...) {
+  "mo"
+}
+
+#' @exportMethod vec_ptype_full.mo
+#' @importFrom vctrs vec_ptype_full
+#' @export
+vec_ptype_full.mo <- function(x, ...) {
+  "mo"
+}
+
+#' @rdname AMR-vctrs
+#' @export
+vec_ptype2.mo <- function(x, y, ...) {
+  UseMethod("vec_ptype2.mo", y)
+}
+
+#' @method vec_ptype2.mo default
+#' @export
+vec_ptype2.mo.default <- function(x, y, ..., x_arg = "x", y_arg = "y") {
+  vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
+}
+
+#' @method vec_ptype2.mo character
+#' @export
+vec_ptype2.mo.character <- function(x, y, ...) {
+  x
+}
+
+#' @method vec_ptype2.character mo
+#' @importFrom vctrs vec_ptype2.character
+#' @export
+vec_ptype2.character.mo <- function(x, y, ...) {
+  y
+}
+
+#' @rdname AMR-vctrs
+#' @export
+vec_cast.mo <- function(x, to, ...) {
+  UseMethod("vec_cast.mo")
+}
+
+#' @method vec_cast.mo mo
+#' @export
+vec_cast.mo.mo <- function(x, to, ...) {
+  as.mo(x)
+}
+
+#' @method vec_cast.mo character
+#' @export
+vec_cast.mo.character <- function(x, to, ...) {
+  as.mo(x)
+}
+
+#' @method vec_cast.mo default
+#' @export
+vec_cast.mo.default <- function(x, to, ...) {
+  vec_default_cast(x, to)
+}
+
+# @method vec_cast.character mo
+#' @exportMethod vec_cast.character.mo
+#' @importFrom vctrs vec_cast
+#' @export
+vec_cast.character.mo <- function(x, to, ...) {
+  # purrr::map_chr(x, stringr::str_c, collapse = " ")
+  unclass(x)
+}
+
+
+# Class ab ----------------------------------------------------------------
+
+
+#' @exportMethod vec_ptype_abbr.ab
+#' @importFrom vctrs vec_ptype_abbr
+#' @export
+vec_ptype_abbr.ab <- function(x, ...) {
+  "ab"
+}
+
+#' @exportMethod vec_ptype_full.ab
+#' @importFrom vctrs vec_ptype_full
+#' @export
+vec_ptype_full.ab <- function(x, ...) {
+  "ab"
+}
+
+#' @rdname AMR-vctrs
+#' @export
+vec_ptype2.ab <- function(x, y, ...) {
+  UseMethod("vec_ptype2.ab", y)
+}
+
+#' @method vec_ptype2.ab default
+#' @export
+vec_ptype2.ab.default <- function(x, y, ..., x_arg = "x", y_arg = "y") {
+  vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
+}
+
+#' @method vec_ptype2.ab character
+#' @export
+vec_ptype2.ab.character <- function(x, y, ...) {
+  x
+}
+
+#' @method vec_ptype2.character ab
+#' @importFrom vctrs vec_ptype2.character
+#' @export
+vec_ptype2.character.ab <- function(x, y, ...) {
+  y
+}
+
+#' @rdname AMR-vctrs
+#' @export
+vec_cast.ab <- function(x, to, ...) {
+  UseMethod("vec_cast.ab")
+}
+
+#' @method vec_cast.ab ab
+#' @export
+vec_cast.ab.ab <- function(x, to, ...) {
+  as.ab(x)
+}
+
+#' @method vec_cast.ab character
+#' @export
+vec_cast.ab.character <- function(x, to, ...) {
+  as.ab(x)
+}
+
+#' @method vec_cast.ab default
+#' @export
+vec_cast.ab.default <- function(x, to, ...) {
+  vec_default_cast(x, to)
+}
+
+# @method vec_cast.character ab
+#' @exportMethod vec_cast.character.ab
+#' @importFrom vctrs vec_cast
+#' @export
+vec_cast.character.ab <- function(x, to, ...) {
+  # purrr::map_chr(x, stringr::str_c, collapse = " ")
+  unclass(x)
+}
+
+
+# Class disk --------------------------------------------------------------
+
+
+#' @exportMethod vec_ptype_abbr.disk
+#' @importFrom vctrs vec_ptype_abbr
+#' @export
+vec_ptype_abbr.disk <- function(x, ...) {
+  "disk"
+}
+
+#' @exportMethod vec_ptype_full.disk
+#' @importFrom vctrs vec_ptype_full
+#' @export
+vec_ptype_full.disk <- function(x, ...) {
+  "disk"
+}
+
+
+# Class rsi --------------------------------------------------------------
+
+
+#' @exportMethod vec_ptype_abbr.rsi
+#' @importFrom vctrs vec_ptype_abbr
+#' @export
+vec_ptype_abbr.rsi <- function(x, ...) {
+  "rsi"
+}
+
+#' @exportMethod vec_ptype_full.rsi
+#' @importFrom vctrs vec_ptype_full
+#' @export
+vec_ptype_full.rsi <- function(x, ...) {
+  "rsi"
+}
+
+
+# Class mic --------------------------------------------------------------
+
+
+#' @exportMethod vec_ptype_abbr.mic
+#' @importFrom vctrs vec_ptype_abbr
+#' @export
+vec_ptype_abbr.mic <- function(x, ...) {
+  "mic"
+}
+
+#' @exportMethod vec_ptype_full.mic
+#' @importFrom vctrs vec_ptype_full
+#' @export
+vec_ptype_full.mic <- function(x, ...) {
+  "mic"
+}