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62 lines
3.6 KiB
R
Executable File
62 lines
3.6 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 #
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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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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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expect_equal(AMR:::percentage(0.25), "25%")
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expect_equal(AMR:::percentage(0.5), "50%")
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expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%")
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expect_equal(AMR:::percentage(0.1234), "12.3%")
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# round up 0.5
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expect_equal(AMR:::percentage(0.0054), "0.5%")
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expect_equal(AMR:::percentage(0.0055), "0.6%")
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# test functions on all R versions - R < 3.3 did not contain these
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expect_equal(strrep("A", 5), "AAAAA")
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expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
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expect_equal(trimws(" test "), "test")
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expect_equal(trimws(" test ", "l"), "test ")
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expect_equal(trimws(" test ", "r"), " test")
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expect_equal(AMR:::trimws2(" test "), "test")
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expect_equal(AMR:::trimws2(" test ", "l"), "test ")
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expect_equal(AMR:::trimws2(" test ", "r"), " test")
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expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
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expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
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expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
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expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
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expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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}
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# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
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}
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