AMR/R/add_custom_antimicrobials.R

104 lines
4.8 KiB
R
Raw Normal View History

2022-10-10 20:20:39 +02:00
# ==================================================================== #
# 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"
2022-10-10 21:03:39 +02:00
#' @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, although this requires to load the `AMR` package at every start-up:
2022-10-10 20:20:39 +02:00
#'
#' ```r
2022-10-10 21:03:39 +02:00
#' # Open .Rprofile file
#' utils::file.edit("~/.Rprofile")
#'
#' # Add custom antibiotic codes:
2022-10-10 20:20:39 +02:00
#' 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
2022-10-10 21:03:39 +02:00
#' # returns NA and throws a warning (which is now suppressed):
#' suppressWarnings(
#' as.ab("test")
#' )
2022-10-10 20:20:39 +02:00
#'
2022-10-10 21:03:39 +02:00
#' # now add a manual entry - it will be considered by as.ab() and
2022-10-10 20:20:39 +02:00
#' # 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")
2022-10-10 21:03:39 +02:00
#'
#' ab_info("test")
2022-10-10 20:20:39 +02:00
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.")
}