mirror of
https://github.com/msberends/AMR.git
synced 2026-11-16 00:10:57 +01:00
dr. M.S. (Matthijs) Berends
53d0704271
- New sir_combine() to combine SIR results of multiple antimicrobials into one variable; antibiogram(), wisca() and the count/proportion functions now use the same engine (antibiogram() and wisca() output unchanged) - With multiple antimicrobials, count_*() and proportion_*() now follow the documented combination therapy rules: resistance() is the proportion of failing combinations, count_all() excludes isolates with an unknown combination result, and WT/NWT/NS/NI are handled correctly - where() is now decided at runtime instead of at installation, fixing antibiogram() and wisca() without tidyselect (e.g. CRAN binaries without dplyr) - Imports from data.table and cli moved to .onLoad(); data.table functions are only used while it is loaded; the like() example no longer unloads data.table, which crashed R - Static test that fails on code outside functions depending on suggested packages - New check-without-dplyr workflow: installs AMR with all suggested packages, removes dplyr (and tidyselect), then runs all unit tests and examples against the installed package - g.test() now returns the degrees of freedom as 'parameter', so they are printed - Fix R CMD check NOTEs (hidden .claude folder, lost braces in inherited g.test and ggplot_pca docs)
92 lines
4.9 KiB
R
92 lines
4.9 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 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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# Run all unit tests and all examples against the INSTALLED AMR package, in a library where some suggested packages are not available.
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# Used by .github/workflows/check-without-dplyr.yaml; run from the root of the repository:
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# Rscript .github/scripts/test_installed_without.R dplyr tidyselect
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# The package must have been installed BEFORE the listed packages were made unavailable, as binary packages from CRAN are built on machines that have all suggested packages: code that depends on what was available at installation (instead of at runtime) then fails, which R CMD check cannot detect as it reinstalls the package.
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unavailable <- commandArgs(trailingOnly = TRUE)
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if (length(unavailable) == 0) {
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stop("provide the package(s) that must be unavailable, e.g.: Rscript test_installed_without.R dplyr tidyselect")
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}
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still_available <- unavailable[vapply(unavailable, requireNamespace, logical(1), quietly = TRUE)]
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if (length(still_available) > 0) {
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stop("these packages must not be available, but are: ", paste(still_available, collapse = ", "))
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}
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cat("Not available:", paste(unavailable, collapse = ", "), "\n")
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cat("AMR", format(utils::packageVersion("AMR")), "installed in", find.package("AMR"), "\n\n")
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Sys.setenv(NOT_CRAN = "true")
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library(AMR)
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# 1. all unit tests, against the installed package
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cat("== Unit tests ==\n")
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results <- as.data.frame(testthat::test_dir(
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"tests/testthat",
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package = "AMR",
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load_package = "installed",
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reporter = "summary",
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stop_on_failure = FALSE
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))
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n_failed <- sum(results$failed) + sum(results$error)
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cat("\nTests: ", sum(results$nb), " expectations, ", sum(results$failed), " failed, ", sum(results$error), " errored, ", sum(results$skipped), " skipped\n", sep = "")
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# 2. all examples, including \donttest{} (not \dontrun{}), against the installed package
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cat("\n== Examples ==\n")
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rd_db <- tools::Rd_db("AMR")
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failed_examples <- character(0)
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n_examples <- 0
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for (rd in sort(names(rd_db))) {
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ex_file <- tempfile(fileext = ".R")
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tools::Rd2ex(rd_db[[rd]], ex_file, commentDonttest = FALSE)
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if (!file.exists(ex_file)) next
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n_examples <- n_examples + 1
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# print the name first, so that a crash of R itself shows which help page caused it
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cat(rd, "\n")
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ok <- tryCatch(
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{
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utils::capture.output(suppressMessages(suppressWarnings(source(ex_file, local = new.env(parent = globalenv()), echo = FALSE))))
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TRUE
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},
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error = function(e) {
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cat("FAILED: ", rd, ": ", conditionMessage(e), "\n", sep = "")
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FALSE
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}
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)
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if (!ok) failed_examples <- c(failed_examples, rd)
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grDevices::graphics.off()
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}
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cat("Examples: ", length(failed_examples), " of ", n_examples, " help pages failed\n", sep = "")
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if (n_failed > 0 || length(failed_examples) > 0) {
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stop(n_failed, " test(s) failed and ", length(failed_examples), " example(s) failed without ", paste(unavailable, collapse = " and "), call. = FALSE)
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}
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cat("\nAll tests and examples passed without ", paste(unavailable, collapse = " and "), ".\n", sep = "")
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