AMR/R/vctrs.R

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
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# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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://msberends.github.io/AMR/ #
# ==================================================================== #
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# 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
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# S3: ab_selector
vec_ptype2.character.ab_selector <- function(x, y, ...) {
x
}
vec_ptype2.ab_selector.character <- function(x, y, ...) {
y
}
vec_cast.character.ab_selector <- function(x, to, ...) {
unclass(x)
}
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# S3: ab_selector_any_all
vec_ptype2.logical.ab_selector_any_all <- function(x, y, ...) {
x
}
vec_ptype2.ab_selector_any_all.logical <- function(x, y, ...) {
y
}
vec_cast.logical.ab_selector_any_all <- function(x, to, ...) {
unclass(x)
}
# S3: ab
vec_ptype2.character.ab <- function(x, y, ...) {
x
}
vec_ptype2.ab.character <- function(x, y, ...) {
y
}
vec_cast.character.ab <- function(x, to, ...) {
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as.character(x)
}
vec_cast.ab.character <- function(x, to, ...) {
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return_after_integrity_check(x, "antimicrobial drug code", as.character(AMR_env$AB_lookup$ab))
}
# S3: av
vec_ptype2.character.av <- function(x, y, ...) {
x
}
vec_ptype2.av.character <- function(x, y, ...) {
y
}
vec_cast.character.av <- function(x, to, ...) {
as.character(x)
}
vec_cast.av.character <- function(x, to, ...) {
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return_after_integrity_check(x, "antiviral drug code", as.character(AMR_env$AV_lookup$av))
}
# S3: mo
vec_ptype2.character.mo <- function(x, y, ...) {
x
}
vec_ptype2.mo.character <- function(x, y, ...) {
y
}
vec_cast.character.mo <- function(x, to, ...) {
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as.character(x)
}
vec_cast.mo.character <- function(x, to, ...) {
return_after_integrity_check(x, "microorganism code", as.character(AMR::microorganisms$mo))
}
# S3: disk
vec_ptype2.integer.disk <- function(x, y, ...) {
x
}
vec_ptype2.disk.integer <- function(x, y, ...) {
y
}
vec_cast.integer.disk <- function(x, to, ...) {
unclass(x)
}
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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)
}
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# S3: mic
vec_cast.character.mic <- function(x, to, ...) {
as.character(x)
}
vec_cast.double.mic <- function(x, to, ...) {
as.double(x)
}
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vec_cast.mic.double <- function(x, to, ...) {
as.mic(x)
}
vec_cast.mic.character <- function(x, to, ...) {
as.mic(x)
}
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vec_math.mic <- function(.fn, x, ...) {
.fn(as.double(x), ...)
}
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# S3: rsi
vec_ptype2.character.rsi <- function(x, y, ...) {
x
}
vec_ptype2.rsi.character <- function(x, y, ...) {
y
}
vec_cast.character.rsi <- function(x, to, ...) {
as.character(x)
}
vec_cast.rsi.character <- function(x, to, ...) {
as.rsi(x)
}