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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
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60
tests/testthat/test-mean_amr_distance.R
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@ -27,37 +27,39 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
vctr_disk <- as.disk(c(20:25))
vctr_mic <- as.mic(2^c(0:5))
vctr_sir <- as.sir(c("S", "S", "I", "I", "R", "R"))
test_that("mean_amr_distance works", {
vctr_disk <- as.disk(c(20:25))
vctr_mic <- as.mic(2^c(0:5))
vctr_sir <- as.sir(c("S", "S", "I", "I", "R", "R"))
expect_identical(
mean_amr_distance(vctr_disk),
(as.double(vctr_disk) - mean(as.double(vctr_disk))) / sd(as.double(vctr_disk))
)
expect_identical(
mean_amr_distance(vctr_disk),
(as.double(vctr_disk) - mean(as.double(vctr_disk))) / sd(as.double(vctr_disk))
)
expect_identical(
mean_amr_distance(vctr_mic),
(log2(vctr_mic) - mean(log2(vctr_mic))) / sd(log2(vctr_mic))
)
expect_identical(
mean_amr_distance(vctr_mic),
(log2(vctr_mic) - mean(log2(vctr_mic))) / sd(log2(vctr_mic))
)
expect_identical(
mean_amr_distance(vctr_sir, combine_SI = FALSE),
(c(1, 1, 2, 2, 3, 3) - mean(c(1, 1, 2, 2, 3, 3))) / sd(c(1, 1, 2, 2, 3, 3))
)
expect_identical(
mean_amr_distance(vctr_sir, combine_SI = TRUE),
(c(1, 1, 1, 1, 3, 3) - mean(c(1, 1, 1, 1, 3, 3))) / sd(c(1, 1, 1, 1, 3, 3))
)
expect_identical(
mean_amr_distance(vctr_sir, combine_SI = FALSE),
(c(1, 1, 2, 2, 3, 3) - mean(c(1, 1, 2, 2, 3, 3))) / sd(c(1, 1, 2, 2, 3, 3))
)
expect_identical(
mean_amr_distance(vctr_sir, combine_SI = TRUE),
(c(1, 1, 1, 1, 3, 3) - mean(c(1, 1, 1, 1, 3, 3))) / sd(c(1, 1, 1, 1, 3, 3))
)
expect_equal(
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk)),
c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
tolerance = 0.00001
)
expect_equal(
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk)),
c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
tolerance = 0.00001
)
expect_equal(
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk), 2:3),
c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
tolerance = 0.00001
)
expect_equal(
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk), 2:3),
c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
tolerance = 0.00001
)
})