mirror of https://github.com/msberends/AMR.git
50 lines
3.6 KiB
R
50 lines
3.6 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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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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if (pkg_is_available("dplyr")) {
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expect_true(example_isolates %>% filter_ab_class("carbapenem") %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_aminoglycosides() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_betalactams() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_carbapenems() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_1st_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_2nd_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_3rd_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_4th_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% mutate(ceftaroline = CTX) %>% filter_5th_cephalosporins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_fluoroquinolones() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_glycopeptides() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_macrolides() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_oxazolidinones() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_penicillins() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_tetracyclines() %>% nrow() < nrow(example_isolates))
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expect_true(example_isolates %>% filter_carbapenems("R", "all") %>% nrow() > 0)
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expect_error(example_isolates %>% filter_carbapenems(result = "test"))
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expect_error(example_isolates %>% filter_carbapenems(scope = "test"))
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expect_message(example_isolates %>% select(1:3) %>% filter_carbapenems())
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}
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