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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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37
tests/testthat/test-first_isolate.R
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@ -46,17 +46,28 @@ expect_equal(
)
# for phenotype determination
expect_equal(AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
FALSE)
expect_equal(AMR:::duplicated_antibiogram(c("RRR", "SSS"),
points_threshold = 2, ignore_I = TRUE, type = "points"),
c(FALSE, FALSE))
expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
points_threshold = 2, ignore_I = TRUE, type = "points"),
c(FALSE, TRUE, FALSE))
expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
points_threshold = 2, ignore_I = TRUE, type = "points"),
c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE))
expect_equal(
AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
FALSE
)
expect_equal(
AMR:::duplicated_antibiogram(c("RRR", "SSS"),
points_threshold = 2, ignore_I = TRUE, type = "points"
),
c(FALSE, FALSE)
)
expect_equal(
AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
points_threshold = 2, ignore_I = TRUE, type = "points"
),
c(FALSE, TRUE, FALSE)
)
expect_equal(
AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
points_threshold = 2, ignore_I = TRUE, type = "points"
),
c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)
)
# Phenotype-based, using key antimicrobials
expect_equal(
@ -89,7 +100,9 @@ expect_true(
col_icu = example_isolates$ward == "ICU",
info = TRUE,
icu_exclude = TRUE
), na.rm = TRUE) < 950
),
na.rm = TRUE
) < 950
)
# set 1500 random observations to be of specimen type 'Urine'