2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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# TITLE #
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2021-02-02 23:57:35 +01:00
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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2018-12-16 22:45:12 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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# SOURCE #
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2020-07-08 14:48:06 +02:00
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# https://github.com/msberends/AMR #
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2018-12-16 22:45:12 +01:00
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# #
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# LICENCE #
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2020-12-27 00:30:28 +01:00
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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2020-10-08 11:16:03 +02:00
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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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2018-12-16 22:45:12 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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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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2020-01-05 17:22:09 +01:00
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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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2020-10-08 11:16:03 +02:00
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# #
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# Visit our website for the full manual and a complete tutorial about #
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2021-02-02 23:57:35 +01:00
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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2021-05-15 21:36:22 +02:00
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expect_identical(suppressWarnings(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3))),
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c("***", "**", "*", ".", " ", NA, NA))
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2018-11-05 13:20:32 +01:00
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2021-05-15 21:36:22 +02:00
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expect_warning(key_antibiotics(example_isolates))
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expect_identical(suppressWarnings(key_antibiotics(example_isolates)),
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key_antimicrobials(example_isolates, antifungal = NULL))
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2018-11-05 13:20:32 +01:00
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2021-05-15 21:36:22 +02:00
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expect_warning(key_antibiotics_equal("S", "S"))
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expect_identical(suppressWarnings(key_antibiotics_equal("S", "S")),
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antimicrobials_equal("S", "S", type = "keyantimicrobials"))
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2018-11-05 13:20:32 +01:00
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2021-05-15 21:36:22 +02:00
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expect_warning(filter_first_weighted_isolate(example_isolates))
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expect_identical(suppressWarnings(filter_first_weighted_isolate(example_isolates)),
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filter_first_isolate(example_isolates))
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2021-05-19 22:55:42 +02:00
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expect_warning(filter_ab_class(example_isolates, "mycobact"))
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expect_warning(filter_aminoglycosides(example_isolates))
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expect_warning(filter_betalactams(example_isolates))
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expect_warning(filter_carbapenems(example_isolates))
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expect_warning(filter_cephalosporins(example_isolates))
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expect_warning(filter_1st_cephalosporins(example_isolates))
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expect_warning(filter_2nd_cephalosporins(example_isolates))
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expect_warning(filter_3rd_cephalosporins(example_isolates))
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expect_warning(filter_4th_cephalosporins(example_isolates))
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expect_warning(filter_5th_cephalosporins(example_isolates))
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expect_warning(filter_fluoroquinolones(example_isolates))
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expect_warning(filter_glycopeptides(example_isolates))
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expect_warning(filter_macrolides(example_isolates))
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expect_warning(filter_oxazolidinones(example_isolates))
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expect_warning(filter_penicillins(example_isolates))
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expect_warning(filter_tetracyclines(example_isolates))
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