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AMR/R/vctrs.R

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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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 the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# These are all S3 implementations for the vctrs package,
# that is used internally by tidyverse packages such as dplyr.
# They are to convert AMR-specific classes to bare characters and integers.
# All of them will be exported using s3_register() in R/zzz.R when loading the package.
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
# LIST ALL EXPORTS
# this prevents the requirement for putting `vctrs` as a the dependency in Imports
# (NOTE 2024-02-22 this is the right way - it should be 2 '.'-separated S3 classes in the second argument)
# S3: amr_selector
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.amr_selector)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.amr_selector)
# S3: amr_selector_any_all
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, logical.amr_selector_any_all)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, amr_selector_any_all.logical)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, logical.amr_selector_any_all)
# S3: ab
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, ab.ab)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.ab)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, ab.character)
# S3: av
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, av.av)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.av)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, av.character)
# S3: mo
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mo.mo)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mo)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mo.character)
# S3: disk
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_full, disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype_abbr, disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, disk.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.integer)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.double)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.disk)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, disk.character)
# S3: mic
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, mic.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, double.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, integer.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, factor.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.double)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.integer)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.factor)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, mic.mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_math, mic)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_arith, mic)
# S3: sir
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.default)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, sir.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_ptype2, character.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, character.sir)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.character)
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(vctrs::vec_cast, sir.sir)
# S3: amr_selector ----
# this does not need a .default method since it's used internally only
vec_ptype2.character.amr_selector <- function(x, y, ...) {
x
}
vec_ptype2.amr_selector.character <- function(x, y, ...) {
y
}
vec_cast.character.amr_selector <- function(x, to, ...) {
unclass(x)
}
# S3: amr_selector_any_all ----
# this does not need a .default method since it's used internally only
vec_ptype2.logical.amr_selector_any_all <- function(x, y, ...) {
x
}
vec_ptype2.amr_selector_any_all.logical <- function(x, y, ...) {
y
}
vec_cast.logical.amr_selector_any_all <- function(x, to, ...) {
unclass(x)
}
# S3: ab ----
vec_ptype2.ab.default <- function(x, y, ..., x_arg = "", y_arg = "") {
x
}
vec_ptype2.ab.ab <- function(x, y, ...) {
x
}
vec_cast.character.ab <- function(x, to, ...) {
as.character(x)
}
vec_cast.ab.character <- function(x, to, ...) {
return_after_integrity_check(x, "antimicrobial drug code", as.character(AMR_env$AB_lookup$ab))
}
# S3: av ----
vec_ptype2.av.default <- function(x, y, ..., x_arg = "", y_arg = "") {
x
}
vec_ptype2.av.av <- function(x, y, ...) {
x
}
vec_cast.character.av <- function(x, to, ...) {
as.character(x)
}
vec_cast.av.character <- function(x, to, ...) {
return_after_integrity_check(x, "antiviral drug code", as.character(AMR_env$AV_lookup$av))
}
# S3: mo ----
vec_ptype2.mo.default <- function(x, y, ..., x_arg = "", y_arg = "") {
x
}
vec_ptype2.mo.mo <- function(x, y, ...) {
x
}
vec_cast.character.mo <- function(x, to, ...) {
as.character(x)
}
vec_cast.mo.character <- function(x, to, ...) {
add_MO_lookup_to_AMR_env()
return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
}
# S3: disk ----
vec_ptype_full.disk <- function(x, ...) {
"disk"
}
vec_ptype_abbr.disk <- function(x, ...) {
"dsk"
}
vec_ptype2.disk.default <- function(x, y, ..., x_arg = "", y_arg = "") {
NA_disk_[0]
}
vec_ptype2.disk.disk <- function(x, y, ...) {
NA_disk_[0]
}
vec_cast.disk.disk <- function(x, to, ...) {
as.disk(x)
}
vec_cast.integer.disk <- function(x, to, ...) {
unclass(x)
}
vec_cast.disk.integer <- function(x, to, ...) {
as.disk(x)
}
vec_cast.double.disk <- function(x, to, ...) {
unclass(x)
}
vec_cast.disk.double <- function(x, to, ...) {
as.disk(x)
}
vec_cast.character.disk <- function(x, to, ...) {
unclass(x)
}
vec_cast.disk.character <- function(x, to, ...) {
as.disk(x)
}
# S3: mic ----
vec_ptype2.mic.default <- function(x, y, ..., x_arg = "", y_arg = "") {
# this will make sure that currently implemented MIC levels are returned
NA_mic_[0]
}
vec_ptype2.mic.mic <- function(x, y, ...) {
# this will make sure that currently implemented MIC levels are returned
NA_mic_[0]
}
vec_cast.mic.mic <- function(x, to, ...) {
# this will make sure that currently implemented MIC levels are returned
as.mic(x)
}
vec_cast.character.mic <- function(x, to, ...) {
as.character(x)
}
vec_cast.double.mic <- function(x, to, ...) {
as.double(x)
}
vec_cast.integer.mic <- function(x, to, ...) {
as.integer(x)
}
vec_cast.factor.mic <- function(x, to, ...) {
factor(as.character(x))
}
vec_cast.mic.double <- function(x, to, ...) {
as.mic(x)
}
vec_cast.mic.character <- function(x, to, ...) {
as.mic(x)
}
vec_cast.mic.integer <- function(x, to, ...) {
as.mic(x)
}
vec_cast.mic.factor <- function(x, to, ...) {
as.mic(x)
}
vec_math.mic <- function(.fn, x, ...) {
.fn(as.double(x), ...)
}
vec_arith.mic <- function(op, x, y, ...) {
vctrs::vec_arith(op, as.double(x), as.double(y))
}
# S3: sir ----
vec_ptype2.sir.default <- function(x, y, ..., x_arg = "", y_arg = "") {
NA_sir_[0]
}
vec_ptype2.sir.sir <- function(x, y, ...) {
NA_sir_[0]
}
vec_ptype2.character.sir <- function(x, y, ...) {
NA_sir_[0]
}
vec_cast.sir.sir <- function(x, to, ...) {
# this makes sure that old SIR objects (with S/I/R) are converted to the current structure (S/SDD/I/R/NI)
as.sir(x)
}
vec_cast.character.sir <- function(x, to, ...) {
as.character(x)
}
vec_cast.sir.character <- function(x, to, ...) {
as.sir(x)
}
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