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prepare for CRAN

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-10-20 14:51:48 +02:00
parent 7dc96794be
commit 7cda9e575b
46 changed files with 7863 additions and 5663 deletions
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20
inst/tinytest/test-first_isolate.R
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@ -42,7 +42,7 @@ expect_equal(
)
expect_equal(
sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
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)
# Phenotype-based, using key antimicrobials
@ -53,7 +53,7 @@ expect_equal(
type = "keyantimicrobials",
antifungal = NULL, info = TRUE
), na.rm = TRUE),
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)
expect_equal(
sum(first_isolate(
@ -62,7 +62,7 @@ expect_equal(
type = "keyantimicrobials",
antifungal = NULL, info = TRUE, ignore_I = FALSE
), na.rm = TRUE),
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)
@ -93,7 +93,7 @@ expect_true(
col_specimen = "specimen",
filter_specimen = "Urine",
info = TRUE
), na.rm = TRUE) < 1501
), na.rm = TRUE) < 1400
)
# same, but now exclude ICU
expect_true(
@ -107,7 +107,7 @@ expect_true(
col_icu = x$ward == "ICU",
icu_exclude = TRUE,
info = TRUE
), na.rm = TRUE) < 1501
), na.rm = TRUE) < 1000
)
# "No isolates found"
@ -193,7 +193,7 @@ expect_equal(
),
na.rm = TRUE
),
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)
# unknown MOs
@ -201,23 +201,23 @@ test_unknown <- example_isolates
test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
expect_equal(
sum(first_isolate(test_unknown, include_unknown = FALSE)),
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)
expect_equal(
sum(first_isolate(test_unknown, include_unknown = TRUE)),
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)
test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
expect_equal(
sum(first_isolate(test_unknown)),
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)
# empty sir results
expect_equal(
sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
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)
# shortcuts