AMR/tests/testthat/test-mic.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
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# SOURCE #
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# https://github.com/msberends/AMR #
# #
# 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 #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
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# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("mic.R")
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test_that("mic works", {
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skip_on_cran()
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expect_true(as.mic(8) == as.mic("8"))
expect_true(as.mic("1") > as.mic("<=0.0625"))
expect_true(as.mic("1") < as.mic(">=32"))
expect_true(is.mic(as.mic(8)))
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expect_equal(as.double(as.mic(">=32")), 32)
expect_equal(as.numeric(as.mic(">=32")), 32)
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expect_equal(as.integer(as.mic(">=32")), 32)
expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
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# all levels should be valid MICs
x <- as.mic(c(2, 4))
expect_s3_class(x[1], "mic")
expect_s3_class(x[[1]], "mic")
expect_s3_class(c(x[1], x[9]), "mic")
expect_s3_class(unique(x[1], x[9]), "mic")
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expect_s3_class(droplevels(c(x[1], x[9])), "mic")
x[2] <- 32
expect_s3_class(x, "mic")
expect_warning(as.mic("INVALID VALUE"))
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pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_output(print(as.mic(c(1, 2, 4, 8))))
expect_equal(summary(as.mic(c(2, 8))),
structure(c("Class" = "mic",
"<NA>" = "0",
"Min." = "2",
"Max." = "8"), class = c("summaryDefault", "table")))
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library(dplyr, warn.conflicts = FALSE)
expect_output(print(tibble(m = as.mic(2:4))))
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})