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24f24ecaf8
* Generalise interpretive rules for multi-guideline support (#268) - Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider column (value: "EUCAST") to distinguish future CLSI rows - Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R; filter by rule.provider == guideline when applying rules in interpretive_rules() - Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class "custom_interpretive_rules"; old function becomes a deprecated wrapper in zz_deprecated.R; backward-compat S3 dispatch shims added for old class - Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors - Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF for transitional compatibility until sysdata.rda is regenerated https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP * Fix namespace load failure: remove assignInNamespace from .onLoad (#268) assignInNamespace cannot add NEW bindings to a locked package namespace (R locks namespace bindings before .onLoad runs). Replace the .onLoad shim with a runtime fallback inside interpretive_rules(): if INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive it from EUCAST_RULES_DF by adding the rule.provider column. This also fixes the screening_abx line to reuse the already-resolved interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF reference. https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP * fixes * fixes --------- Co-authored-by: Claude <noreply@anthropic.com>
63 lines
3.9 KiB
R
Executable File
63 lines
3.9 KiB
R
Executable File
# ==================================================================== #
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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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/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://amr-for-r.org #
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# ==================================================================== #
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#' Download and Unpack an AMR Course Repository
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#'
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#' 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.
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#' @param github_repo A character string specifying the GitHub repository with username and repo name, e.g. `"https://github.com/username/repo"`.
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#' @param branch A character string specifying the branch to download. Defaults to `"main"`.
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#' @param ... Additional arguments passed on to [usethis::use_course()].
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#' @details
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#' 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.
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#'
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#' The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
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#' @return
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#' 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.
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#' @seealso [usethis::use_course()]
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#' @export
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#' @examples
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#' \dontrun{
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#'
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#' # Let this run by users, e.g., webinar participants
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#' amr_course("https://github.com/my_user_name/our_AMR_course")
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#' }
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amr_course <- function(github_repo, branch = "main", ...) {
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if (!"usethis" %in% rownames(utils::installed.packages())) {
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if ("rlang" %in% rownames(utils::installed.packages())) {
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rlang::check_installed("usethis")
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} else {
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stop("Package usethis is not installed. Please run: install.packages(\"usethis\")", call. = FALSE)
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}
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}
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url <- paste0(github_repo, "/archive/refs/heads/", branch, ".zip")
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use_course <- import_fn("use_course", "usethis")
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message("This will download and unpack the contents of a repository.\n")
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use_course(url, ...)
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}
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