2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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# TITLE #
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2020-10-08 11:16:03 +02:00
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# Antimicrobial Resistance (AMR) 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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# how to conduct AMR 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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2018-08-25 22:01:14 +02:00
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context("mic.R")
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2018-03-27 17:43:42 +02:00
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test_that("mic works", {
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2020-07-31 10:50:08 +02:00
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skip_on_cran()
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2018-03-27 17:43:42 +02:00
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expect_true(as.mic(8) == as.mic("8"))
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expect_true(as.mic("1") > as.mic("<=0.0625"))
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expect_true(as.mic("1") < as.mic(">=32"))
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expect_true(is.mic(as.mic(8)))
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2018-04-02 16:05:09 +02:00
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2018-03-27 17:43:42 +02:00
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expect_equal(as.double(as.mic(">=32")), 32)
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2018-08-24 11:08:20 +02:00
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expect_equal(as.numeric(as.mic(">=32")), 32)
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2018-03-27 17:43:42 +02:00
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expect_equal(as.integer(as.mic(">=32")), 32)
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expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
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2018-04-02 16:05:09 +02:00
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2018-08-24 11:08:20 +02:00
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# all levels should be valid MICs
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2020-09-25 14:44:50 +02:00
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x <- as.mic(c(2, 4))
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expect_s3_class(x[1], "mic")
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expect_s3_class(x[[1]], "mic")
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expect_s3_class(c(x[1], x[9]), "mic")
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expect_s3_class(unique(x[1], x[9]), "mic")
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2020-12-13 20:44:32 +01:00
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expect_s3_class(droplevels(c(x[1], x[9])), "mic")
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x[2] <- 32
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expect_s3_class(x, "mic")
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2018-08-24 11:08:20 +02:00
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expect_warning(as.mic("INVALID VALUE"))
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2020-09-30 10:24:53 +02:00
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2020-09-19 15:15:57 +02:00
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pdf(NULL) # prevent Rplots.pdf being created
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expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
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expect_silent(plot(as.mic(c(1, 2, 4, 8))))
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expect_output(print(as.mic(c(1, 2, 4, 8))))
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2020-09-18 16:05:53 +02:00
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expect_equal(summary(as.mic(c(2, 8))),
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structure(c("Class" = "mic",
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"<NA>" = "0",
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"Min." = "2",
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"Max." = "8"), class = c("summaryDefault", "table")))
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2020-12-13 20:44:32 +01:00
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library(dplyr, warn.conflicts = FALSE)
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expect_output(print(tibble(m = as.mic(2:4))))
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2018-03-27 17:43:42 +02:00
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})
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