mirror of https://github.com/msberends/AMR.git
81 lines
3.7 KiB
R
81 lines
3.7 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 #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. 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://msberends.github.io/AMR/ #
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# ==================================================================== #
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# we use {tinytest} instead of {testthat} because it does not rely on recent R versions - we want to test on R >= 3.0.
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# Run them in RStudio using:
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# rstudioapi::jobRunScript("tests/tinytest.R", name = "AMR Unit Tests", workingDir = getwd(), exportEnv = "tinytest_results")
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# test only on GitHub Actions and at using RStudio jobs - not on CRAN as tests are lengthy
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if (tryCatch(isTRUE(AMR:::import_fn("isJob", "rstudioapi")()), error = function(e) FALSE) ||
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identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
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# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
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.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
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if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
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library(AMR)
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# set language
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set_AMR_locale("English")
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# set some functions if on old R
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if (getRversion() < "3.2.0") {
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anyNA <- AMR:::anyNA
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dir.exists <- AMR:::dir.exists
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file.size <- AMR:::file.size
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file.mtime <- AMR:::file.mtime
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isNamespaceLoaded <- AMR:::isNamespaceLoaded
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lengths <- AMR:::lengths
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}
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if (getRversion() < "3.3.0") {
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strrep <- AMR:::strrep
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}
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if (getRversion() < "3.5.0") {
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isFALSE <- AMR:::isFALSE
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}
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if (getRversion() < "3.6.0") {
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str2lang <- AMR:::str2lang
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# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
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trimws <- AMR:::trimws
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}
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if (getRversion() < "4.0.0") {
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deparse1 <- AMR:::deparse1
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}
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# start the unit tests
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out <- test_package("AMR",
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testdir = ifelse(dir.exists("inst/tinytest"),
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"inst/tinytest",
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"tinytest"
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),
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verbose = 99,
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color = FALSE
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)
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cat("\n\nSUMMARY:\n")
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print(summary(out))
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}
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}
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