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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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72
tests/testthat/test-g.test.R
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@ -27,43 +27,45 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# GOODNESS-OF-FIT
test_that("g.test works", {
# GOODNESS-OF-FIT
# example 1: clearfield rice vs. red rice
x <- c(772, 1611, 737)
expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
0.12574,
tolerance = 0.0001
)
# example 2: red crossbills
x <- c(1752, 1895)
expect_equal(g.test(x)$p.value,
0.017873,
tolerance = 0.0001
)
expect_error(g.test(0))
expect_error(g.test(c(0, 1), 0))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
# expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
# INDEPENDENCE
x <- as.data.frame(
matrix(
data = round(runif(4) * 100000, 0),
ncol = 2,
byrow = TRUE
# example 1: clearfield rice vs. red rice
x <- c(772, 1611, 737)
expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
0.12574,
tolerance = 0.0001
)
)
# fisher.test() is always better for 2x2 tables:
# expect_warning(g.test(x))
expect_true(suppressWarnings(g.test(x)$p.value) < 1)
# example 2: red crossbills
x <- c(1752, 1895)
expect_equal(g.test(x)$p.value,
0.017873,
tolerance = 0.0001
)
# expect_warning(g.test(x = c(772, 1611, 737), y = c(780, 1560, 780), rescale.p = TRUE))
expect_error(g.test(0))
expect_error(g.test(c(0, 1), 0))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
# expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
# INDEPENDENCE
x <- as.data.frame(
matrix(
data = round(runif(4) * 100000, 0),
ncol = 2,
byrow = TRUE
)
)
# fisher.test() is always better for 2x2 tables:
# expect_warning(g.test(x))
expect_true(suppressWarnings(g.test(x)$p.value) < 1)
# expect_warning(g.test(x = c(772, 1611, 737), y = c(780, 1560, 780), rescale.p = TRUE))
expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
})