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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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54
tests/testthat/test-disk.R
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@ -27,33 +27,35 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_true(as.disk(8) == as.disk("8"))
expect_true(is.disk(as.disk(8)))
test_that("disk works", {
expect_true(as.disk(8) == as.disk("8"))
expect_true(is.disk(as.disk(8)))
expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
# all levels should be valid disks
x <- as.disk(c(20, 40))
expect_inherits(x[1], "disk")
expect_inherits(x[[1]], "disk")
expect_inherits(c(x[1], x[9]), "disk")
expect_inherits(unique(x[1], x[9]), "disk")
# expect_warning(as.disk("INVALID VALUE"))
x[2] <- 32
expect_inherits(x, "disk")
# all levels should be valid disks
x <- as.disk(c(20, 40))
expect_inherits(x[1], "disk")
expect_inherits(x[[1]], "disk")
expect_inherits(c(x[1], x[9]), "disk")
expect_inherits(unique(x[1], x[9]), "disk")
# expect_warning(as.disk("INVALID VALUE"))
x[2] <- 32
expect_inherits(x, "disk")
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.disk(12)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_output(print(as.disk(12)))
if (AMR:::pkg_is_available("tibble")) {
expect_stdout(print(tibble::tibble(d = as.disk(12))))
}
if (AMR:::pkg_is_available("tibble")) {
expect_output(print(tibble::tibble(d = as.disk(12))))
}
})