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(v3.0.1.9034) Add amr_course()

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dr. M.S. (Matthijs) Berends
2026-03-11 16:07:31 +01:00
parent 353eaa3f38
commit 4dc3ec0008
8 changed files with 110 additions and 17 deletions
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62
R/amr_course.R Normal file
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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 #
# ==================================================================== #
#' Download and Unpack an AMR Course Repository
#'
#' Downloads and unpacks a GitHub repository containing course materials, using [usethis::use_course()]. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
#' @param github_repo A character string specifying the GitHub repository with username and repo name, e.g. `"https://github.com/username/repo"`.
#' @param branch A character string specifying the branch to download. Defaults to `"main"`.
#' @param ... Additional arguments passed on to [usethis::use_course()].
#' @details
#' This function constructs a ZIP archive URL from the provided `github_repo` and `branch`, then delegates to [usethis::use_course()] to handle the download and extraction.
#'
#' The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
#' @return
#' Called for its side effect. [usethis::use_course()] will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever [usethis::use_course()] returns.
#' @seealso [usethis::use_course()]
#' @export
#' @examples
#' \dontrun{
#'
#' # Let this run by users, e.g., webinar participants
#' amr_course("https://github.com/my_user_name/our_AMR_course")
#' }
amr_course <- function(github_repo, branch = "main", ...) {
if (!"usethis" %in% rownames(utils::installed.packages())) {
if ("rlang" %in% rownames(utils::installed.packages())) {
rlang::check_installed("usethis")
} else {
stop("Package usethis is not installed. Please run: install.packages(\"usethis\")", call. = FALSE)
}
}
url <- paste0(github_repo, "/archive/refs/heads/", branch, ".zip")
use_course <- import_fn("use_course", "usethis")
message("This will download and unpack the contents of a repository.\n")
use_course(url, ...)
}

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R/interpretive_rules.R
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#' Apply Interpretive Rules
#'
#' @description
#' **WORK IN PROGRESS**
#'
# TODO Remove this remark before next release
#' **The `interpretive_rules()` function is new, to allow CLSI 'rules' too. The old `eucast_rules()` function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.**
#'
#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
#'
#' To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see *Details*.