mirror of
https://github.com/msberends/AMR.git
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157 lines
4.8 KiB
R
157 lines
4.8 KiB
R
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# 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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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# These are all S3 implementations for the vctrs package,
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# that is used internally by tidyverse packages such as dplyr.
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# They are to convert AMR-specific classes to bare characters and integers.
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# All of them will be exported using s3_register() in R/zzz.R when loading the package.
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# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
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# S3: ab_selector
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vec_ptype2.character.ab_selector <- function(x, y, ...) {
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x
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}
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vec_ptype2.ab_selector.character <- function(x, y, ...) {
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y
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}
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vec_cast.character.ab_selector <- function(x, to, ...) {
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unclass(x)
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}
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# S3: ab_selector_any_all
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vec_ptype2.logical.ab_selector_any_all <- function(x, y, ...) {
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x
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}
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vec_ptype2.ab_selector_any_all.logical <- function(x, y, ...) {
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y
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}
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vec_cast.logical.ab_selector_any_all <- function(x, to, ...) {
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unclass(x)
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}
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# S3: ab
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vec_ptype2.character.ab <- function(x, y, ...) {
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x
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}
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vec_ptype2.ab.character <- function(x, y, ...) {
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y
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}
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vec_cast.character.ab <- function(x, to, ...) {
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as.character(x)
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}
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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))
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}
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# S3: av
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vec_ptype2.character.av <- function(x, y, ...) {
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x
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}
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vec_ptype2.av.character <- function(x, y, ...) {
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y
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}
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vec_cast.character.av <- function(x, to, ...) {
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as.character(x)
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}
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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))
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}
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# S3: mo
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vec_ptype2.character.mo <- function(x, y, ...) {
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x
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}
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vec_ptype2.mo.character <- function(x, y, ...) {
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y
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}
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vec_cast.character.mo <- function(x, to, ...) {
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as.character(x)
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}
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vec_cast.mo.character <- function(x, to, ...) {
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return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
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}
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# S3: disk
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vec_ptype2.integer.disk <- function(x, y, ...) {
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x
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}
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vec_ptype2.disk.integer <- function(x, y, ...) {
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y
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}
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vec_cast.integer.disk <- function(x, to, ...) {
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unclass(x)
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}
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vec_cast.disk.integer <- function(x, to, ...) {
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as.disk(x)
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}
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vec_cast.double.disk <- function(x, to, ...) {
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unclass(x)
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}
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vec_cast.disk.double <- function(x, to, ...) {
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as.disk(x)
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}
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vec_cast.character.disk <- function(x, to, ...) {
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unclass(x)
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}
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vec_cast.disk.character <- function(x, to, ...) {
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as.disk(x)
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}
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# S3: mic
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vec_cast.character.mic <- function(x, to, ...) {
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as.character(x)
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}
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vec_cast.double.mic <- function(x, to, ...) {
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as.double(x)
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}
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vec_cast.mic.double <- function(x, to, ...) {
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as.mic(x)
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}
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vec_cast.mic.character <- function(x, to, ...) {
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as.mic(x)
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}
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vec_math.mic <- function(.fn, x, ...) {
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.fn(as.double(x), ...)
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}
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# S3: rsi
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vec_ptype2.character.rsi <- function(x, y, ...) {
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x
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}
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vec_ptype2.rsi.character <- function(x, y, ...) {
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y
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}
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vec_cast.character.rsi <- function(x, to, ...) {
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as.character(x)
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}
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vec_cast.rsi.character <- function(x, to, ...) {
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as.rsi(x)
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}
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