mirror of
https://github.com/msberends/AMR.git
synced 2025-11-04 06:34:07 +01:00
99 lines
4.6 KiB
R
99 lines
4.6 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# 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 #
|
|
# 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/ #
|
|
# ==================================================================== #
|
|
|
|
#' Add Manual Antimicrobials to This Package
|
|
#'
|
|
#' With [add_custom_antimicrobials()] you can add your own manual antimicrobial codes to the `AMR` package.
|
|
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
|
|
#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, for example:
|
|
#'
|
|
#' ```r
|
|
#' library(AMR)
|
|
#' add_custom_antimicrobials(
|
|
#' data.frame(ab = "TEST",
|
|
#' name = "Test Antibiotic",
|
|
#' group = "Test Group")
|
|
#' )
|
|
#' ```
|
|
#'
|
|
#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
|
|
#' @rdname add_custom_antimicrobials
|
|
#' @export
|
|
#' @examples
|
|
#' \donttest{
|
|
#'
|
|
#' # returns NA and throws a warning:
|
|
#' as.ab("test")
|
|
#'
|
|
#' # now a manual entry - it will be considered by as.ab() and
|
|
#' # all ab_*() functions
|
|
#' add_custom_antimicrobials(
|
|
#' data.frame(ab = "TEST",
|
|
#' name = "Test Antibiotic",
|
|
#' group = "Test Group")
|
|
#' )
|
|
#'
|
|
#' "test" is now a new antibiotic:
|
|
#' as.ab("test")
|
|
#' ab_name("test")
|
|
#' ab_group("test")
|
|
#' }
|
|
add_custom_antimicrobials <- function(x) {
|
|
meet_criteria(x, allow_class = "data.frame")
|
|
stop_ifnot(all(c("ab", "name") %in% colnames(x)),
|
|
"`x` must contain columns \"ab\" and \"name\".")
|
|
stop_if(any(x$ab %in% AB_lookup$ab),
|
|
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AB_lookup$ab]), " already exist in the internal `antibiotics` data set.")
|
|
|
|
x <- x[, colnames(AB_lookup)[colnames(AB_lookup) %in% colnames(x)], drop = FALSE]
|
|
x$generalised_name <- generalise_antibiotic_name(x$name)
|
|
x$generalised_all <- as.list(x$generalised_name)
|
|
|
|
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
|
|
if (!is.null(bind_rows)) {
|
|
new_df <- bind_rows(AB_lookup, x)
|
|
} else {
|
|
new_df <- rbind(AB_lookup, x, stringsAsFactors = FALSE)
|
|
}
|
|
|
|
assignInNamespace(x = "AB_lookup",
|
|
value = new_df,
|
|
ns = asNamespace("AMR"))
|
|
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to internal `antibiotics` data set.")
|
|
}
|
|
|
|
#' @rdname add_custom_antimicrobials
|
|
#' @export
|
|
clear_custom_antimicrobials <- function() {
|
|
assignInNamespace(x = "AB_lookup",
|
|
value = create_AB_lookup(),
|
|
ns = asNamespace("AMR"))
|
|
message_("Manual antimicrobials cleared.")
|
|
}
|